1
|
Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ. Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. EMBO J 2024; 43:2127-2165. [PMID: 38580776 PMCID: PMC11148168 DOI: 10.1038/s44318-024-00084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024] Open
Abstract
The in vitro oxygen microenvironment profoundly affects the capacity of cell cultures to model physiological and pathophysiological states. Cell culture is often considered to be hyperoxic, but pericellular oxygen levels, which are affected by oxygen diffusivity and consumption, are rarely reported. Here, we provide evidence that several cell types in culture actually experience local hypoxia, with important implications for cell metabolism and function. We focused initially on adipocytes, as adipose tissue hypoxia is frequently observed in obesity and precedes diminished adipocyte function. Under standard conditions, cultured adipocytes are highly glycolytic and exhibit a transcriptional profile indicative of physiological hypoxia. Increasing pericellular oxygen diverted glucose flux toward mitochondria, lowered HIF1α activity, and resulted in widespread transcriptional rewiring. Functionally, adipocytes increased adipokine secretion and sensitivity to insulin and lipolytic stimuli, recapitulating a healthier adipocyte model. The functional benefits of increasing pericellular oxygen were also observed in macrophages, hPSC-derived hepatocytes and cardiac organoids. Our findings demonstrate that oxygen is limiting in many terminally-differentiated cell types, and that considering pericellular oxygen improves the quality, reproducibility and translatability of culture models.
Collapse
Affiliation(s)
- Joycelyn Tan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sam Virtue
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Guillaume Bidault
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Fatima Lugtu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ioannis Kamzolas
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Lu Liang
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Martin Dale
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James A Horscroft
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Alice P Sowton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Marcella Ma
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stefania Carobbio
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, 27834, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| |
Collapse
|
2
|
Jones AE, Rios A, Ibrahimovic N, Chavez C, Bayley NA, Ball AB, Hsieh WY, Sammarco A, Bianchi AR, Cortez AA, Graeber TG, Hoffmann A, Bensinger SJ, Divakaruni AS. The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587096. [PMID: 38585887 PMCID: PMC10996702 DOI: 10.1101/2024.03.28.587096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Metabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [m(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence m(IL-4) differentiation. Rather, we discovered that exogenous CoA provides a weak TLR4 signal which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88-linked signals prime for IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism, and suggests that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.
Collapse
Affiliation(s)
- Anthony E Jones
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy Rios
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neira Ibrahimovic
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carolina Chavez
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas A Bayley
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andréa B Ball
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Yuan Hsieh
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alessandro Sammarco
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amber R Bianchi
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angel A Cortez
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steven J Bensinger
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Lead contact
| |
Collapse
|
3
|
Xia W, Fang X, Gao Y, Wu W, Han Y, Liu R, Yang H, Chen H, Gao H. Advances of stable isotope technology in food safety analysis and nutrient metabolism research. Food Chem 2023; 408:135191. [PMID: 36527919 DOI: 10.1016/j.foodchem.2022.135191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/21/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Food quality, safety, and the regulatory metabolism of food nutrients in cells are primary factors in determining human health. However, residues of undesirable or hazardous compounds in food products and dysregulation in the nutrient metabolism inevitably occur occasionally. For years, chromatography-mass spectrometry technology has been recognized as an essential research tool in food analysis and nutrient metabolism research, and it is more accurate and robust when coupled with stable isotopes. In this study, we summarize the applications of stable isotope technology in the quantification of contaminant residues (pesticides, veterinary drugs, mycotoxins, polycyclic aromatic hydrocarbons, and other hazardous compounds) in foods and in the nutrients (glucose, lipids, amino acids and proteins) metabolism research. The aim of this review was to serve as a reference for providing effective analysis techniques for protecting food quality and human health, and to pave the way for the broader application of stable isotope technology.
Collapse
Affiliation(s)
- Wei Xia
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Xiangjun Fang
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Yuan Gao
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Weijie Wu
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Yanchao Han
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Ruiling Liu
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Hailong Yang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China.
| | - Hangjun Chen
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China.
| | - Haiyan Gao
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China.
