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Colville A, Liu JY, Rodriguez-Mateo C, Thomas S, Ishak HD, Zhou R, Klein JDD, Morgens DW, Goshayeshi A, Salvi JS, Yao D, Spees K, Dixon SJ, Liu C, Rhee JW, Lai C, Wu JC, Bassik MC, Rando TA. Death-seq identifies regulators of cell death and senolytic therapies. Cell Metab 2023; 35:1814-1829.e6. [PMID: 37699398 PMCID: PMC10597643 DOI: 10.1016/j.cmet.2023.08.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Selectively ablating damaged cells is an evolving therapeutic approach for age-related disease. Current methods for genome-wide screens to identify genes whose deletion might promote the death of damaged or senescent cells are generally underpowered because of the short timescales of cell death as well as the difficulty of scaling non-dividing cells. Here, we establish "Death-seq," a positive-selection CRISPR screen optimized to identify enhancers and mechanisms of cell death. Our screens identified synergistic enhancers of cell death induced by the known senolytic ABT-263. The screen also identified inducers of cell death and senescent cell clearance in models of age-related diseases by a related compound, ABT-199, which alone is not senolytic but exhibits less toxicity than ABT-263. Death-seq enables the systematic screening of cell death pathways to uncover molecular mechanisms of regulated cell death subroutines and identifies drug targets for the treatment of diverse pathological states such as senescence, cancer, and fibrosis.
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Affiliation(s)
- Alex Colville
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jie-Yu Liu
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cristina Rodriguez-Mateo
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samantha Thomas
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heather D Ishak
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ronghao Zhou
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julian D D Klein
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Armon Goshayeshi
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jayesh S Salvi
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - June-Wha Rhee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Celine Lai
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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2
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Benjamin DI, Both P, Benjamin JS, Nutter CW, Tan JH, Kang J, Machado LA, Klein JDD, de Morree A, Kim S, Liu L, Dulay H, Feraboli L, Louie SM, Nomura DK, Rando TA. Fasting induces a highly resilient deep quiescent state in muscle stem cells via ketone body signaling. Cell Metab 2022; 34:902-918.e6. [PMID: 35584694 PMCID: PMC9177797 DOI: 10.1016/j.cmet.2022.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 12/15/2021] [Accepted: 04/25/2022] [Indexed: 01/11/2023]
Abstract
Short-term fasting is beneficial for the regeneration of multiple tissue types. However, the effects of fasting on muscle regeneration are largely unknown. Here, we report that fasting slows muscle repair both immediately after the conclusion of fasting as well as after multiple days of refeeding. We show that ketosis, either endogenously produced during fasting or a ketogenic diet or exogenously administered, promotes a deep quiescent state in muscle stem cells (MuSCs). Although deep quiescent MuSCs are less poised to activate, slowing muscle regeneration, they have markedly improved survival when facing sources of cellular stress. Furthermore, we show that ketone bodies, specifically β-hydroxybutyrate, directly promote MuSC deep quiescence via a nonmetabolic mechanism. We show that β-hydroxybutyrate functions as an HDAC inhibitor within MuSCs, leading to acetylation and activation of an HDAC1 target protein p53. Finally, we demonstrate that p53 activation contributes to the deep quiescence and enhanced resilience observed during fasting.
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Affiliation(s)
- Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pieter Both
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joel S Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher W Nutter
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jenna H Tan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leo A Machado
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Julian D D Klein
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hunter Dulay
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ludovica Feraboli
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon M Louie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA; Neurology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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3
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de Morree A, Klein JDD, Gan Q, Farup J, Urtasun A, Kanugovi A, Bilen B, van Velthoven CTJ, Quarta M, Rando TA. Alternative polyadenylation of Pax3 controls muscle stem cell fate and muscle function. Science 2020; 366:734-738. [PMID: 31699935 DOI: 10.1126/science.aax1694] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
Abstract
Adult stem cells are essential for tissue homeostasis. In skeletal muscle, muscle stem cells (MuSCs) reside in a quiescent state, but little is known about the mechanisms that control homeostatic turnover. Here we show that, in mice, the variation in MuSC activation rate among different muscles (for example, limb versus diaphragm muscles) is determined by the levels of the transcription factor Pax3. We further show that Pax3 levels are controlled by alternative polyadenylation of its transcript, which is regulated by the small nucleolar RNA U1. Isoforms of the Pax3 messenger RNA that differ in their 3' untranslated regions are differentially susceptible to regulation by microRNA miR206, which results in varying levels of the Pax3 protein in vivo. These findings highlight a previously unrecognized mechanism of the homeostatic regulation of stem cell fate by multiple RNA species.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Julian D D Klein
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiang Gan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jean Farup
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.,Departments of Clinical Medicine and Biomedicine, Research Laboratory for Biochemical Pathology, Aarhus University, Aarhus, Denmark
| | - Andoni Urtasun
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Abhijnya Kanugovi
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Biter Bilen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Marco Quarta
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.,Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.,Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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4
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Baar MP, Brandt RMC, Putavet DA, Klein JDD, Derks KWJ, Bourgeois BRM, Stryeck S, Rijksen Y, van Willigenburg H, Feijtel DA, van der Pluijm I, Essers J, van Cappellen WA, van IJcken WF, Houtsmuller AB, Pothof J, de Bruin RWF, Madl T, Hoeijmakers JHJ, Campisi J, de Keizer PLJ. Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging. Cell 2017; 169:132-147.e16. [PMID: 28340339 DOI: 10.1016/j.cell.2017.02.031] [Citation(s) in RCA: 837] [Impact Index Per Article: 119.6] [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: 08/11/2016] [Revised: 12/29/2016] [Accepted: 02/22/2017] [Indexed: 02/06/2023]
Abstract
The accumulation of irreparable cellular damage restricts healthspan after acute stress or natural aging. Senescent cells are thought to impair tissue function, and their genetic clearance can delay features of aging. Identifying how senescent cells avoid apoptosis allows for the prospective design of anti-senescence compounds to address whether homeostasis can also be restored. Here, we identify FOXO4 as a pivot in senescent cell viability. We designed a FOXO4 peptide that perturbs the FOXO4 interaction with p53. In senescent cells, this selectively causes p53 nuclear exclusion and cell-intrinsic apoptosis. Under conditions where it was well tolerated in vivo, this FOXO4 peptide neutralized doxorubicin-induced chemotoxicity. Moreover, it restored fitness, fur density, and renal function in both fast aging XpdTTD/TTD and naturally aged mice. Thus, therapeutic targeting of senescent cells is feasible under conditions where loss of health has already occurred, and in doing so tissue homeostasis can effectively be restored.
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Affiliation(s)
- Marjolein P Baar
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Diana A Putavet
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Julian D D Klein
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Benjamin R M Bourgeois
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Sarah Stryeck
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Yvonne Rijksen
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Hester van Willigenburg
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Danny A Feijtel
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Radiation Oncology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wilfred F van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ron W F de Bruin
- Department of Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Tobias Madl
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Judith Campisi
- The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Lawrence Berkeley National Laboratories, Berkeley, CA 94720, USA
| | - Peter L J de Keizer
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA.
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