1
|
Kumar A, Vaca-Dempere M, Mortimer T, Deryagin O, Smith JG, Petrus P, Koronowski KB, Greco CM, Segalés J, Andrés E, Lukesova V, Zinna VM, Welz PS, Serrano AL, Perdiguero E, Sassone-Corsi P, Benitah SA, Muñoz-Cánoves P. Brain-muscle communication prevents muscle aging by maintaining daily physiology. Science 2024; 384:563-572. [PMID: 38696572 DOI: 10.1126/science.adj8533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/26/2024] [Indexed: 05/04/2024]
Abstract
A molecular clock network is crucial for daily physiology and maintaining organismal health. We examined the interactions and importance of intratissue clock networks in muscle tissue maintenance. In arrhythmic mice showing premature aging, we created a basic clock module involving a central and a peripheral (muscle) clock. Reconstituting the brain-muscle clock network is sufficient to preserve fundamental daily homeostatic functions and prevent premature muscle aging. However, achieving whole muscle physiology requires contributions from other peripheral clocks. Mechanistically, the muscle peripheral clock acts as a gatekeeper, selectively suppressing detrimental signals from the central clock while integrating important muscle homeostatic functions. Our research reveals the interplay between the central and peripheral clocks in daily muscle function and underscores the impact of eating patterns on these interactions.
Collapse
Affiliation(s)
- Arun Kumar
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Mireia Vaca-Dempere
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Thomas Mortimer
- Institute for Research in Biomedicine (IRB), Barcelona, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Oleg Deryagin
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jacob G Smith
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Petrus
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Medicine (H7), Karolinska Institutet, Stockholm 141 86, Sweden
| | - Kevin B Koronowski
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Carolina M Greco
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital IRCCS, 20089, Rozzano (Milan), Italy
| | - Jessica Segalés
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eva Andrés
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Vera Lukesova
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB), Barcelona, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Patrick-Simon Welz
- Cancer Research Programme, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Antonio L Serrano
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Altos Labs Inc., San Diego Institute of Science, San Diego, CA 92121, USA
| | - Eusebio Perdiguero
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Altos Labs Inc., San Diego Institute of Science, San Diego, CA 92121, USA
| | - Paolo Sassone-Corsi
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB), Barcelona, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Pura Muñoz-Cánoves
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Altos Labs Inc., San Diego Institute of Science, San Diego, CA 92121, USA
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
2
|
Mortimer T, Zinna VM, Atalay M, Laudanna C, Deryagin O, Posas G, Smith JG, García-Lara E, Vaca-Dempere M, Monteiro de Assis LV, Heyde I, Koronowski KB, Petrus P, Greco CM, Forrow S, Oster H, Sassone-Corsi P, Welz PS, Muñoz-Cánoves P, Benitah SA. The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis. Cell Stem Cell 2024:S1934-5909(24)00140-1. [PMID: 38701785 DOI: 10.1016/j.stem.2024.04.013] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]
Abstract
In mammals, the circadian clock network drives daily rhythms of tissue-specific homeostasis. To dissect daily inter-tissue communication, we constructed a mouse minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By transcriptomic and functional characterization of this isolated connection, we identified a gatekeeping function of the peripheral tissue clock with respect to systemic inputs. The epidermal clock concurrently integrates and subverts brain signals to ensure timely execution of epidermal daily physiology. Timely cell-cycle termination in the epidermal stem cell compartment depends upon incorporation of clock-driven signals originating from the brain. In contrast, the epidermal clock corrects or outcompetes potentially disruptive feeding-related signals to ensure the optimal timing of DNA replication. Together, we present an approach for cataloging the systemic dependencies of daily temporal organization in a tissue and identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.
Collapse
Affiliation(s)
- Thomas Mortimer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Muge Atalay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Carmelo Laudanna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Oleg Deryagin
- Universitat Pompeu Fabra (UPF), Department of Medicine and Life Sciences (MELIS), 08003 Barcelona, Spain
| | - Guillem Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Jacob G Smith
- Universitat Pompeu Fabra (UPF), Department of Medicine and Life Sciences (MELIS), 08003 Barcelona, Spain; Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Elisa García-Lara
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Mireia Vaca-Dempere
- Universitat Pompeu Fabra (UPF), Department of Medicine and Life Sciences (MELIS), 08003 Barcelona, Spain
| | | | - Isabel Heyde
- Institute of Neurobiology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Kevin B Koronowski
- Department of Biochemistry & Structural Biology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Medicine (H7), Karolinska Institute, 141 86 Stockholm, Sweden
| | - Carolina M Greco
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcinni 4, Pieve Emanuele, 20090 Milan, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Stephen Forrow
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Patrick-Simon Welz
- Hospital del Mar Research Institute, Cancer Research Programme, 08003 Barcelona, Spain.
| | - Pura Muñoz-Cánoves
- Universitat Pompeu Fabra (UPF), Department of Medicine and Life Sciences (MELIS), 08003 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Altos Labs Inc, San Diego Institute of Science, San Diego, CA 92121, USA.
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
| |
Collapse
|
3
|
Hong SH, Castro G, Wang D, Nofsinger R, Kane M, Folias A, Atkins AR, Yu RT, Napoli JL, Sassone-Corsi P, de Rooij DG, Liddle C, Downes M, Evans RM. Targeting nuclear receptor corepressors for reversible male contraception. Proc Natl Acad Sci U S A 2024; 121:e2320129121. [PMID: 38377195 PMCID: PMC10907271 DOI: 10.1073/pnas.2320129121] [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] [Received: 11/30/2023] [Accepted: 01/06/2024] [Indexed: 02/22/2024] Open
Abstract
Despite numerous female contraceptive options, nearly half of all pregnancies are unintended. Family planning choices for men are currently limited to unreliable condoms and invasive vasectomies with questionable reversibility. Here, we report the development of an oral contraceptive approach based on transcriptional disruption of cyclical gene expression patterns during spermatogenesis. Spermatogenesis involves a continuous series of self-renewal and differentiation programs of spermatogonial stem cells (SSCs) that is regulated by retinoic acid (RA)-dependent activation of receptors (RARs), which control target gene expression through association with corepressor proteins. We have found that the interaction between RAR and the corepressor silencing mediator of retinoid and thyroid hormone receptors (SMRT) is essential for spermatogenesis. In a genetically engineered mouse model that negates SMRT-RAR binding (SMRTmRID mice), the synchronized, cyclic expression of RAR-dependent genes along the seminiferous tubules is disrupted. Notably, the presence of an RA-resistant SSC population that survives RAR de-repression suggests that the infertility attributed to the loss of SMRT-mediated repression is reversible. Supporting this notion, we show that inhibiting the action of the SMRT complex with chronic, low-dose oral administration of a histone deacetylase inhibitor reversibly blocks spermatogenesis and fertility without affecting libido. This demonstration validates pharmacologic targeting of the SMRT repressor complex for non-hormonal male contraception.
Collapse
Affiliation(s)
- Suk-Hyun Hong
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Glenda Castro
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Dan Wang
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Russell Nofsinger
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Maureen Kane
- Department of Nutritional Sciences and Toxicology, The University of California, Berkeley, CA94720
| | - Alexandra Folias
- Department of Nutritional Sciences and Toxicology, The University of California, Berkeley, CA94720
| | - Annette R. Atkins
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Ruth T. Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Joseph L. Napoli
- Department of Nutritional Sciences and Toxicology, The University of California, Berkeley, CA94720
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, CA92697
| | - Dirk G. de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Christopher Liddle
- Storr Liver Centre, The Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead, NSW2145, Australia
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Ronald M. Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| |
Collapse
|
4
|
Smith JG, Molendijk J, Blazev R, Chen WH, Zhang Q, Litwin C, Zinna VM, Welz PS, Benitah SA, Greco CM, Sassone-Corsi P, Muñoz-Cánoves P, Parker BL, Koronowski KB. Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice. Mol Cell Proteomics 2023; 22:100655. [PMID: 37793502 PMCID: PMC10651687 DOI: 10.1016/j.mcpro.2023.100655] [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] [Received: 06/15/2023] [Revised: 09/01/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Molecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding are well defined at the transcriptional level, their impact on governing protein abundance in peripheral tissues is unclear. Here, we determine the relative contributions of local molecular clocks and daily feeding cycles on liver and muscle proteomes during the active phase in mice. LC-MS/MS was performed on liver and gastrocnemius muscle harvested 4 h into the dark phase from WT, Bmal1 KO, and dual liver- and muscle-Bmal1-rescued mice under either ad libitum feeding or time-restricted feeding during the dark phase. Feeding-fasting cycles had only minimal effects on levels of liver proteins and few, if any, on the muscle proteome. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver and 80 proteins in muscle. Local rescue of liver and muscle Bmal1 restored ∼50% of proteins in liver and ∼25% in muscle. These included proteins involved in fatty acid oxidation in liver and carbohydrate metabolism in muscle. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 in liver and muscle were enriched for secreted proteins. We found that the abundance of fibroblast growth factor 1, a liver secreted protein, requires BMAL1 and that autocrine fibroblast growth factor 1 signaling modulates mitochondrial respiration in hepatocytes. In liver and muscle, BMAL1 is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and many metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.
