1
|
Jakobsen ST, Jensen RAM, Madsen MS, Ravnsborg T, Vaagenso CS, Siersbæk MS, Einarsson H, Andersson R, Jensen ON, Siersbæk R. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch. Nat Genet 2024; 56:663-674. [PMID: 38454021 DOI: 10.1038/s41588-024-01676-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.
Collapse
Affiliation(s)
- Simon T Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rikke A M Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria S Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hjorleifur Einarsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rasmus Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
2
|
Larsen FT, Hansen D, Terkelsen MK, Bendixen SM, Avolio F, Wernberg CW, Lauridsen MM, Grønkjaer LL, Jacobsen BG, Klinggaard EG, Mandrup S, Di Caterino T, Siersbæk MS, Indira Chandran V, Graversen JH, Krag A, Grøntved L, Ravnskjaer K. Stellate cell expression of SPARC-related modular calcium-binding protein 2 is associated with human non-alcoholic fatty liver disease severity. JHEP Rep 2023; 5:100615. [PMID: 36687468 PMCID: PMC9850195 DOI: 10.1016/j.jhepr.2022.100615] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022] Open
Abstract
Background & Aims Histological assessment of liver biopsies is the gold standard for diagnosis of non-alcoholic steatohepatitis (NASH), the progressive form of non-alcoholic fatty liver disease (NAFLD), despite its well-established limitations. Therefore, non-invasive biomarkers that can offer an integrated view of the liver are needed to improve diagnosis and reduce sampling bias. Hepatic stellate cells (HSCs) are central in the development of hepatic fibrosis, a hallmark of NASH. Secreted HSC-specific proteins may, therefore, reflect disease state in the NASH liver and serve as non-invasive diagnostic biomarkers. Methods We performed RNA-sequencing on liver biopsies from a histologically characterised cohort of obese patients (n = 30, BMI >35 kg/m2) to identify and evaluate HSC-specific genes encoding secreted proteins. Bioinformatics was used to identify potential biomarkers and their expression at single-cell resolution. We validated our findings using single-molecule fluorescence in situ hybridisation (smFISH) and ELISA to detect mRNA in liver tissue and protein levels in plasma, respectively. Results Hepatic expression of SPARC-related modular calcium-binding protein 2 (SMOC2) was increased in NASH compared to no-NAFLD (p.adj <0.001). Single-cell RNA-sequencing data indicated that SMOC2 was primarily expressed by HSCs, which was validated using smFISH. Finally, plasma SMOC2 was elevated in NASH compared to no-NAFLD (p <0.001), with a predictive accuracy of AUROC 0.88. Conclusions Increased SMOC2 in plasma appears to reflect HSC activation, a key cellular event associated with NASH progression, and may serve as a non-invasive biomarker of NASH. Impact and implications Non-alcoholic fatty liver disease (NAFLD) and its progressive form, non-alcoholic steatohepatitis (NASH), are the most common forms of chronic liver diseases. Currently, liver biopsies are the gold standard for diagnosing NAFLD. Blood-based biomarkers to complement liver biopsies for diagnosis of NAFLD are required. We found that activated hepatic stellate cells, a cell type central to NAFLD pathogenesis, upregulate expression of the secreted protein SPARC-related modular calcium-binding protein 2 (SMOC2). SMOC2 was elevated in blood samples from patients with NASH and may hold promise as a blood-based biomarker for the diagnosis of NAFLD.
