1
|
Tsouka S, Kumar P, Seubnooch P, Freiburghaus K, St-Pierre M, Dufour JF, Masoodi M. Transcriptomics-driven metabolic pathway analysis reveals similar alterations in lipid metabolism in mouse MASH model and human. COMMUNICATIONS MEDICINE 2024; 4:39. [PMID: 38443644 PMCID: PMC10914730 DOI: 10.1038/s43856-024-00465-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent chronic liver disease worldwide, and can rapidly progress to metabolic dysfunction-associated steatohepatitis (MASH). Accurate preclinical models and methodologies are needed to understand underlying metabolic mechanisms and develop treatment strategies. Through meta-analysis of currently proposed mouse models, we hypothesized that a diet- and chemical-induced MASH model closely resembles the observed lipid metabolism alterations in humans. METHODS We developed transcriptomics-driven metabolic pathway analysis (TDMPA), a method to aid in the evaluation of metabolic resemblance. TDMPA uses genome-scale metabolic models to calculate enzymatic reaction perturbations from gene expression data. We performed TDMPA to score and compare metabolic pathway alterations in MASH mouse models to human MASH signatures. We used an already-established WD+CCl4-induced MASH model and performed functional assays and lipidomics to confirm TDMPA findings. RESULTS Both human MASH and mouse models exhibit numerous altered metabolic pathways, including triglyceride biosynthesis, fatty acid beta-oxidation, bile acid biosynthesis, cholesterol metabolism, and oxidative phosphorylation. We confirm a significant reduction in mitochondrial functions and bioenergetics, as well as in acylcarnitines for the mouse model. We identify a wide range of lipid species within the most perturbed pathways predicted by TDMPA. Triglycerides, phospholipids, and bile acids are increased significantly in mouse MASH liver, confirming our initial observations. CONCLUSIONS We introduce TDMPA, a methodology for evaluating metabolic pathway alterations in metabolic disorders. By comparing metabolic signatures that typify human MASH, we show a good metabolic resemblance of the WD+CCl4 mouse model. Our presented approach provides a valuable tool for defining metabolic space to aid experimental design for assessing metabolism.
Collapse
Affiliation(s)
- Sofia Tsouka
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Pavitra Kumar
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Patcharamon Seubnooch
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Katrin Freiburghaus
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Marie St-Pierre
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Jean-François Dufour
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
- Centre des Maladie Digestives, Lausanne, Switzerland
| | - Mojgan Masoodi
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland.
| |
Collapse
|
2
|
Seubnooch P, Montani M, Tsouka S, Claude E, Rafiqi U, Perren A, Dufour JF, Masoodi M. Characterisation of hepatic lipid signature distributed across the liver zonation using mass spectrometry imaging. JHEP Rep 2023; 5:100725. [PMID: 37284141 PMCID: PMC10240278 DOI: 10.1016/j.jhepr.2023.100725] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 06/08/2023] Open
Abstract
Background & Aims Lipid metabolism plays an important role in liver pathophysiology. The liver lobule asymmetrically distributes oxygen and nutrition, resulting in heterogeneous metabolic functions. Periportal and pericentral hepatocytes have different metabolic functions, which lead to generating liver zonation. We developed spatial metabolic imaging using desorption electrospray ionisation mass spectrometry to investigate lipid distribution across liver zonation with high reproducibility and accuracy. Methods Fresh frozen livers from healthy mice with control diet were analysed using desorption electrospray ionisation mass spectrometry imaging. Imaging was performed at 50 μm × 50 μm pixel size. Regions of interest (ROIs) were manually created by co-registering with histological data to determine the spatial hepatic lipids across liver zonation. The ROIs were confirmed by double immunofluorescence. The mass list of specific ROIs was automatically created, and univariate and multivariate statistical analysis were performed to identify statistically significant lipids across liver zonation. Results A wide range of lipid species was identified, including fatty acids, phospholipids, triacylglycerols, diacylglycerols, ceramides, and sphingolipids. We characterised hepatic lipid signatures in three different liver zones (periportal zone, midzone, and pericentral zone) and validated the reproducibility of our method for measuring a wide range of lipids. Fatty acids were predominantly detected in the periportal region, whereas phospholipids were distributed in both the periportal and pericentral zones. Interestingly, phosphatidylinositols, PI(36:2), PI(36:3), PI(36:4), PI(38:5), and PI(40:6) were located predominantly in the midzone (zone 2). Triacylglycerols and diacylglycerols were detected mainly in the pericentral region. De novo triacylglycerol biosynthesis appeared to be the most influenced pathway across the three zones. Conclusions The ability to accurately assess zone-specific hepatic lipid distribution in the liver could lead to a better understanding of lipid metabolism during the progression of liver disease. Impact and Implications Zone-specific hepatic lipid metabolism could play an important role in lipid homoeostasis during disease progression. Herein, we defined the zone-specific references of hepatic lipid species in the three liver zones using molecular imaging. The de novo triacylglycerol biosynthesis was highlighted as the most influenced pathway across the three zones.