| |
Collapse
|
4
|
Turner R, Mukherjee R, Wallace M, Sanchez-Gurmaches J. Quantitative Determination of De Novo Fatty Acid Synthesis in Brown Adipose Tissue Using Deuterium Oxide. J Vis Exp 2023:10.3791/64219. [PMID: 37246886 PMCID: PMC10913692 DOI: 10.3791/64219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
Fatty acid synthesis is a complex and highly energy demanding metabolic pathway with important functional roles in the control of whole-body metabolic homeostasis and other physiological and pathological processes. Contrary to other key metabolic pathways, such as glucose disposal, fatty acid synthesis is not routinely functionally assessed, leading to incomplete interpretations of metabolic status. In addition, there is a lack of publicly available detailed protocols suitable for newcomers in the field. Here, we describe an inexpensive quantitative method utilizing deuterium oxide and gas chromatography mass spectrometry (GCMS) for the analysis of total fatty acid de novo synthesis in brown adipose tissue in vivo. This method measures the synthesis of the products of fatty acid synthase independently of a carbon source, and it is potentially useful for virtually any tissue, in any mouse model, and under any external perturbation. Details on the sample preparation for GCMS and downstream calculations are provided. We focus on the analysis of brown fat due to its high levels of de novo fatty acid synthesis and critical roles in maintaining metabolic homeostasis.
Collapse
Affiliation(s)
- Rory Turner
- UCD Conway Institute and UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin
| | - Rajib Mukherjee
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati
| | - Martina Wallace
- UCD Conway Institute and UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin;
| | - Joan Sanchez-Gurmaches
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati; Department of Pediatrics, University of Cincinnati College of Medicine;
| |
Collapse
|
5
|
Alcoriza-Balaguer MI, García-Cañaveras JC, Benet M, Juan-Vidal O, Lahoz A. FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism. Brief Bioinform 2023; 24:7066347. [PMID: 36857618 PMCID: PMC10025582 DOI: 10.1093/bib/bbad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The use of stable isotope tracers and mass spectrometry (MS) is the gold standard method for the analysis of fatty acid (FA) metabolism. Yet, current state-of-the-art tools provide limited and difficult-to-interpret information about FA biosynthetic routes. Here we present FAMetA, an R package and a web-based application (www.fameta.es) that uses 13C mass isotopologue profiles to estimate FA import, de novo lipogenesis, elongation and desaturation in a user-friendly platform. The FAMetA workflow covers the required functionalities needed for MS data analyses. To illustrate its utility, different in vitro and in vivo experimental settings are used in which FA metabolism is modified. Thanks to the comprehensive characterization of FA biosynthesis and the easy-to-interpret graphical representations compared to previous tools, FAMetA discloses unnoticed insights into how cells reprogram their FA metabolism and, when combined with FASN, SCD1 and FADS2 inhibitors, it enables the identification of new FAs by the metabolic reconstruction of their synthesis route.
Collapse
Affiliation(s)
- María I Alcoriza-Balaguer
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
| | - Juan C García-Cañaveras
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
| | - Marta Benet
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
| | - Oscar Juan-Vidal
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
| | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain
| |
Collapse
|
6
|
Lien EC, Westermark AM, Zhang Y, Yuan C, Li Z, Lau AN, Sapp KM, Wolpin BM, Vander Heiden MG. Low glycaemic diets alter lipid metabolism to influence tumour growth. Nature 2021; 599:302-307. [PMID: 34671163 PMCID: PMC8628459 DOI: 10.1038/s41586-021-04049-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/17/2021] [Indexed: 11/08/2022]
Abstract
Dietary interventions can change metabolite levels in the tumour microenvironment, which might then affect cancer cell metabolism to alter tumour growth1-5. Although caloric restriction (CR) and a ketogenic diet (KD) are often thought to limit tumour progression by lowering blood glucose and insulin levels6-8, we found that only CR inhibits the growth of select tumour allografts in mice, suggesting that other mechanisms contribute to tumour growth inhibition. A change in nutrient availability observed with CR, but not with KD, is lower lipid levels in the plasma and tumours. Upregulation of stearoyl-CoA desaturase (SCD), which synthesises monounsaturated fatty acids, is required for cancer cells to proliferate in a lipid-depleted environment, and CR also impairs tumour SCD activity to cause an imbalance between unsaturated and saturated fatty acids to slow tumour growth. Enforcing cancer cell SCD expression or raising circulating lipid levels through a higher-fat CR diet confers resistance to the effects of CR. By contrast, although KD also impairs tumour SCD activity, KD-driven increases in lipid availability maintain the unsaturated to saturated fatty acid ratios in tumours, and changing the KD fat composition to increase tumour saturated fatty acid levels cooperates with decreased tumour SCD activity to slow tumour growth. These data suggest that diet-induced mismatches between tumour fatty acid desaturation activity and the availability of specific fatty acid species determine whether low glycaemic diets impair tumour growth.