Collapse
Affiliation(s)
- Jacob G Smith
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Jeffrey Molendijk
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wan Hsi Chen
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, Texas, USA; Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA
| | - Qing Zhang
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Christopher Litwin
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Hospital del Mar Research Institute Barcelona, Cancer Research Program, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Carolina M Greco
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, California, USA
| | - Pura Muñoz-Cánoves
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Inc, San Diego Institute of Science, San Diego, California, USA
| | - Benjamin L Parker
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Kevin B Koronowski
- Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA; Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA.
| |
Collapse
|
5
|
Crosio C, Heitz E, Allis CD, Borrelli E, Sassone-Corsi P. Correction: Chromatin remodeling and neuronal response: multiple signaling pathways induce specific histone H3 modifications and early gene expression in hippocampal neurons. J Cell Sci 2023; 136:jcs261542. [PMID: 37650454 DOI: 10.1242/jcs.261542] [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: 09/01/2023] Open
|
6
|
Smith JG, Koronowski KB, Mortimer T, Sato T, Greco CM, Petrus P, Verlande A, Chen S, Samad M, Deyneka E, Mathur L, Blazev R, Molendijk J, Kumar A, Deryagin O, Vaca-Dempere M, Sica V, Liu P, Orlando V, Parker BL, Baldi P, Welz PS, Jang C, Masri S, Benitah SA, Muñoz-Cánoves P, Sassone-Corsi P. Liver and muscle circadian clocks cooperate to support glucose tolerance in mice. Cell Rep 2023; 42:112588. [PMID: 37267101 PMCID: PMC10592114 DOI: 10.1016/j.celrep.2023.112588] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 03/14/2022] [Revised: 03/28/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Physiology is regulated by interconnected cell and tissue circadian clocks. Disruption of the rhythms generated by the concerted activity of these clocks is associated with metabolic disease. Here we tested the interactions between clocks in two critical components of organismal metabolism, liver and skeletal muscle, by rescuing clock function either in each organ separately or in both organs simultaneously in otherwise clock-less mice. Experiments showed that individual clocks are partially sufficient for tissue glucose metabolism, yet the connections between both tissue clocks coupled to daily feeding rhythms support systemic glucose tolerance. This synergy relies in part on local transcriptional control of the glucose machinery, feeding-responsive signals such as insulin, and metabolic cycles that connect the muscle and liver. We posit that spatiotemporal mechanisms of muscle and liver play an essential role in the maintenance of systemic glucose homeostasis and that disrupting this diurnal coordination can contribute to metabolic disease.
Collapse
Affiliation(s)
- Jacob G Smith
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain.
| | - Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
| | - Thomas Mortimer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Laboratory of Nutritional Biochemistry, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Carolina M Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Medicine (H7), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Amandine Verlande
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Ekaterina Deyneka
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Lavina Mathur
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Ronnie Blazev
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jeffrey Molendijk
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Arun Kumar
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Oleg Deryagin
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Mireia Vaca-Dempere
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Valentina Sica
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Peng Liu
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Valerio Orlando
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Benjamin L Parker
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Program in Cancer Research, Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Cholsoon Jang
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
| | - Pura Muñoz-Cánoves
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Altos Labs, Inc., San Diego Institute of Science, San Diego, CA 92121, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| |
Collapse
|
7
|
Sato S, Hishida T, Kinouchi K, Hatanaka F, Li Y, Nguyen Q, Chen Y, Wang PH, Kessenbrock K, Li W, Izpisua Belmonte JC, Sassone-Corsi P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming. Cell Rep 2023; 42:112590. [PMID: 37261952 DOI: 10.1016/j.celrep.2023.112590] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Distinct metabolic conditions rewire circadian-clock-controlled signaling pathways leading to the de novo construction of signal transduction networks. However, it remains unclear whether metabolic hallmarks unique to pluripotent stem cells (PSCs) are connected to clock functions. Reprogramming somatic cells to a pluripotent state, here we highlighted non-canonical functions of the circadian repressor CRY1 specific to PSCs. Metabolic reprogramming, including AMPK inactivation and SREBP1 activation, was coupled with the accumulation of CRY1 in PSCs. Functional assays verified that CRY1 is required for the maintenance of self-renewal capacity, colony organization, and metabolic signatures. Genome-wide occupancy of CRY1 identified CRY1-regulatory genes enriched in development and differentiation in PSCs, albeit not somatic cells. Last, cells lacking CRY1 exhibit differential gene expression profiles during induced PSC (iPSC) reprogramming, resulting in impaired iPSC reprogramming efficiency. Collectively, these results suggest the functional implication of CRY1 in pluripotent reprogramming and ontogenesis, thereby dictating PSC identity.
Collapse
Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Fumiaki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| |
Collapse
|
8
|
Mendoza-Viveros L, Marmolejo-Gutierrez C, Cid-Castro C, Escalante-Covarrubias Q, Montellier E, Carreño-Vázquez E, Noriega LG, Velázquez-Villegas LA, Tovar AR, Sassone-Corsi P, Aguilar-Arnal L, Orozco-Solis R. Astrocytic circadian clock control of energy expenditure by transcriptional stress responses in the ventromedial hypothalamus. Glia 2023; 71:1626-1647. [PMID: 36919670 DOI: 10.1002/glia.24360] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
Hypothalamic circuits compute systemic information to control metabolism. Astrocytes residing within the hypothalamus directly sense nutrients and hormones, integrating metabolic information, and modulating neuronal responses. Nevertheless, the role of the astrocytic circadian clock on the control of energy balance remains unclear. We used mice with a targeted ablation of the core-clock gene Bmal1 within Gfap-expressing astrocytes to gain insight on the role played by this transcription factor in astrocytes. While this mutation does not substantially affect the phenotype in mice fed normo-caloric diet, under high-fat diet we unmasked a thermogenic phenotype consisting of increased energy expenditure, and catabolism in brown adipose and overall metabolic improvement consisting of better glycemia control, and body composition. Transcriptomic analysis in the ventromedial hypothalamus revealed an enhanced response to moderate cellular stress, including ER-stress response, unfolded protein response and autophagy. We identified Xbp1 and Atf1 as two key transcription factors enhancing cellular stress responses. Therefore, we unveiled a previously unknown role of the astrocytic circadian clock modulating energy balance through the regulation of cellular stress responses within the VMH.
Collapse
Affiliation(s)
- Lucia Mendoza-Viveros
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, México City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), México City, México
| | | | - Carolina Cid-Castro
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, México City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), México City, México
| | | | | | | | - Lilia G Noriega
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Armando R Tovar
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Lorena Aguilar-Arnal
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, México City, Mexico
| | - Ricardo Orozco-Solis
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), México City, México
| |
Collapse
|
9
|
Petrus P, Cervantes M, Samad M, Sato T, Chao A, Sato S, Koronowski KB, Park G, Alam Y, Mejhert N, Seldin MM, Monroy Kuhn JM, Dyar KA, Lutter D, Baldi P, Kaiser P, Jang C, Sassone-Corsi P. Tryptophan metabolism is a physiological integrator regulating circadian rhythms. Mol Metab 2022; 64:101556. [PMID: 35914650 PMCID: PMC9382333 DOI: 10.1016/j.molmet.2022.101556] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE The circadian clock aligns physiology with the 24-hour rotation of Earth. Light and food are the main environmental cues (zeitgebers) regulating circadian rhythms in mammals. Yet, little is known about the interaction between specific dietary components and light in coordinating circadian homeostasis. Herein, we focused on the role of essential amino acids. METHODS Mice were fed diets depleted of specific essential amino acids and their behavioral rhythms were monitored and tryptophan was selected for downstream analyses. The role of tryptophan metabolism in modulating circadian homeostasis was studied using isotope tracing as well as transcriptomic- and metabolomic- analyses. RESULTS Dietary tryptophan depletion alters behavioral rhythms in mice. Furthermore, tryptophan metabolism was shown to be regulated in a time- and light- dependent manner. A multi-omics approach and combinatory diet/light interventions demonstrated that tryptophan metabolism modulates temporal regulation of metabolism and transcription programs by buffering photic cues. Specifically, tryptophan metabolites regulate central circadian functions of the suprachiasmatic nucleus and the core clock machinery in the liver. CONCLUSIONS Tryptophan metabolism is a modulator of circadian homeostasis by integrating environmental cues. Our findings propose tryptophan metabolism as a potential point for pharmacologic intervention to modulate phenotypes associated with disrupted circadian rhythms.
Collapse
Affiliation(s)
- Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine (UCI), Irvine, CA, USA
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Alina Chao
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697, USA
| | - Shogo Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Grace Park
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697, USA
| | - Yasmine Alam
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697, USA
| | - Niklas Mejhert
- Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Marcus M Seldin
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - José Manuel Monroy Kuhn
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Kenneth A Dyar
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Metabolic Physiology, Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Zentrum Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dominik Lutter
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine (UCI), Irvine, CA, USA
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| |
Collapse
|
10
|
Petrus P, Smith JG, Koronowski KB, Chen S, Sato T, Greco CM, Mortimer T, Welz PS, Zinna VM, Shimaji K, Cervantes M, Punzo D, Baldi P, Muñoz-Cánoves P, Sassone-Corsi P, Aznar Benitah S. The central clock suffices to drive the majority of circulatory metabolic rhythms. Sci Adv 2022; 8:eabo2896. [PMID: 35767612 PMCID: PMC9242453 DOI: 10.1126/sciadv.abo2896] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/09/2022] [Indexed: 05/17/2023]
Abstract
Life on Earth anticipates recurring 24-hour environmental cycles via genetically encoded molecular clocks active in all mammalian organs. Communication between these clocks controls circadian homeostasis. Intertissue communication is mediated, in part, by temporal coordination of metabolism. Here, we characterize the extent to which clocks in different organs control systemic metabolic rhythms, an area that remains largely unexplored. We analyzed the metabolome of serum from mice with tissue-specific expression of the clock gene Bmal1. Having functional hepatic and muscle clocks can only drive a minority (13%) of systemic metabolic rhythms. Conversely, limiting Bmal1 expression to the central pacemaker in the brain restores rhythms to 57% of circulatory metabolites. Rhythmic feeding imposed on clockless mice resulted in a similar rescue, indicating that the central clock mainly regulates metabolic rhythms via behavior. These findings explicate the circadian communication between tissues and highlight the importance of the central clock in governing those signals.