Collapse
Affiliation(s)
- Patcharamon Seubnooch
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Matteo Montani
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Sofia Tsouka
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | | | - Umara Rafiqi
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Aurel Perren
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Jean-Francois Dufour
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Mojgan Masoodi
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| |
Collapse
|
3
|
Smith OE, Roussel V, Morin F, Ongaro L, Zhou X, Bertucci MC, Bernard DJ, Murphy BD. Steroidogenic Factor 1 Regulation of the Hypothalamic-Pituitary-Ovarian Axis of Adult Female Mice. Endocrinology 2022; 163:6542939. [PMID: 35247045 PMCID: PMC8974829 DOI: 10.1210/endocr/bqac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 11/19/2022]
Abstract
The orphan nuclear receptor steroidogenic factor-1 (SF-1 or NR5A1) is an indispensable regulator of adrenal and gonadal formation, playing roles in sex determination, hypothalamic development, and pituitary function. This study aimed to identify the roles of SF-1 in postnatal female reproductive function. Using a progesterone receptor-driven Cre recombinase, we developed a novel murine model, characterized by conditional depletion of SF-1 [PR-Cre;Nr5a1f/f; conditional knockout (cKO)] in the hypothalamic-pituitary-gonadal axis. Mature female cKO were infertile due to the absence of ovulation. Reduced gonadotropin concentrations in the pituitary gland that were nevertheless sufficient to maintain regular estrous cycles were observed in mature cKO females. The cKO ovaries showed abnormal lipid accumulation in the stroma, associated with an irregular expression of cholesterol homeostatic genes such as Star, Scp2, and Acat1. The depletion of SF-1 in granulosa cells prevented appropriate cumulus oöphorus expansion, characterized by reduced expression of Areg, Ereg, and Ptgs2. Exogenous delivery of gonadotropins to cKO females to induce ovulation did not restore fertility and was associated with impaired formation and function of corpora lutea accompanied by reduced expression of the steroidogenic genes Cyp11a1 and Cyp19a1 and attenuated progesterone production. Surgical transplantation of cKO ovaries to ovariectomized control animals (Nr5a1f/f) resulted in 2 separate phenotypes, either sterility or apparently normal fertility. The deletion of SF-1 in the pituitary and in granulosa cells near the moment of ovulation demonstrated that this nuclear receptor functions across the pituitary-gonadal axis and plays essential roles in gonadotropin synthesis, cumulus expansion, and luteinization.