Collapse
Key Words
- AUROC, area under the receiver operating characteristic curve
- ECM, extracellular matrix
- HSC, hepatic stellate cells
- LSM, liver stiffness measurement
- MCP, matricellular protein
- NAFL, non-alcoholic fatty liver
- NAFLD
- NAFLD, non-alcoholic fatty liver disease
- NAS, NAFLD activity score
- NASH
- PCA, principal component analysis
- SAF, steatosis, activity, and fibrosis
- SE, sensitivity
- SMOC2
- SMOC2, SPARC-related modular calcium-binding protein 2
- SP, specificity
- SPARC, secreted protein acidic and cysteine-rich
- VSMCs, vascular smooth muscle cells
- WGCNA, weighted gene co-expression network analysis
- aHSC, activated HSC
- hepatic stellate cells
- non-invasive biomarker
- qHSC, quiescent HSC
- smFISH, single-molecule fluorescence in situ hybridisation
- transcriptomics
Collapse
Affiliation(s)
- Frederik T. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Daniel Hansen
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Mike K. Terkelsen
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Sofie M. Bendixen
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Fabio Avolio
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Charlotte W. Wernberg
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Department of Gastroenterology and Hepatology, University Hospital of
Southern Denmark, Esbjerg, Denmark
- Center for Liver Research (FLASH), Department of Gastroenterology and
Hepatology, Odense University Hospital, Odense, Denmark
| | - Mette M. Lauridsen
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Department of Gastroenterology and Hepatology, University Hospital of
Southern Denmark, Esbjerg, Denmark
| | - Lea L. Grønkjaer
- Department of Gastroenterology and Hepatology, University Hospital of
Southern Denmark, Esbjerg, Denmark
| | - Birgitte G. Jacobsen
- Department of Gastroenterology and Hepatology, University Hospital of
Southern Denmark, Esbjerg, Denmark
| | - Ellen G. Klinggaard
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Tina Di Caterino
- Department of Pathology, Odense University Hospital, Odense,
Denmark
| | - Majken S. Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Vineesh Indira Chandran
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense,
Denmark
| | - Jonas H. Graversen
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense,
Denmark
| | - Aleksander Krag
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Center for Liver Research (FLASH), Department of Gastroenterology and
Hepatology, Odense University Hospital, Odense, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern
Denmark, Odense, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of
Southern Denmark, Odense, Denmark
- Corresponding author. Address: Department of Biochemistry and Molecular
Biology, Campusvej 55, 5230 Odense M, Denmark. Tel.: +45 65508906/+45
93979317.
| |
Collapse
|
3
|
Præstholm SM, Correia CM, Goitea VE, Siersbæk MS, Jørgensen M, Havelund JF, Pedersen TÅ, Færgeman NJ, Grøntved L. Impaired glucocorticoid receptor expression in liver disrupts feeding-induced gene expression, glucose uptake, and glycogen storage. Cell Rep 2021; 37:109938. [PMID: 34731602 DOI: 10.1016/j.celrep.2021.109938] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/08/2021] [Revised: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022] Open
Abstract
The transition from a fasted to a fed state is associated with extensive transcriptional remodeling in hepatocytes facilitated by hormonal- and nutritional-regulated transcription factors. Here, we use a liver-specific glucocorticoid receptor (GR) knockout (L-GRKO) model to investigate the temporal hepatic expression of GR target genes in response to feeding. Interestingly, in addition to the well-described fasting-regulated genes, we identify a subset of hepatic feeding-induced genes that requires GR for full expression. This includes Gck, which is important for hepatic glucose uptake, utilization, and storage. We show that insulin and glucocorticoids cooperatively regulate hepatic Gck expression in a direct GR-dependent manner by a 4.6 kb upstream GR binding site operating as a Gck enhancer. L-GRKO blunts preprandial and early postprandial Gck expression, which ultimately affects early postprandial hepatic glucose uptake, phosphorylation, and glycogen storage. Thus, GR is positively involved in feeding-induced gene expression and important for postprandial glucose metabolism in the liver.