Collapse
Affiliation(s)
- Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jacob G. Smith
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), E-08003 Barcelona, Spain
| | - Kevin B. Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Siwei Chen
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Laboratory of Nutritional Biochemistry, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Carolina M. Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital IRCCS, Via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Thomas Mortimer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Patrick-Simon Welz
- Hospital del Mar Medical Research Institute (IMIM), Cancer Research Programme, 08003 Barcelona, Spain
| | - Valentina M. Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Kohei Shimaji
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Daniela Punzo
- School of Medicine, Department of Microbiology and Molecular Genetics, INSERMU1233, Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), E-08003 Barcelona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Spanish National Center on Cardiovascular Research (CNIC), E-28029 Madrid, Spain
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
11
|
Smith JG, Sato T, Shimaji K, Koronowski KB, Petrus P, Cervantes M, Kinouchi K, Lutter D, Dyar KA, Sassone-Corsi P. Antibiotic-induced microbiome depletion remodels daily metabolic cycles in the brain. Life Sci 2022; 303:120601. [PMID: 35561749 DOI: 10.1016/j.lfs.2022.120601] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiome influences cognition and behavior in mammals, yet its metabolic impact on the brain is only starting to be defined. Using metabolite profiling of antibiotics-treated mice, we reveal the microbiome as a key input controlling circadian metabolic cycles in the brain. Intra and inter-region analyses characterise the influence of the microbiome on the suprachiasmatic nucleus, containing the central clockwork, as well as the hippocampus and cortex, regions involved in learning and behavior.
Collapse
Affiliation(s)
- Jacob G Smith
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Kohei Shimaji
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA; Division of Endocrinology, Metabolism, and Nephrology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Dominik Lutter
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Kenneth A Dyar
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Metabolic Physiology, Institute for Diabetes and Cancer, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| |
Collapse
|
12
|
Sato T, Sassone-Corsi P. Nutrition, metabolism, and epigenetics: pathways of circadian reprogramming. EMBO Rep 2022; 23:e52412. [PMID: 35412705 PMCID: PMC9066069 DOI: 10.15252/embr.202152412] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 01/07/2021] [Revised: 10/28/2021] [Accepted: 03/30/2022] [Indexed: 01/07/2023] Open
Abstract
Food intake profoundly affects systemic physiology. A large body of evidence has indicated a link between food intake and circadian rhythms, and ~24-h cycles are deemed essential for adapting internal homeostasis to the external environment. Circadian rhythms are controlled by the biological clock, a molecular system remarkably conserved throughout evolution. The circadian clock controls the cyclic expression of numerous genes, a regulatory program common to all mammalian cells, which may lead to various metabolic and physiological disturbances if hindered. Although the circadian clock regulates multiple metabolic pathways, metabolic states also provide feedback on the molecular clock. Therefore, a remarkable feature is reprogramming by nutritional challenges, such as a high-fat diet, fasting, ketogenic diet, and caloric restriction. In addition, various factors such as energy balance, histone modifications, and nuclear receptor activity are involved in the remodeling of the clock. Herein, we review the interaction of dietary components with the circadian system and illustrate the relationships linking the molecular clock to metabolism and critical roles in the remodeling process.
Collapse
Affiliation(s)
- Tomoki Sato
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, INSERM U1233, University of California, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, INSERM U1233, University of California, Irvine, CA, USA
| |
Collapse
|
13
|
Cervantes M, Lewis RG, Della-Fazia MA, Borrelli E, Sassone-Corsi P. Dopamine D2 receptor signaling in the brain modulates circadian liver metabolomic profiles. Proc Natl Acad Sci U S A 2022; 119:e2117113119. [PMID: 35271395 PMCID: PMC8931347 DOI: 10.1073/pnas.2117113119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/16/2021] [Accepted: 02/08/2022] [Indexed: 02/04/2023] Open
Abstract
SignificanceWe analyzed the liver metabolome of mice deficient in the expression of the dopamine D2 receptor (D2R) in striatal medium spiny neurons (iMSN-D2RKO) and found profound changes in the liver circadian metabolome compared to control mice. Additionally, we show activation of dopaminergic circuits by acute cocaine administration in iMSN-D2RKO mice reprograms the circadian liver metabolome in response to cocaine. D2R signaling in MSNs is key for striatal output and essential for regulating the first response to the cellular and rewarding effects of cocaine. Our results suggest changes in dopamine signaling in specific striatal neurons evoke major changes in liver physiology. Dysregulation of liver metabolism could contribute to an altered allostatic state and therefore be involved in continued use of drugs.
Collapse
Affiliation(s)
- Marlene Cervantes
- INSERM U1233, Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - Robert G. Lewis
- INSERM U1233, Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697
| | | | - Emiliana Borrelli
- INSERM U1233, Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697
| | - Paolo Sassone-Corsi
- INSERM U1233, Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| |
Collapse
|
14
|
Sato S, Dyar KA, Treebak JT, Jepsen SL, Ehrlich AM, Ashcroft SP, Trost K, Kunzke T, Prade VM, Small L, Basse AL, Schönke M, Chen S, Samad M, Baldi P, Barrès R, Walch A, Moritz T, Holst JJ, Lutter D, Zierath JR, Sassone-Corsi P. Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis. Cell Metab 2022; 34:329-345.e8. [PMID: 35030324 DOI: 10.1016/j.cmet.2021.12.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [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: 09/29/2020] [Revised: 11/22/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
Abstract
Tissue sensitivity and response to exercise vary according to the time of day and alignment of circadian clocks, but the optimal exercise time to elicit a desired metabolic outcome is not fully defined. To understand how tissues independently and collectively respond to timed exercise, we applied a systems biology approach. We mapped and compared global metabolite responses of seven different mouse tissues and serum after an acute exercise bout performed at different times of the day. Comparative analyses of intra- and inter-tissue metabolite dynamics, including temporal profiling and blood sampling across liver and hindlimb muscles, uncovered an unbiased view of local and systemic metabolic responses to exercise unique to time of day. This comprehensive atlas of exercise metabolism provides clarity and physiological context regarding the production and distribution of canonical and novel time-dependent exerkine metabolites, such as 2-hydroxybutyrate (2-HB), and reveals insight into the health-promoting benefits of exercise on metabolism.
Collapse
Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kenneth A Dyar
- Metabolic Physiology, Institute for Diabetes and Cancer, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara L Jepsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Amy M Ehrlich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen P Ashcroft
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kajetan Trost
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Verena M Prade
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lewin Small
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Astrid Linde Basse
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Milena Schönke
- Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Moritz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Dominik Lutter
- German Center for Diabetes Research, Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| |
Collapse
|
15
|
Petrus P, Sassone-Corsi P. Circadian Analysis of Rodent Locomotor Activity in Home Cages. Methods Mol Biol 2022; 2482:211-215. [PMID: 35610429 DOI: 10.1007/978-1-0716-2249-0_14] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rhythmic locomotor activity is a commonly used readout of general circadian function in animals. For instance, measuring the activity of rodents in their home cages can provide information about circadian phase and period in response to genetic, pharmacological, and environmental manipulations. Herein, the use of infrared light sensors to measure circadian locomotor activity is described. Furthermore, we provide information about data handling, analysis and software use as well as points to consider when performing the experiment.
Collapse
Affiliation(s)
- Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA
| |
Collapse
|
16
|
Koronowski KB, Sassone-Corsi P. Real-Time Measurement of Energy Metabolism Over Circadian Time Using Indirect Calorimetry-Enabled Metabolic Cages. Methods Mol Biol 2022; 2482:301-310. [PMID: 35610435 DOI: 10.1007/978-1-0716-2249-0_20] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Indirect calorimetry probes the relationship between fuel consumed and energy produced, and in doing so provides an estimation of whole-body energy expenditure and fuel preference. When assayed continuously in real-time, rhythms appear and illuminate the temporal regulation of energy metabolism by the circadian clock. Here we describe a method for recording circadian energy metabolism in mice using indirect calorimetry-enabled metabolic cages, encompassing mouse entrainment, experimental design, data acquisition and analysis, troubleshooting of common problems, and important considerations. This method is adaptable to the end user's equipment and serves as an effective tool to study, for example, mutant mice, dietary interventions, drug treatments, or circadian disruption.
Collapse
Affiliation(s)
- Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA
| |
Collapse
|
17
|
Greco CM, Koronowski KB, Smith JG, Shi J, Kunderfranco P, Carriero R, Chen S, Samad M, Welz PS, Zinna VM, Mortimer T, Chun SK, Shimaji K, Sato T, Petrus P, Kumar A, Vaca-Dempere M, Deryagian O, Van C, Kuhn JMM, Lutter D, Seldin MM, Masri S, Li W, Baldi P, Dyar KA, Muñoz-Cánoves P, Benitah SA, Sassone-Corsi P. Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms. Sci Adv 2021; 7:eabi7828. [PMID: 34550736 PMCID: PMC8457671 DOI: 10.1126/sciadv.abi7828] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/29/2021] [Indexed: 05/28/2023]
Abstract
The mammalian circadian clock, expressed throughout the brain and body, controls daily metabolic homeostasis. Clock function in peripheral tissues is required, but not sufficient, for this task. Because of the lack of specialized animal models, it is unclear how tissue clocks interact with extrinsic signals to drive molecular oscillations. Here, we isolated the interaction between feeding and the liver clock by reconstituting Bmal1 exclusively in hepatocytes (Liver-RE), in otherwise clock-less mice, and controlling timing of food intake. We found that the cooperative action of BMAL1 and the transcription factor CEBPB regulates daily liver metabolic transcriptional programs. Functionally, the liver clock and feeding rhythm are sufficient to drive temporal carbohydrate homeostasis. By contrast, liver rhythms tied to redox and lipid metabolism required communication with the skeletal muscle clock, demonstrating peripheral clock cross-talk. Our results highlight how the inner workings of the clock system rely on communicating signals to maintain daily metabolism.