Collapse
Affiliation(s)
- Olivia E Smith
- Centre de recherche en reproduction et fertilité (CRRF), Université de Montréal, Saint Hyacinthe, Québec, Canada
| | - Vickie Roussel
- Centre de recherche en reproduction et fertilité (CRRF), Université de Montréal, Saint Hyacinthe, Québec, Canada
| | - Fanny Morin
- Centre de recherche en reproduction et fertilité (CRRF), Université de Montréal, Saint Hyacinthe, Québec, Canada
| | - Luisina Ongaro
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Xiang Zhou
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Micka C Bertucci
- School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Bruce D Murphy
- Centre de recherche en reproduction et fertilité (CRRF), Université de Montréal, Saint Hyacinthe, Québec, Canada
- Correspondence: Bruce D. Murphy, PhD, Centre de Recherche en Reproduction et Fertilité, Université de Montréal, Saint-Hyacinthe, Québec, J2S 7C6, Canada. E-mail:
| |
Collapse
|
4
|
Weger BD, Gobet C, David FPA, Atger F, Martin E, Phillips NE, Charpagne A, Weger M, Naef F, Gachon F. Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proc Natl Acad Sci U S A 2021; 118:e2015803118. [PMID: 33452134 PMCID: PMC7826335 DOI: 10.1073/pnas.2015803118] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The circadian clock and feeding rhythms are both important regulators of rhythmic gene expression in the liver. To further dissect the respective contributions of feeding and the clock, we analyzed differential rhythmicity of liver tissue samples across several conditions. We developed a statistical method tailored to compare rhythmic liver messenger RNA (mRNA) expression in mouse knockout models of multiple clock genes, as well as PARbZip output transcription factors (Hlf/Dbp/Tef). Mice were exposed to ad libitum or night-restricted feeding under regular light-dark cycles. During ad libitum feeding, genetic ablation of the core clock attenuated rhythmic-feeding patterns, which could be restored by the night-restricted feeding regimen. High-amplitude mRNA expression rhythms in wild-type livers were driven by the circadian clock, but rhythmic feeding also contributed to rhythmic gene expression, albeit with significantly lower amplitudes. We observed that Bmal1 and Cry1/2 knockouts differed in their residual rhythmic gene expression. Differences in mean expression levels between wild types and knockouts correlated with rhythmic gene expression in wild type. Surprisingly, in PARbZip knockout mice, the mean expression levels of PARbZip targets were more strongly impacted than their rhythms, potentially due to the rhythmic activity of the D-box-repressor NFIL3. Genes that lost rhythmicity in PARbZip knockouts were identified to be indirect targets. Our findings provide insights into the diurnal transcriptome in mouse liver as we identified the differential contributions of several core clock regulators. In addition, we gained more insights on the specific effects of the feeding-fasting cycle.
Collapse
Affiliation(s)
- Benjamin D Weger
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
| | - Cédric Gobet
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Fabrice P A David
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Gene Expression Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- BioInformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Florian Atger
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Eva Martin
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Nicholas E Phillips
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Aline Charpagne
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland;
| | - Frédéric Gachon
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland;
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
| |
Collapse
|
5
|
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. PLoS One 2020; 15:e0239711. [PMID: 32986734 PMCID: PMC7521718 DOI: 10.1371/journal.pone.0239711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/12/2020] [Indexed: 01/12/2023] Open
Abstract
As newer single-cell protocols generate increasingly more cells at reduced sequencing depths, the value of a higher read depth may be overlooked. Using data from three different single-cell RNA-seq protocols that lend themselves to having either higher read depth (Smart-seq) or many cells (MARS-seq and 10X), we evaluate their ability to recapitulate biological signals in the context of spatial reconstruction. Overall, we find gene expression profiles after spatial reconstruction analysis are highly reproducible between datasets despite being generated by different protocols and using different computational algorithms. While UMI-based protocols such as 10X and MARS-seq allow for capturing more cells, Smart-seq's higher sensitivity and read-depth allow for analysis of lower expressed genes and isoforms. Additionally, we evaluate trade-offs for each protocol by performing subsampling analyses and find that optimizing the balance between sequencing depth and number of cells within a protocol is necessary for efficient use of resources. Our analysis emphasizes the importance of selecting a protocol based on the biological questions and features of interest.