Collapse
Affiliation(s)
- Stine M Præstholm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Catarina M Correia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Victor E Goitea
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mathilde Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper F Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | | | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
| |
Collapse
|
4
|
Larsen AMH, Kuczek DE, Kalvisa A, Siersbæk MS, Thorseth ML, Johansen AZ, Carretta M, Grøntved L, Vang O, Madsen DH. Collagen Density Modulates the Immunosuppressive Functions of Macrophages. J Immunol 2020; 205:1461-1472. [PMID: 32839214 DOI: 10.4049/jimmunol.1900789] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Tumor-associated macrophages (TAMs) support tumor growth by suppressing the activity of tumor-infiltrating T cells. Consistently, TAMs are considered a major limitation for the efficacy of cancer immunotherapy. However, the molecular reason behind the acquisition of an immunosuppressive TAM phenotype is not fully clarified. During tumor growth, the extracellular matrix (ECM) is degraded and substituted with a tumor-specific collagen-rich ECM. The collagen density of this tumor ECM has been associated with poor patient prognosis but the reason for this is not well understood. In this study, we investigated whether the collagen density could modulate the immunosuppressive activity of TAMs. The murine macrophage cell line RAW 264.7 was three-dimensionally cultured in collagen matrices of low and high collagen densities mimicking healthy and tumor tissue, respectively. Collagen density did not affect proliferation or viability of the macrophages. However, whole-transcriptome analysis revealed a striking response to the surrounding collagen density, including the regulation of immune regulatory genes and genes encoding chemokines. These transcriptional changes were shown to be similar in murine bone marrow-derived macrophages and TAMs isolated from murine tumors. Strikingly, coculture assays with primary T cells showed that macrophages cultured in high-density collagen were less efficient at attracting cytotoxic T cells and capable of inhibiting T cell proliferation more than macrophages cultured in low-density collagen. Our study demonstrates that a high collagen density can instruct macrophages to acquire an immunosuppressive phenotype. This mechanism could reduce the efficacy of immunotherapy and explain the link between high collagen density and poor prognosis.
Collapse
Affiliation(s)
- Anne Mette H Larsen
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark.,Department for Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Dorota E Kuczek
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| | - Adrija Kalvisa
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; and
| | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; and
| | - Marie-Louise Thorseth
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| | - Astrid Z Johansen
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark.,Department of Oncology, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| | - Marco Carretta
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; and
| | - Ole Vang
- Department for Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Daniel H Madsen
- National Center for Cancer Immune Therapy, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark; .,Department of Oncology, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| |
Collapse
|
5
|
Kuczek DE, Larsen AMH, Thorseth ML, Carretta M, Kalvisa A, Siersbæk MS, Simões AMC, Roslind A, Engelholm LH, Noessner E, Donia M, Svane IM, Straten PT, Grøntved L, Madsen DH. Collagen density regulates the activity of tumor-infiltrating T cells. J Immunother Cancer 2019; 7:68. [PMID: 30867051 PMCID: PMC6417085 DOI: 10.1186/s40425-019-0556-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/04/2019] [Indexed: 11/14/2022] Open
Abstract
Background Tumor progression is accompanied by dramatic remodeling of the surrounding extracellular matrix leading to the formation of a tumor-specific ECM, which is often more collagen-rich and of increased stiffness. The altered ECM of the tumor supports cancer growth and metastasis, but it is unknown if this effect involves modulation of T cell activity. To investigate if a high-density tumor-specific ECM could influence the ability of T cells to kill cancer cells, we here studied how T cells respond to 3D culture in different collagen densities. Methods T cells cultured in 3D conditions surrounded by a high or low collagen density were imaged using confocal fluorescent microscopy. The effects of the different collagen densities on T cell proliferation, survival, and differentiation were examined using flow cytometry. Cancer cell proliferation in similar 3D conditions was also measured. Triple-negative breast cancer specimens were analyzed for the number of infiltrating CD8+ T cells and for the collagen density. Whole-transcriptome analyses were applied to investigate in detail the effects of collagen density on T cells. Computational analyses were used to identify transcription factors involved in the collagen density-induced gene regulation. Observed changes were confirmed by qRT-PCR analysis. Results T cell proliferation was significantly reduced in a high-density matrix compared to a low-density matrix and prolonged culture in a high-density matrix led to a higher ratio of CD4+ to CD8+ T cells. The proliferation of cancer cells was unaffected by the surrounding