Collapse
Affiliation(s)
- Carolina M. Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kevin B. Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jacob G. Smith
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jiejun Shi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Kunderfranco
- Bioinformatics Unit, Humanitas Clinical and Research Center–IRCCS, Rozzano 20089, Italy
| | - Roberta Carriero
- Bioinformatics Unit, Humanitas Clinical and Research Center–IRCCS, Rozzano 20089, Italy
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Program in Cancer Research, Hospital del Mar Medical Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Valentina M. Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Thomas Mortimer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Sung Kook Chun
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kohei Shimaji
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Arun Kumar
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Mireia Vaca-Dempere
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Oleg Deryagian
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Cassandra Van
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - José Manuel Monroy Kuhn
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Dominik Lutter
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Marcus M. Seldin
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Wei Li
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Kenneth A. Dyar
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Metabolic Physiology, Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
- Spanish National Center on Cardiovascular Research (CNIC), Madrid 28029, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| |
Collapse
|
18
|
Koronowski KB, Greco CM, Huang H, Kim JK, Fribourgh JL, Crosby P, Mathur L, Ren X, Partch CL, Jang C, Qiao F, Zhao Y, Sassone-Corsi P. Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation. Cell Rep 2021; 36:109487. [PMID: 34348140 PMCID: PMC8372761 DOI: 10.1016/j.celrep.2021.109487] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 05/01/2020] [Revised: 05/03/2021] [Accepted: 07/14/2021] [Indexed: 01/20/2023] Open
Abstract
Ketone bodies are bioactive metabolites that function as energy substrates, signaling molecules, and regulators of histone modifications. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, and associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification, and one-carbon metabolic pathways. Kbhb inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, in parallel with altered metabolite levels. Our results illuminate the role of Kbhb in hepatic metabolism under ketogenic conditions and demonstrate a functional consequence of this modification on a central metabolic enzyme.
Collapse
Affiliation(s)
- Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Carolina M Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - He Huang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jin-Kwang Kim
- Department of Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lavina Mathur
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cholsoon Jang
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Feng Qiao
- Department of Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| |
Collapse
|
19
|
Bellet MM, Stincardini C, Costantini C, Gargaro M, Pieroni S, Castelli M, Piobbico D, Sassone-Corsi P, Della-Fazia MA, Romani L, Servillo G. The Circadian Protein PER1 Modulates the Cellular Response to Anticancer Treatments. Int J Mol Sci 2021; 22:ijms22062974. [PMID: 33804124 PMCID: PMC8001324 DOI: 10.3390/ijms22062974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 01/30/2023] Open
Abstract
The circadian clock driven by the daily light–dark and temperature cycles of the environment regulates fundamental physiological processes and perturbations of these sophisticated mechanisms may result in pathological conditions, including cancer. While experimental evidence is building up to unravel the link between circadian rhythms and tumorigenesis, it is becoming increasingly apparent that the response to antitumor agents is similarly dependent on the circadian clock, given the dependence of each drug on the circadian regulation of cell cycle, DNA repair and apoptosis. However, the molecular mechanisms that link the circadian machinery to the action of anticancer treatments is still poorly understood, thus limiting the application of circadian rhythms-driven pharmacological therapy, or chronotherapy, in the clinical practice. Herein, we demonstrate the circadian protein period 1 (PER1) and the tumor suppressor p53 negatively cross-regulate each other’s expression and activity to modulate the sensitivity of cancer cells to anticancer treatments. Specifically, PER1 physically interacts with p53 to reduce its stability and impair its transcriptional activity, while p53 represses the transcription of PER1. Functionally, we could show that PER1 reduced the sensitivity of cancer cells to drug-induced apoptosis, both in vitro and in vivo in NOD scid gamma (NSG) mice xenotransplanted with a lung cancer cell line. Therefore, our results emphasize the importance of understanding the relationship between the circadian clock and tumor regulatory proteins as the basis for the future development of cancer chronotherapy.
Collapse
Affiliation(s)
- Marina Maria Bellet
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
- Correspondence: (M.M.B.); (G.S.); Tel.: +39-0755858238 (M.M.B.); +39-0755858110 (G.S.)
| | - Claudia Stincardini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Stefania Pieroni
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Marilena Castelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Danilo Piobbico
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, CA 92617, USA;
| | - Maria Agnese Della-Fazia
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Giuseppe Servillo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
- Correspondence: (M.M.B.); (G.S.); Tel.: +39-0755858238 (M.M.B.); +39-0755858110 (G.S.)
| |
Collapse
|
20
|
Abstract
Circadian clocks temporally coordinate physiology and align it with geophysical time, which enables diverse life-forms to anticipate daily environmental cycles. In complex organisms, clock function originates from the molecular oscillator within each cell and builds upward anatomically into an organism-wide system. Recent advances have transformed our understanding of how clocks are connected to achieve coherence across tissues. Circadian misalignment, often imposed in modern society, disrupts coordination among clocks and has been linked to diseases ranging from metabolic syndrome to cancer. Thus, uncovering the physiological circuits whereby biological clocks achieve coherence will inform on both challenges and opportunities in human health.
Collapse
Affiliation(s)
- Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| |
Collapse
|
21
|
Helbling JC, Kinouchi K, Trifilieff P, Sassone-Corsi P, Moisan MP. Combined Gene Expression and Chromatin Immunoprecipitation From a Single Mouse Hippocampus. Curr Protoc 2021; 1:e33. [PMID: 33566459 DOI: 10.1002/cpz1.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
All neuronal cells hold the same genetic information but vary by their structural and functional plasticity depending on the brain area and environmental influences. Such variability involves specific gene regulation, which is driven by transcription factors (TFs). In the field of neuroscience, epigenetics is the main mechanism that has been investigated to understand the dynamic modulation of gene expression by behavioral responses, stress responses, memory processes, etc. Nowadays, gene expression analyzed by real-time quantitative PCR and TF binding estimated by chromatin immunoprecipitation (ChIP) enables one to dissect this regulation. Because of the wide range of transgenic models, as well as cost-effective aspects, mouse models are widely used neuroscience. Thus, we have set up a protocol that allows extraction of both RNA for gene expression analysis and chromatin for ChIP experiment from a single mouse hippocampus. Using such protocols, information regarding gene expression and regulatory molecular mechanisms from the same animal can be integrated and correlated with neurobiological and behavioral outcomes. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Hippocampus isolation from mouse brain Basic Protocol 2: RNA extraction and gene expression analysis from a mouse half hippocampus Basic Protocol 3: ChIP from one hemisphere side mouse hippocampus.
Collapse
Affiliation(s)
| | - Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California Irvine, Irvine, California
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan
| | - Pierre Trifilieff
- University of Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, Bordeaux, France
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California Irvine, Irvine, California
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, Irvine, California
| | - Marie-Pierre Moisan
- University of Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, Bordeaux, France
| |
Collapse
|
22
|
Greco CM, Cervantes M, Fustin JM, Ito K, Ceglia N, Samad M, Shi J, Koronowski KB, Forne I, Ranjit S, Gaucher J, Kinouchi K, Kojima R, Gratton E, Li W, Baldi P, Imhof A, Okamura H, Sassone-Corsi P. S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling. Sci Adv 2020; 6:eabc5629. [PMID: 33328229 PMCID: PMC7744083 DOI: 10.1126/sciadv.abc5629] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/30/2020] [Indexed: 05/03/2023]
Abstract
Circadian gene expression driven by transcription activators CLOCK and BMAL1 is intimately associated with dynamic chromatin remodeling. However, how cellular metabolism directs circadian chromatin remodeling is virtually unexplored. We report that the S-adenosylhomocysteine (SAH) hydrolyzing enzyme adenosylhomocysteinase (AHCY) cyclically associates to CLOCK-BMAL1 at chromatin sites and promotes circadian transcriptional activity. SAH is a potent feedback inhibitor of S-adenosylmethionine (SAM)-dependent methyltransferases, and timely hydrolysis of SAH by AHCY is critical to sustain methylation reactions. We show that AHCY is essential for cyclic H3K4 trimethylation, genome-wide recruitment of BMAL1 to chromatin, and subsequent circadian transcription. Depletion or targeted pharmacological inhibition of AHCY in mammalian cells markedly decreases the amplitude of circadian gene expression. In mice, pharmacological inhibition of AHCY in the hypothalamus alters circadian locomotor activity and rhythmic transcription within the suprachiasmatic nucleus. These results reveal a previously unappreciated connection between cellular metabolism, chromatin dynamics, and circadian regulation.
Collapse
Affiliation(s)
- Carolina Magdalen Greco
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA.
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA
| | - Jean-Michel Fustin
- Graduate School of Pharmaceutical Sciences, Department of Systems Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Kakeru Ito
- Graduate School of Pharmaceutical Sciences, Department of Systems Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Nicholas Ceglia
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine (UCI), Irvine, CA, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine (UCI), Irvine, CA, USA
| | - Jiejun Shi
- Department of Biological Chemistry, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin Brian Koronowski
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA
| | - Ignasi Forne
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine (UCI), Irvine, CA, USA
| | - Jonathan Gaucher
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA
| | - Rika Kojima
- Graduate School of Pharmaceutical Sciences, Department of Systems Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine (UCI), Irvine, CA, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine (UCI), Irvine, CA, USA
| | - Axel Imhof
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Hitoshi Okamura
- Graduate School of Pharmaceutical Sciences, Department of Systems Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism; U1233 INSERM; Department of Biological Chemistry, School of Medicine, University of California, Irvine (UCI), Irvine, CA, USA.
| |
Collapse
|
23
|
Abstract
Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
Collapse
Affiliation(s)
- Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
| |
Collapse
|
24
|
Hawley JA, Sassone-Corsi P, Zierath JR. Chrono-nutrition for the prevention and treatment of obesity and type 2 diabetes: from mice to men. Diabetologia 2020; 63:2253-2259. [PMID: 32761356 DOI: 10.1007/s00125-020-05238-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 03/04/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
The proliferation in the rate of diagnosis of obesity and type 2 diabetes mellitus continues unabated, with current recommendations for primary lifestyle changes (i.e. modification to dietary patterns) having a limited impact in reducing the incidence of these metabolic diseases. Part of the reason for the failure to alter nutritional practices is that current dietary recommendations may be unrealistic for the majority of adults. Indeed, round-the-clock access to energy-dense, nutrient-poor food makes long-term changes to dietary habits challenging. Hence, there is urgent need for innovations in the delivery of evidence-based diet interventions to rescue some of the deleterious effects on circadian biology induced by our modern-day lifestyle. With the growing appreciation that the duration over which food is consumed during a day has profound effects on numerous physiological and metabolic processes, we discuss dietary protocols that modify the timing of food intake to deliberately alter the feeding-fasting cycle. Such chrono-nutrition functions to optimise metabolism by timing nutrient intake to the acrophases of metabolic rhythms to improve whole-body insulin sensitivity and glycaemic control, and thereby positively impact metabolic health. Graphical abstract.