Collapse
|
6
|
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: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [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
|
7
|
Dyar KA, Hubert MJ, Mir AA, Ciciliot S, Lutter D, Greulich F, Quagliarini F, Kleinert M, Fischer K, Eichmann TO, Wright LE, Peña Paz MI, Casarin A, Pertegato V, Romanello V, Albiero M, Mazzucco S, Rizzuto R, Salviati L, Biolo G, Blaauw B, Schiaffino S, Uhlenhaut NH. Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock. PLoS Biol 2018; 16:e2005886. [PMID: 30096135 PMCID: PMC6105032 DOI: 10.1371/journal.pbio.2005886] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/22/2018] [Accepted: 07/27/2018] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks are fundamental physiological regulators of energy homeostasis, but direct transcriptional targets of the muscle clock machinery are unknown. To understand how the muscle clock directs rhythmic metabolism, we determined genome-wide binding of the master clock regulators brain and muscle ARNT-like protein 1 (BMAL1) and REV-ERBα in murine muscles. Integrating occupancy with 24-hr gene expression and metabolomics after muscle-specific loss of BMAL1 and REV-ERBα, here we unravel novel molecular mechanisms connecting muscle clock function to daily cycles of lipid and protein metabolism. Validating BMAL1 and REV-ERBα targets using luciferase assays and in vivo rescue, we demonstrate how a major role of the muscle clock is to promote diurnal cycles of neutral lipid storage while coordinately inhibiting lipid and protein catabolism prior to awakening. This occurs by BMAL1-dependent activation of Dgat2 and REV-ERBα-dependent repression of major targets involved in lipid metabolism and protein turnover (MuRF-1, Atrogin-1). Accordingly, muscle-specific loss of BMAL1 is associated with metabolic inefficiency, impaired muscle triglyceride biosynthesis, and accumulation of bioactive lipids and amino acids. Taken together, our data provide a comprehensive overview of how genomic binding of BMAL1 and REV-ERBα is related to temporal changes in gene expression and metabolite fluctuations.
Collapse
Affiliation(s)
- Kenneth Allen Dyar
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Michaël Jean Hubert
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Ashfaq Ali Mir
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | | | - Dominik Lutter
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Franziska Greulich
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Fabiana Quagliarini
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Maximilian Kleinert
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Katrin Fischer
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | | | | | | | - Alberto Casarin
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Vanessa Pertegato
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | | | - Mattia Albiero
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Sara Mazzucco
- Clinica Medica, Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Gianni Biolo
- Clinica Medica, Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - N. Henriette Uhlenhaut
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
- Gene Center, Ludwig-Maximilians-Universitaet (LMU), Munich, Germany
| |
Collapse
|
8
|
Circadian- and UPR-dependent control of CPEB4 mediates a translational response to counteract hepatic steatosis under ER stress. Nat Cell Biol 2017; 19:94-105. [PMID: 28092655 DOI: 10.1038/ncb3461] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/09/2016] [Indexed: 12/18/2022]
Abstract
The cytoplasmic polyadenylation element-binding (CPEB) proteins regulate pre-mRNA processing and translation of CPE-containing mRNAs in early embryonic development and synaptic activity. However, specific functions in adult organisms are poorly understood. Here we show that CPEB4 is required for adaptation to high-fat-diet- and ageing-induced endoplasmic reticulum (ER) stress, and subsequent hepatosteatosis. Stress-activated liver CPEB4 expression is dual-mode regulated. First, Cpeb4 mRNA transcription is controlled by the circadian clock, and then its translation is regulated by the unfolded protein response (UPR) through upstream open reading frames within the 5'UTR. Thus, the CPEB4 protein is synthesized only following ER stress but the induction amplitude is circadian. In turn, CPEB4 activates a second wave of UPR translation required to maintain ER and mitochondrial homeostasis. Our results suggest that combined transcriptional and translational Cpeb4 regulation generates a 'circadian mediator', which coordinates hepatic UPR activity with periods of high ER-protein-folding demand. Accordingly, CPEB4 deficiency results in non-alcoholic fatty liver disease.
Collapse
|