collagen-density. Consistently, we observed a reduction in the number of infiltrating CD8+ T-cells in mammary tumors with high collagen-density indicating that collagen-density has a role in regulating T cell abundance in human breast cancer. Whole-transcriptome analysis of 3D-cultured T cells revealed that a high-density matrix induces downregulation of cytotoxic activity markers and upregulation of regulatory T cell markers. These transcriptional changes were predicted to involve autocrine TGF-β signaling and they were accompanied by an impaired ability of tumor-infiltrating T cells to kill autologous cancer cells. Conclusions Our study identifies a new immune modulatory mechanism, which could be essential for suppression of T cell activity in the tumor microenvironment. Electronic supplementary material The online version of this article (10.1186/s40425-019-0556-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dorota E Kuczek
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Anne Mette H Larsen
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark.,Roskilde University Center, Roskilde, Denmark
| | - Marie-Louise Thorseth
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Marco Carretta
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Adrija Kalvisa
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ana Micaela C Simões
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Anne Roslind
- Department of Pathology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Lars H Engelholm
- Finsen Laboratory, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Elfriede Noessner
- Immunoanalytics: Tissue control of Immunocytes, German Research Center for Environmental Health, Helmholtz Zentrum München, Munich, Germany
| | - Marco Donia
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Per Thor Straten
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark.,Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Daniel H Madsen
- Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark. .,Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
| |
Collapse
|
6
|
Kalvisa A, Siersbæk MS, Præstholm SM, Christensen LJL, Nielsen R, Stohr O, Vettorazzi S, Tuckermann J, White M, Mandrup S, Grøntved L. Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver. PLoS Biol 2018; 16:e2006249. [PMID: 30532187 PMCID: PMC6301715 DOI: 10.1371/journal.pbio.2006249] [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: 04/04/2018] [Revised: 12/20/2018] [Accepted: 11/16/2018] [Indexed: 02/01/2023] Open
Abstract
Hepatic circadian gene transcription is tightly coupled to feeding behavior, which has a profound impact on metabolic disorders associated with diet-induced obesity. Here, we describe a genomics approach to uncover mechanisms controlling hepatic postprandial gene expression. Combined transcriptomic and cistromic analysis identified hundreds of circadian-regulated genes and enhancers controlled by feeding. Postprandial suppression of enhancer activity was associated with reduced glucocorticoid receptor (GR) and Forkhead box O1 (FOXO1) occupancy of chromatin correlating with reduced serum corticosterone levels and increased serum insulin levels. Despite substantial co-occupancy of feeding-regulated enhancers by GR and FOXO1, selective disruption of corticosteroid and/or insulin signaling resulted in dysregulation of specific postprandial regulated gene programs. In combination, these signaling pathways operate a major part of the genes suppressed by feeding. Importantly, the feeding response was disrupted in diet-induced obese animals, which was associated with dysregulation of several corticosteroid- and insulin-regulated genes, providing mechanistic insights to dysregulated circadian gene transcription associated with obesity. The liver is an essential organ regulating metabolic homeostasis in response to fluctuations of metabolites induced by daily rhythms of food intake. Homeostasis is maintained by precise dynamic regulation of signaling pathways controlling a wealth of enzymatic reactions involving lipid, bile acid, amino acid and glucose synthesis, storage, and redistribution in hepatocytes. Precise temporal expression of hepatic enzymes is crucial for metabolic homeostasis; a major part of circadian hepatic protein expression is regulated by precisely timed gene transcription. Here, we use a genomics approach to identify genes and regulatory regions of the genome involved in feeding-regulated gene expression. We find that transcription factors acting downstream of glucocorticoid and insulin signaling are enriched at regulatory regions repressed by feeding. Importantly, insulin and glucocorticoid signaling operate to cooperatively control the majority of feeding-mediated gene repression, and these signaling pathways are dysregulated in diet-induced obesity impacting dynamic hepatic gene expression.
Collapse
Affiliation(s)
- Adrija Kalvisa
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Majken S. Siersbæk
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Stine M. Præstholm
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Line J. L. Christensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Oliver Stohr
- Division of Endocrinology, Boston Children's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sabine Vettorazzi
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Jan Tuckermann
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Morris White
- Division of Endocrinology, Boston Children's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- * E-mail:
| |
Collapse
|