Collapse
Affiliation(s)
- John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia.
| | - Paolo Sassone-Corsi
- INSERM U1233-Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
25
|
Debski KJ, Ceglia N, Ghestem A, Ivanov AI, Brancati GE, Bröer S, Bot AM, Müller JA, Schoch S, Becker A, Löscher W, Guye M, Sassone-Corsi P, Lukasiuk K, Baldi P, Bernard C. The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental temporal lobe epilepsy. Sci Adv 2020; 6:eaat5979. [PMID: 33036982 PMCID: PMC10764101 DOI: 10.1126/sciadv.aat5979] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Gene and protein expressions display circadian oscillations, which can be disrupted in diseases in most body organs. Whether these oscillations occur in the healthy hippocampus and whether they are altered in epilepsy are not known. We identified more than 1200 daily oscillating transcripts in the hippocampus of control mice and 1600 in experimental epilepsy, with only one-fourth oscillating in both conditions. Comparison of gene oscillations in control and epilepsy predicted time-dependent alterations in energy metabolism, which were verified experimentally. Although aerobic glycolysis remained constant from morning to afternoon in controls, it increased in epilepsy. In contrast, oxidative phosphorylation increased in control and decreased in epilepsy. Thus, the control hippocampus shows circadian molecular remapping, which is altered in epilepsy. We suggest that the hippocampus operates in a different functioning mode in epilepsy. These alterations need to be considered when studying epilepsy mechanisms, designing drug treatments, and timing their delivery.
Collapse
Affiliation(s)
- K J Debski
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
- Bioinformatics Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - N Ceglia
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3435, USA
| | - A Ghestem
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - A I Ivanov
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - G E Brancati
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - S Bröer
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - A M Bot
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - J A Müller
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - S Schoch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - A Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - W Löscher
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - M Guye
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France
- APHM, Hôpital Universitaire Timone, CEMEREM, Marseille, France
| | - P Sassone-Corsi
- Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - K Lukasiuk
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - P Baldi
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3435, USA
| | - C Bernard
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France.
| |
Collapse
|
26
|
Lundell LS, Parr EB, Devlin BL, Ingerslev LR, Altıntaş A, Sato S, Sassone-Corsi P, Barrès R, Zierath JR, Hawley JA. Time-restricted feeding alters lipid and amino acid metabolite rhythmicity without perturbing clock gene expression. Nat Commun 2020; 11:4643. [PMID: 32938935 PMCID: PMC7495469 DOI: 10.1038/s41467-020-18412-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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] [Received: 05/02/2019] [Accepted: 08/16/2020] [Indexed: 12/20/2022] Open
Abstract
Time-restricted feeding (TRF) improves metabolism independent of dietary macronutrient composition or energy restriction. To elucidate mechanisms underpinning the effects of short-term TRF, we investigated skeletal muscle and serum metabolic and transcriptomic profiles from 11 men with overweight/obesity after TRF (8 h day-1) and extended feeding (EXF, 15 h day-1) in a randomised cross-over design (trial registration: ACTRN12617000165381). Here we show that muscle core clock gene expression was similar after both interventions. TRF increases the amplitude of oscillating muscle transcripts, but not muscle or serum metabolites. In muscle, TRF induces rhythmicity of several amino acid transporter genes and metabolites. In serum, lipids are the largest class of periodic metabolites, while the majority of phase-shifted metabolites are amino acid related. In conclusion, short-term TRF in overweight men affects the rhythmicity of serum and muscle metabolites and regulates the rhythmicity of genes controlling amino acid transport, without perturbing core clock gene expression.
Collapse
Affiliation(s)
- Leonidas S Lundell
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Evelyn B Parr
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia
| | - Brooke L Devlin
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shogo Sato
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia.
| |
Collapse
|
27
|
Brami-Cherrier K, Lewis RG, Cervantes M, Liu Y, Tognini P, Baldi P, Sassone-Corsi P, Borrelli E. Cocaine-mediated circadian reprogramming in the striatum through dopamine D2R and PPARγ activation. Nat Commun 2020; 11:4448. [PMID: 32895370 PMCID: PMC7477550 DOI: 10.1038/s41467-020-18200-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 01/16/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Substance abuse disorders are linked to alteration of circadian rhythms, although the molecular and neuronal pathways implicated have not been fully elucidated. Addictive drugs, such as cocaine, induce a rapid increase of dopamine levels in the brain. Here, we show that acute administration of cocaine triggers reprogramming in circadian gene expression in the striatum, an area involved in psychomotor and rewarding effects of drugs. This process involves the activation of peroxisome protein activator receptor gamma (PPARγ), a nuclear receptor involved in inflammatory responses. PPARγ reprogramming is altered in mice with cell-specific ablation of the dopamine D2 receptor (D2R) in the striatal medium spiny neurons (MSNs) (iMSN-D2RKO). Administration of a specific PPARγ agonist in iMSN-D2RKO mice elicits substantial rescue of cocaine-dependent control of circadian genes. These findings have potential implications for development of strategies to treat substance abuse disorders. Drugs of abuse have been shown to perturb circadian rhythms. Here, the authors show in mice that cocaine exposure modulates circadian gene expression in the striatum through a previously unappreciated pathway that involves dopamine D2 receptors and the nuclear receptor PPARγ.
Collapse
Affiliation(s)
- Karen Brami-Cherrier
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Robert G Lewis
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Yu Liu
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine, Irvine, CA, 92697, USA
| | - Paola Tognini
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine, Irvine, CA, 92697, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA.
| | - Emiliana Borrelli
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
| |
Collapse
|
28
|
Greco CM, Garetto S, Montellier E, Liu Y, Chen S, Baldi P, Sassone-Corsi P, Lucci J. A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome. Sci Rep 2020; 10:12915. [PMID: 32737396 PMCID: PMC7395094 DOI: 10.1038/s41598-020-69469-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/14/2019] [Accepted: 07/01/2020] [Indexed: 12/29/2022] Open
Abstract
Metabolic syndrome has increased at a worrisome level. Lifestyle changes are not sufficient to prevent and improve the adverse effects of obesity, thus novel interventions are necessary. The aim of this study was to investigate the use and metabolic outcomes of a non-pharmacological intervention in a high-fat diet (HFD) fed mouse model, capable of recapitulating key aspects of metabolic syndrome. We show that Policaptil Gel Retard has remarkable, beneficial effects on metabolic dysfunction caused by consumption of HFD. We describe the mechanism by which such effects are obtained, highlighting the fact that the amelioration of metabolic function observed upon Policaptil Gel Retard administration is profound and of systemic nature, despite being originated by sequestering, therefore non-pharmacological events elicited in the gut lumen.
Collapse
Affiliation(s)
- Carolina Magdalen Greco
- Department of Biological Chemistry, School of Medicine, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine (UCI), Irvine, CA, 92697, USA
| | - Stefano Garetto
- Natural Bio-Medicine SpA, Loc. Aboca 20, 52037, Sansepolcro, AR, Italy.,Innovation & Medical Science Division, Aboca SpA Società Agricola, Loc. Aboca 20, 52037, Sansepolcro, AR, Italy
| | - Emilie Montellier
- Department of Biological Chemistry, School of Medicine, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine (UCI), Irvine, CA, 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, UCI, Irvine, CA, 92697, USA
| | - Siwei Chen
- Department of Computer Science, Institute for Genomics and Bioinformatics, UCI, Irvine, CA, 92697, USA
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, UCI, Irvine, CA, 92697, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, School of Medicine, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine (UCI), Irvine, CA, 92697, USA.
| | - Jacopo Lucci
- Natural Bio-Medicine SpA, Loc. Aboca 20, 52037, Sansepolcro, AR, Italy. .,Innovation & Medical Science Division, Aboca SpA Società Agricola, Loc. Aboca 20, 52037, Sansepolcro, AR, Italy.
| |
Collapse
|
29
|
Abstract
Circadian rhythms govern physiology and metabolism, leading to controlled homeostasis. We discuss the impact of circadian rhythms on society and the challenges for the imminent future of personalized medicine.
Collapse
Affiliation(s)
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California Irvine, Irvine, CA
| |
Collapse
|
30
|
Cervantes M, Forné I, Ranjit S, Gratton E, Imhof A, Sassone-Corsi P. BMAL1 Associates with NOP58 in the Nucleolus and Contributes to Pre-rRNA Processing. iScience 2020; 23:101151. [PMID: 32450515 PMCID: PMC7256328 DOI: 10.1016/j.isci.2020.101151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 02/14/2020] [Revised: 03/30/2020] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
The transcription factor BMAL1 is a core element of the circadian clock that contributes to cyclic control of genes transcribed by RNA polymerase II. By using biochemical cellular fractionation and immunofluorescence analyses we reveal a previously uncharacterized nucleolar localization for BMAL1. We used an unbiased approach to determine the BMAL1 interactome by mass spectrometry and identified NOP58 as a prominent nucleolar interactor. NOP58, a core component of the box C/D small nucleolar ribonucleoprotein complex, associates with Snord118 to control specific pre-ribosomal RNA (pre-rRNA) processing steps. These results suggest a non-canonical role of BMAL1 in ribosomal RNA regulation. Indeed, we show that BMAL1 controls NOP58-associated Snord118 nucleolar levels and cleavage of unique pre-rRNA intermediates. Our findings identify an unsuspected function of BMAL1 in the nucleolus that appears distinct from its canonical role in the circadian clock system. BMAL1 displays a circadian-independent localization in the nucleolus Bmal1-deficient cells show altered nucleolar morphology Interactome proteomics reveals that BMAL1 associates with nucleolar proteins BMAL1 appears to play a non-canonical, non-circadian role in pre-rRNA processing
Collapse
Affiliation(s)
- Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich 80539, Germany
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich 80539, Germany
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
31
|
Welz PS, Zinna VM, Symeonidi A, Koronowski KB, Kinouchi K, Smith JG, Guillén IM, Castellanos A, Furrow S, Aragón F, Crainiciuc G, Prats N, Caballero JM, Hidalgo A, Sassone-Corsi P, Benitah SA. BMAL1-Driven Tissue Clocks Respond Independently to Light to Maintain Homeostasis. Cell 2020; 177:1436-1447.e12. [PMID: 31150620 DOI: 10.1016/j.cell.2019.05.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/23/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
Circadian rhythms control organismal physiology throughout the day. At the cellular level, clock regulation is established by a self-sustained Bmal1-dependent transcriptional oscillator network. However, it is still unclear how different tissues achieve a synchronized rhythmic physiology. That is, do they respond independently to environmental signals, or require interactions with each other to do so? We show that unexpectedly, light synchronizes the Bmal1-dependent circadian machinery in single tissues in the absence of Bmal1 in all other tissues. Strikingly, light-driven tissue autonomous clocks occur without rhythmic feeding behavior and are lost in constant darkness. Importantly, tissue-autonomous Bmal1 partially sustains homeostasis in otherwise arrhythmic and prematurely aging animals. Our results therefore support a two-branched model for the daily synchronization of tissues: an autonomous response branch, whereby light entrains circadian clocks without any commitment of other Bmal1-dependent clocks, and a memory branch using other Bmal1-dependent clocks to "remember" time in the absence of external cues.
Collapse
Affiliation(s)
- Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Aikaterini Symeonidi
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Kevin B Koronowski
- Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Jacob G Smith
- Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Inés Marín Guillén
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Andrés Castellanos
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Stephen Furrow
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ferrán Aragón
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Georgiana Crainiciuc
- Area of Developmental and Cell Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Andrés Hidalgo
- Area of Developmental and Cell Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; Institute for Cardiovascular Prevention, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA.
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; ICREA, Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain.
| |
Collapse
|
32
|
Abstract
The circadian clock is an endogenous, time-tracking system that directs multiple metabolic and physiological functions required for homeostasis. The master or central clock located within the suprachiasmatic nucleus in the hypothalamus governs peripheral clocks present in all systemic tissues, contributing to their alignment and ultimately to temporal coordination of physiology. Accumulating evidence reveals the presence of additional clocks in the brain and suggests the possibility that circadian circuits may feed back to these from the periphery. Here, we highlight recent advances in the communications between clocks and discuss how they relate to circadian physiology and metabolism.
Collapse
Affiliation(s)
- Carolina Magdalen Greco
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, USA.
| |
Collapse
|
33
|
Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Rep 2019; 25:3299-3314.e6. [PMID: 30566858 DOI: 10.1016/j.celrep.2018.11.077] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 12/14/2017] [Revised: 09/08/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The circadian clock operates as intrinsic time-keeping machinery to preserve homeostasis in response to the changing environment. While food is a known zeitgeber for clocks in peripheral tissues, it remains unclear how lack of food influences clock function. We demonstrate that the transcriptional response to fasting operates through molecular mechanisms that are distinct from time-restricted feeding regimens. First, fasting affects core clock genes and proteins, resulting in blunted rhythmicity of BMAL1 and REV-ERBα both in liver and skeletal muscle. Second, fasting induces a switch in temporal gene expression through dedicated fasting-sensitive transcription factors such as GR, CREB, FOXO, TFEB, and PPARs. Third, the rhythmic genomic response to fasting is sustainable by prolonged fasting and reversible by refeeding. Thus, fasting imposes specialized dynamics of transcriptional coordination between the clock and nutrient-sensitive pathways, thereby achieving a switch to fasting-specific temporal gene regulation.
Collapse
Affiliation(s)
- Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Christophe Magnan
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Nicholas Ceglia
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Nunzia Pastore
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
34
|
Ferreira LL, Cervantes M, Froufe HJC, Egas C, Cunha-Oliveira T, Sassone-Corsi P, Oliveira PJ. Doxorubicin persistently rewires cardiac circadian homeostasis in mice. Arch Toxicol 2019; 94:257-271. [PMID: 31768571 DOI: 10.1007/s00204-019-02626-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/05/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022]
Abstract
Circadian rhythms disruption can be the cause of chronic diseases. External cues, including therapeutic drugs, have been shown to modulate peripheral-circadian clocks. Since anthracycline cardiotoxicity is associated with loss of mitochondrial function and metabolic remodeling, we investigated whether the energetic failure induced by sub-chronic doxorubicin (DOX) treatment in juvenile mice was associated with persistent disruption of circadian regulators. Juvenile C57BL/6J male mice were subjected to a sub-chronic DOX treatment (4 weekly injections of 5 mg/kg DOX) and several cardiac parameters, as well as circadian-gene expression and acetylation patterns, were analyzed after 6 weeks of recovery time. Complementary experiments were performed with Mouse Embryonic Fibroblasts (MEFs) and Human Embryonic Kidney 293 cells. DOX-treated juvenile mice showed cardiotoxicity markers and persistent alterations of transcriptional- and signaling cardiac circadian homeostasis. The results showed a delayed influence of DOX on gene expression, accompanied by changes in SIRT1-mediated cyclic deacetylation. The mechanism behind DOX interference with the circadian clock was further studied in vitro, in which were observed alterations of circadian-gene expression and increased BMAL1 SIRT1-mediated deacetylation. In conclusion, DOX treatment in juvenile mice resulted in disruption of oscillatory molecular mechanisms including gene expression and acetylation profiles.
Collapse
Affiliation(s)
- Luciana L Ferreira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal
| | - Marlene Cervantes
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Hugo J C Froufe
- Next Generation Sequencing Unit, Biocant, Biocant Park, Núcleo 04, Lote 8, Cantanhede, Portugal
| | - Conceição Egas
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal.,Next Generation Sequencing Unit, Biocant, Biocant Park, Núcleo 04, Lote 8, Cantanhede, Portugal
| | - Teresa Cunha-Oliveira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Paulo J Oliveira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal. .,Institute for Interdisciplinary Research (I.I.I.), University of Coimbra, Coimbra, Portugal.
| |
Collapse
|
35
|
Welz PS, Zinna VM, Symeonidi A, Koronowski KB, Kinouchi K, Smith JG, Guillén IM, Castellanos A, Furrow S, Aragón F, Crainiciuc G, Prats N, Caballero JM, Hidalgo A, Sassone-Corsi P, Benitah SA. BMAL1-Driven Tissue Clocks Respond Independently to Light to Maintain Homeostasis. Cell 2019; 178:1029. [PMID: 31398328 DOI: 10.1016/j.cell.2019.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
36
|
Sato S, Basse AL, Schönke M, Chen S, Samad M, Altıntaş A, Laker RC, Dalbram E, Barrès R, Baldi P, Treebak JT, Zierath JR, Sassone-Corsi P. Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis. Cell Metab 2019; 30:92-110.e4. [PMID: 31006592 DOI: 10.1016/j.cmet.2019.03.013] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [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: 08/31/2018] [Revised: 02/06/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022]
Abstract
While the timing of food intake is important, it is unclear whether the effects of exercise on energy metabolism are restricted to unique time windows. As circadian regulation is key to controlling metabolism, understanding the impact of exercise performed at different times of the day is relevant for physiology and homeostasis. Using high-throughput transcriptomic and metabolomic approaches, we identify distinct responses of metabolic oscillations that characterize exercise in either the early rest phase or the early active phase in mice. Notably, glycolytic activation is specific to exercise at the active phase. At the molecular level, HIF1α, a central regulator of glycolysis during hypoxia, is selectively activated in a time-dependent manner upon exercise, resulting in carbohydrate exhaustion, usage of alternative energy sources, and adaptation of systemic energy expenditure. Our findings demonstrate that the time of day is a critical factor to amplify the beneficial impact of exercise on both metabolic pathways within skeletal muscle and systemic energy homeostasis.
Collapse
Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Astrid Linde Basse
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Milena Schönke
- Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Rhianna C Laker
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, University of Copenhagen, Copenhagen, Denmark; Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
37
|
Pastore N, Vainshtein A, Herz NJ, Huynh T, Brunetti L, Klisch TJ, Mutarelli M, Annunziata P, Kinouchi K, Brunetti-Pierri N, Sassone-Corsi P, Ballabio A. Nutrient-sensitive transcription factors TFEB and TFE3 couple autophagy and metabolism to the peripheral clock. EMBO J 2019; 38:embj.2018101347. [PMID: 31126958 DOI: 10.15252/embj.2018101347] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 12/10/2018] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
Autophagy and energy metabolism are known to follow a circadian pattern. However, it is unclear whether autophagy and the circadian clock are coordinated by common control mechanisms. Here, we show that the oscillation of autophagy genes is dependent on the nutrient-sensitive activation of TFEB and TFE3, key regulators of autophagy, lysosomal biogenesis, and cell homeostasis. TFEB and TFE3 display a circadian activation over the 24-h cycle and are responsible for the rhythmic induction of genes involved in autophagy during the light phase. Genetic ablation of TFEB and TFE3 in mice results in deregulated autophagy over the diurnal cycle and altered gene expression causing abnormal circadian wheel-running behavior. In addition, TFEB and TFE3 directly regulate the expression of Rev-erbα (Nr1d1), a transcriptional repressor component of the core clock machinery also involved in the regulation of whole-body metabolism and autophagy. Comparative analysis of the cistromes of TFEB/TFE3 and REV-ERBα showed an extensive overlap of their binding sites, particularly in genes involved in autophagy and metabolic functions. These data reveal a direct link between nutrient and clock-dependent regulation of gene expression shedding a new light on the crosstalk between autophagy, metabolism, and circadian cycles.
Collapse
Affiliation(s)
- Nunzia Pastore
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Anna Vainshtein
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Niculin J Herz
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tuong Huynh
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Tiemo J Klisch
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Sciences, Medical Genetics, Federico II University, Naples, Italy
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
| | - Andrea Ballabio
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Sciences, Medical Genetics, Federico II University, Naples, Italy
| |
Collapse
|
38
|
Dyar KA, Lutter D, Artati A, Ceglia NJ, Liu Y, Armenta D, Jastroch M, Schneider S, de Mateo S, Cervantes M, Abbondante S, Tognini P, Orozco-Solis R, Kinouchi K, Wang C, Swerdloff R, Nadeef S, Masri S, Magistretti P, Orlando V, Borrelli E, Uhlenhaut NH, Baldi P, Adamski J, Tschöp MH, Eckel-Mahan K, Sassone-Corsi P. Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks. Cell 2019; 174:1571-1585.e11. [PMID: 30193114 DOI: 10.1016/j.cell.2018.08.042] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/20/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022]
Abstract
Metabolic diseases are often characterized by circadian misalignment in different tissues, yet how altered coordination and communication among tissue clocks relate to specific pathogenic mechanisms remains largely unknown. Applying an integrated systems biology approach, we performed 24-hr metabolomics profiling of eight mouse tissues simultaneously. We present a temporal and spatial atlas of circadian metabolism in the context of systemic energy balance and under chronic nutrient stress (high-fat diet [HFD]). Comparative analysis reveals how the repertoires of tissue metabolism are linked and gated to specific temporal windows and how this highly specialized communication and coherence among tissue clocks is rewired by nutrient challenge. Overall, we illustrate how dynamic metabolic relationships can be reconstructed across time and space and how integration of circadian metabolomics data from multiple tissues can improve our understanding of health and disease.
Collapse
Affiliation(s)
- Kenneth A Dyar
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Dominik Lutter
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Anna Artati
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764 Neuherberg Germany
| | - Nicholas J Ceglia
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Danny Armenta
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Martin Jastroch
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Sandra Schneider
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Sara de Mateo
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Serena Abbondante
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paola Tognini
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Ricardo Orozco-Solis
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Christina Wang
- Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90509, USA
| | - Ronald Swerdloff
- Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90509, USA
| | - Seba Nadeef
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Selma Masri
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Magistretti
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Valerio Orlando
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Emiliana Borrelli
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764 Neuherberg Germany; Chair of Experimental Genetics, Technical University of Munich, 85350 Freising-Weihenstephan, Germany.
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Division of Metabolic Diseases, Technical University of Munich, 80333 Munich, Germany.
| | - Kristin Eckel-Mahan
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
39
|
Aras E, Ramadori G, Kinouchi K, Liu Y, Ioris RM, Brenachot X, Ljubicic S, Veyrat-Durebex C, Mannucci S, Galié M, Baldi P, Sassone-Corsi P, Coppari R. Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons. Cell Rep 2019; 27:2385-2398.e3. [DOI: 10.1016/j.celrep.2019.04.093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 01/28/2019] [Accepted: 04/19/2019] [Indexed: 12/17/2022] Open
|
40
|
|
41
|
|
42
|
Abstract
The circadian clock is a complex cellular mechanism that, through the control of diverse metabolic and gene expression pathways, governs a large array of cyclic physiological processes. Epidemiological and clinical data reveal a connection between the disruption of circadian rhythms and cancer that is supported by recent preclinical data. In addition, results from animal models and molecular studies underscore emerging links between cancer metabolism and the circadian clock. This has implications for therapeutic approaches, and we discuss the possible design of chronopharmacological strategies.
Collapse
Affiliation(s)
- Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, INSERM U1233, University of California Irvine, Irvine, CA, USA.
| |
Collapse
|
43
|
Kawamura G, Hattori M, Takamatsu K, Tsukada T, Ninomiya Y, Benjamin I, Sassone-Corsi P, Ozawa T, Tamaru T. Cooperative interaction among BMAL1, HSF1, and p53 protects mammalian cells from UV stress. Commun Biol 2018; 1:204. [PMID: 30480104 PMCID: PMC6250677 DOI: 10.1038/s42003-018-0209-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The circadian clock allows physiological systems to adapt to their changing environment by synchronizing their timings in response to external stimuli. Previously, we reported clock-controlled adaptive responses to heat-shock and oxidative stress and showed how the circadian clock interacts with BMAL1 and HSF1. Here, we present a similar clock-controlled adaptation to UV damage. In response to UV irradiation, HSF1 and tumor suppressor p53 regulate the expression of the clock gene Per2 in a time-dependent manner. UV irradiation first activates the HSF1 pathway, which subsequently activates the p53 pathway. Importantly, BMAL1 regulates both HSF1 and p53 through the BMAL1-HSF1 interaction to synchronize the cellular clock. Based on these findings and transcriptome analysis, we propose that the circadian clock protects cells against the UV stress through sequential and hierarchical interactions between the circadian clock, the heat shock response, and a tumor suppressive mechanism.
Collapse
Affiliation(s)
- Genki Kawamura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-0033, Japan
| | - Mitsuru Hattori
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-0033, Japan
| | - Ken Takamatsu
- Department of Physiology & Advanced Research Center for Medical Science, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Teruyo Tsukada
- Nishina Center for Accelerator-Based Science, Riken, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yasuharu Ninomiya
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba, 263-8555, Japan
| | - Ivor Benjamin
- Department of Medicine, Froedtert & Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI, 53226, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, School of Medicine, University of California Irvine, California, 92697, USA
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-0033, Japan.
| | - Teruya Tamaru
- Department of Physiology & Advanced Research Center for Medical Science, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
| |
Collapse
|
44
|
Abstract
Circadian rhythms influence virtually all life forms on our planet, a notion that opens the question on how the circadian cycles of individual organisms may interplay with each other. In mammals, a potentially dangerous environmental stress is represented by encounters with infectious agents. Microbial attack is a major risk for organismal homeostasis and therefore needs to be efficiently counteracted by mechanisms implemented by the host immune system. Accumulating evidence shows that the immune system may anticipate an emerging pathogenic exposure through an enhanced inflammatory state. Notably, the circadian clock orchestrates these anticipatory responses to fluctuating conditions in the external world. In this article, we review the current knowledge about the relationship between the circadian clock and pathogenic infections. We discuss the role of the circadian clock against infection and specific pathogens, the core clock proteins involved in the defense mechanisms, and the specific tissue or cell type in which they function to counteract the infection. Finally, circadian oscillations in the gut microbiome composition and its possible role in protecting against foodborne pathogen colonization are presented.
Collapse
Affiliation(s)
- Paola Tognini
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California, Irvine California 92617
| | - Mari Murakami
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California, Irvine California 92617
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, University of California, Irvine California 92617
| |
Collapse
|
45
|
Ceglia N, Liu Y, Chen S, Agostinelli F, Eckel-Mahan K, Sassone-Corsi P, Baldi P. CircadiOmics: circadian omic web portal. Nucleic Acids Res 2018; 46:W157-W162. [PMID: 29912458 PMCID: PMC6030824 DOI: 10.1093/nar/gky441] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 02/09/2018] [Revised: 04/17/2018] [Accepted: 06/13/2018] [Indexed: 12/29/2022] Open
Abstract
Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian oscillations continues to be the focus of intense research. However, there has been no comprehensive and integrated way for accessing and mining all circadian omic datasets. The latest release of CircadiOmics (http://circadiomics.ics.uci.edu) fills this gap for providing the most comprehensive web server for studying circadian data. The newly updated version contains high-throughput 227 omic datasets corresponding to over 74 million measurements sampled over 24 h cycles. Users can visualize and compare oscillatory trajectories across species, tissues and conditions. Periodicity statistics (e.g. period, amplitude, phase, P-value, q-value etc.) obtained from BIO_CYCLE and other methods are provided for all samples in the repository and can easily be downloaded in the form of publication-ready figures and tables. New features and substantial improvements in performance and data volume make CircadiOmics a powerful web portal for integrated analysis of circadian omic data.
Collapse
Affiliation(s)
- Nicholas Ceglia
- Department of Computer Science, University of California, Irvine, CA 92617, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
| | - Yu Liu
- Department of Computer Science, University of California, Irvine, CA 92617, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
| | - Siwei Chen
- Department of Computer Science, University of California, Irvine, CA 92617, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
| | - Forest Agostinelli
- Department of Computer Science, University of California, Irvine, CA 92617, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
| | - Kristin Eckel-Mahan
- Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Paolo Sassone-Corsi
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
- Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA 92617, USA
- Department of Biochemistry, University of California, Irvine, CA 92617, USA
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, CA 92617, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
- Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA 92617, USA
- Department of Biochemistry, University of California, Irvine, CA 92617, USA
| |
Collapse
|
46
|
Sato S, Parr EB, Devlin BL, Hawley JA, Sassone-Corsi P. Human metabolomics reveal daily variations under nutritional challenges specific to serum and skeletal muscle. Mol Metab 2018; 16:1-11. [PMID: 30293576 PMCID: PMC6157466 DOI: 10.1016/j.molmet.2018.06.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/14/2022] Open
Abstract
Objective Advances in the field of metabolomics and the concomitant development of bioinformatics tools constitute a promising avenue towards the development of precision medicine and personalized profiling for numerous disease states. Studies in animal models have strengthened this concept, but the application in human subjects is scarce. Methods Utilizing high-throughput metabolomics, we have analyzed the metabolome levels of human serum and skeletal muscle in the morning and evening in response to divergent nutritional challenges in order to identify unique signatures present in serum and muscle. Results We reveal dynamic daily variation of human metabolome unique to serum and muscle. The overall effect of nutritional challenges on the serum and muscle metabolome results in a profound rewiring of morning-evening metabolic profiles in human participants in response to the timing and type of dietary challenge. Conclusion We highlight time-of-day and meal-composition dependence of reprogramming of human metabolome by nutritional challenges. Human metabolome identifies the daily variation of metabolite levels. Divergent nutritional challenges reprogram the daily variation of human serum/muscle metabolome. Metabolomics delineates parallels between human serum and skeletal muscle.
Collapse
Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, INSERM U1233, School of Medicine, University of California, Irvine, USA
| | - Evelyn B Parr
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | - Brooke L Devlin
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, INSERM U1233, School of Medicine, University of California, Irvine, USA; Department of Biological Chemistry, School of Medicine, 324 Sprague Hall, University of California, Irvine, USA.
| |
Collapse
|
47
|
Gaucher J, Montellier E, Sassone-Corsi P. Molecular Cogs: Interplay between Circadian Clock and Cell Cycle. Trends Cell Biol 2018; 28:368-379. [DOI: 10.1016/j.tcb.2018.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/21/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
|
48
|
Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB. Guidelines for Genome-Scale Analysis of Biological Rhythms. J Biol Rhythms 2017; 32:380-393. [PMID: 29098954 PMCID: PMC5692188 DOI: 10.1177/0748730417728663] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [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: 12/20/2022]
Abstract
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.
Collapse
Affiliation(s)
- Michael E Hughes
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Katherine C Abruzzi
- 2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA
| | - Ravi Allada
- 3 Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Ron Anafi
- 4 Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Alaaddin Bulak Arpat
- 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.,6 Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gad Asher
- 7 Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Baldi
- 8 Institute for Genomics and Bioinformatics, University of California, Irvine, USA
| | | | | | - Justin Blau
- 11 Department of Biology, New York University, New York, USA
| | - Steve Brown
- 12 Institute of Pharmacology and Toxicology, University of Zürich, Switzerland
| | - M Fernanda Ceriani
- 13 Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Zheng Chen
- 14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA
| | - Joanna C Chiu
- 15 Department of Entomology and Nematology, University of California, Davis, USA
| | - Juergen Cox
- 16 Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexander M Crowell
- 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jason P DeBruyne
- 18 Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Derk-Jan Dijk
- 19 Surrey Sleep Research Centre, University of Surrey, Guildford, UK
| | - Luciano DiTacchio
- 20 The University of Kansas Medical Center, University of Kansas, Kansas City, USA
| | - Francis J Doyle
- 21 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts, USA
| | - Giles E Duffield
- 22 Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jay C Dunlap
- 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Kristin Eckel-Mahan
- 23 Institute of Molecular Medicine, McGovern Medical School, UT Health Houston, Houston, Texas, USA
| | - Karyn A Esser
- 24 Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, USA
| | - Garret A FitzGerald
- 25 Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Daniel B Forger
- 26 Department of Mathematics, University of Michigan, Ann Arbor, USA
| | - Lauren J Francey
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ying-Hui Fu
- 28 Kavli Institute for Fundamental Neuroscience, Weill Institute of Neuroscience, Department of Neurology, University of California, San Francisco, USA
| | - Frédéric Gachon
- 29 Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - David Gatfield
- 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Paul de Goede
- 30 Department of Endocrinology & Metabolism, Academic Medical Center, Amsterdam, the Netherlands
| | - Susan S Golden
- 31 Center for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, USA
| | - Carla Green
- 32 Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA
| | - John Harer
- 33 Department of Mathematics, Duke University, Durham, North Carolina, USA
| | - Stacey Harmer
- 34 Department of Plant Biology, University of California, Davis, USA
| | - Jeff Haspel
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael H Hastings
- 35 Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Hanspeter Herzel
- 36 Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Germany
| | - Erik D Herzog
- 37 Department of Biology, Washington University in St. Louis, Missouri, USA
| | - Christy Hoffmann
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christian Hong
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jacob J Hughey
- 38 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jennifer M Hurley
- 39 Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | | | - Carl Johnson
- 41 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Steve A Kay
- 42 Department of Cell and Molecular Biology, The Scripps Research Institute, University of California, San Diego, La Jolla, USA
| | - Nobuya Koike
- 43 Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Japan
| | - Karl Kornacker
- 44 Division of Sensory Biophysics, The Ohio State University, Columbus, USA
| | - Achim Kramer
- 45 Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Germany
| | - Katja Lamia
- 46 Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Tanya Leise
- 47 Department of Mathematics and Statistics, Amherst College, Amherst, Massachusetts, USA
| | - Scott A Lewis
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jiajia Li
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,48 Department of Biology, University of Missouri-St. Louis, USA
| | - Xiaodong Li
- 49 Department of Cell Biology, College of Life Sciences at Wuhan University, China
| | - Andrew C Liu
- 50 Department of Biological Sciences, University of Memphis, Tennessee, USA
| | - Jennifer J Loros
- 51 Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Tami A Martino
- 52 Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jerome S Menet
- 10 Department of Biology, Texas A&M University, College Station, USA
| | - Martha Merrow
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Andrew J Millar
- 54 SynthSys and School of Biological Sciences, University of Edinburgh, UK
| | - Todd Mockler
- 55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Felix Naef
- 56 The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Emi Nagoshi
- 57 Department of Genetics and Evolution, University of Geneva, Switzerland
| | - Michael N Nitabach
- 58 Department of Cellular and Molecular Physiology, Department of Genetics, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
| | - Maria Olmedo
- 59 Department of Genetics, University of Seville, Spain
| | - Dmitri A Nusinow
- 55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Louis J Ptáček
- 60 Department of Neurology, University of California, San Francisco, USA
| | - David Rand
- 61 Warwick Systems Biology and Mathematics Institute, University of Warwick, Conventry, UK
| | - Akhilesh B Reddy
- 62 The Francis Crick Institute, London, UK, and UCL Institute of Neurology, Queen Square, London, UK
| | - Maria S Robles
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Till Roenneberg
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Michael Rosbash
- 2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA
| | - Marc D Ruben
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Samuel S C Rund
- 63 Centre for Immunity, Infection and Evolution, University of Edinburgh, UK
| | - Aziz Sancar
- 64 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA
| | - Paolo Sassone-Corsi
- 65 Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, USA
| | - Amita Sehgal
- 66 Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Scott Sherrill-Mix
- 67 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Debra J Skene
- 68 Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Kai-Florian Storch
- 69 Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Joseph S Takahashi
- 70 Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA
| | - Hiroki R Ueda
- 71 Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan
| | - Han Wang
- 72 Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, China
| | - Charles Weitz
- 73 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pål O Westermark
- 74 Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Herman Wijnen
- 75 Biological Sciences and Institute for Life Sciences, University of Southampton, UK
| | - Ying Xu
- 76 Cam-Su GRC, Soochow University, Suzhou, China
| | - Gang Wu
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Seung-Hee Yoo
- 14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA
| | - Michael Young
- 77 Laboratory of Genetics, Rockefeller University, New York, New York, USA
| | | | - Tomasz Zielinski
- 54 SynthSys and School of Biological Sciences, University of Edinburgh, UK
| | - John B Hogenesch
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| |
Collapse
|
49
|
Tognini P, Murakami M, Liu Y, Eckel-Mahan KL, Newman JC, Verdin E, Baldi P, Sassone-Corsi P. Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet. Cell Metab 2017; 26:523-538.e5. [PMID: 28877456 DOI: 10.1016/j.cmet.2017.08.015] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/04/2017] [Accepted: 08/15/2017] [Indexed: 12/22/2022]
Abstract
The circadian clock orchestrates rhythms in physiology and behavior, allowing organismal adaptation to daily environmental changes. While food intake profoundly influences diurnal rhythms in the liver, how nutritional challenges are differentially interpreted by distinct tissue-specific clocks remains poorly explored. Ketogenic diet (KD) is considered to have metabolic and therapeutic value, though its impact on circadian homeostasis is virtually unknown. We show that KD has profound and differential effects on liver and intestine clocks. Specifically, the amplitude of clock-controlled genes and BMAL1 chromatin recruitment are drastically altered by KD in the liver, but not in the intestine. KD induces nuclear accumulation of PPARα in both tissues but with different circadian phase. Also, gut and liver clocks respond differently to carbohydrate supplementation to KD. Importantly, KD induces serum and intestinal β-hydroxyl-butyrate levels to robustly oscillate in a circadian manner, an event coupled to tissue-specific cyclic histone deacetylase (HDAC) activity and histone acetylation.
Collapse
Affiliation(s)
- Paola Tognini
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U1233 INSERM, University of California, Irvine, Irvine, CA, USA
| | - Mari Murakami
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U1233 INSERM, University of California, Irvine, Irvine, CA, USA
| | - Yu Liu
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kristin L Eckel-Mahan
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U1233 INSERM, University of California, Irvine, Irvine, CA, USA; Center for Metabolic and Degenerative Diseases, Institute of Molecular Medicine, University of Texas Health Sciences Center, Houston, TX, USA
| | - John C Newman
- Gladstone Institutes, University of California, San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Eric Verdin
- Gladstone Institutes, University of California, San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U1233 INSERM, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
50
|
Orozco-Solis R, Montellier E, Aguilar-Arnal L, Sato S, Vawter MP, Bunney BG, Bunney WE, Sassone-Corsi P. A Circadian Genomic Signature Common to Ketamine and Sleep Deprivation in the Anterior Cingulate Cortex. Biol Psychiatry 2017; 82:351-360. [PMID: 28395871 PMCID: PMC5660920 DOI: 10.1016/j.biopsych.2017.02.1176] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [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: 10/13/2016] [Revised: 02/08/2017] [Accepted: 02/21/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Conventional antidepressants usually require several weeks to achieve a full clinical response in patients with major depressive disorder, an illness associated with dysregulated circadian rhythms and a high incidence of suicidality. Two rapid-acting antidepressant strategies, low-dose ketamine (KT) and sleep deprivation (SD) therapies, dramatically reduce depressive symptoms within 24 hours in a subset of major depressive disorder patients. However, it is unknown whether they exert their actions through shared regulatory mechanisms. To address this question, we performed comparative transcriptomics analyses to identify candidate genes and relevant pathways common to KT and SD. METHODS We used the forced swim test, a standardized behavioral approach to measure antidepressant-like activity of KT and SD. We investigated gene expression changes using high-density microarrays and pathway analyses (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis) in KT- and SD-treated mice compared with saline-treated control male mice. RESULTS We show that KT and SD elicit common transcriptional responses implicating distinct elements of the circadian clock and processes involved in neuronal plasticity. There is an overlap of 64 genes whose expression is common in KT and SD. Specifically, there is downregulation of clock genes including Ciart, Per2, Npas4, Dbp, and Rorb in both KT- and SD-treated mice. CONCLUSIONS We demonstrate a potential involvement of the circadian clock in rapid antidepressant responses. These findings could open new research avenues to help design chronopharmacological strategies to treat major depressive disorder.
Collapse
Affiliation(s)
- Ricardo Orozco-Solis
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, Irvine, California
| | - Emilie Montellier
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, Irvine, California
| | - Lorena Aguilar-Arnal
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, Irvine, California
| | - Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, Irvine, California
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, California
| | - Blynn G Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, California
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, California
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, Irvine, California.
| |
Collapse
|