Collapse
Affiliation(s)
- Evan C Lien
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna M Westermark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yin Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhaoqi Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allison N Lau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
7
|
Leung KL, Sanchita S, Pham CT, Davis BA, Okhovat M, Ding X, Dumesic P, Grogan TR, Williams KJ, Morselli M, Ma F, Carbone L, Li X, Pellegrini M, Dumesic DA, Chazenbalk GD. Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming. Clin Epigenetics 2020; 12:181. [PMID: 33228780 PMCID: PMC7686698 DOI: 10.1186/s13148-020-00970-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background Normal-weight polycystic ovary syndrome (PCOS) women exhibit adipose resistance in vivo accompanied by enhanced subcutaneous (SC) abdominal adipose stem cell (ASC) development to adipocytes with accelerated lipid accumulation per cell in vitro. The present study examines chromatin accessibility, RNA expression and fatty acid (FA) synthesis during SC abdominal ASC differentiation into adipocytes in vitro of normal-weight PCOS versus age- and body mass index-matched normoandrogenic ovulatory (control) women to study epigenetic/genetic characteristics as well as functional alterations of PCOS and control ASCs during adipogenesis. Results SC abdominal ASCs from PCOS women versus controls exhibited dynamic chromatin accessibility during adipogenesis, from significantly less chromatin accessibility at day 0 to greater chromatin accessibility by day 12, with enrichment of binding motifs for transcription factors (TFs) of the AP-1 subfamily at days 0, 3, and 12. In PCOS versus control cells, expression of genes governing adipocyte differentiation (PPARγ, CEBPα, AGPAT2) and function (ADIPOQ, FABP4, LPL, PLIN1, SLC2A4) was increased two–sixfold at days 3, 7, and 12, while that involving Wnt signaling (FZD1, SFRP1, and WNT10B) was decreased. Differential gene expression in PCOS cells at these time points involved triacylglycerol synthesis, lipid oxidation, free fatty acid beta-oxidation, and oxidative phosphorylation of the TCA cycle, with TGFB1 as a significant upstream regulator. There was a broad correspondence between increased chromatin accessibility and increased RNA expression of those 12 genes involved in adipocyte differentiation and function, Wnt signaling, as well as genes involved in the triacylglycerol synthesis functional group at day 12 of adipogenesis. Total content and de novo synthesis of myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1), and oleic (C18:1) acid increased from day 7 to day 12 in all cells, with total content and de novo synthesis of FAs significantly greater in PCOS than controls cells at day 12. Conclusions In normal-weight PCOS women, dynamic chromatin remodeling of SC abdominal ASCs during adipogenesis may enhance adipogenic gene expression as a programmed mechanism to promote greater fat storage.
Collapse
Affiliation(s)
- Karen L Leung
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Smriti Sanchita
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Catherine T Pham
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Brett A Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Sciences University, Portland, OR, 97239, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Sciences University, Portland, OR, 97239, USA
| | - Xiangming Ding
- Technology Center for Genomics and Bioinformatics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | | | - Tristan R Grogan
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Kevin J Williams
- UCLA Lipidomics Lab, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Feiyang Ma
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Sciences University, Portland, OR, 97239, USA.,Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR, 97239, USA.,Department of Medical Information and Clinical Epidemiology, Oregon Health and Sciences University, Portland, OR, 97239, USA.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Xinmin Li
- Technology Center for Genomics and Bioinformatics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel A Dumesic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Gregorio D Chazenbalk
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
| |
Collapse
|
8
|
Hsieh WY, Zhou QD, York AG, Williams KJ, Scumpia PO, Kronenberger EB, Hoi XP, Su B, Chi X, Bui VL, Khialeeva E, Kaplan A, Son YM, Divakaruni AS, Sun J, Smale ST, Flavell RA, Bensinger SJ. Toll-Like Receptors Induce Signal-Specific Reprogramming of the Macrophage Lipidome. Cell Metab 2020; 32:128-143.e5. [PMID: 32516576 PMCID: PMC7891175 DOI: 10.1016/j.cmet.2020.05.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/07/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
Macrophages reprogram their lipid metabolism in response to activation signals. However, a systems-level understanding of how different pro-inflammatory stimuli reshape the macrophage lipidome is lacking. Here, we use complementary "shotgun" and isotope tracer mass spectrometry approaches to define the changes in lipid biosynthesis, import, and composition of macrophages induced by various Toll-like receptors (TLRs) and inflammatory cytokines. "Shotgun" lipidomics data revealed that different TLRs and cytokines induce macrophages to acquire distinct lipidomes, indicating their specificity in reshaping lipid composition. Mechanistic studies showed that differential reprogramming of lipid composition is mediated by the opposing effects of MyD88- and TRIF-interferon-signaling pathways. Finally, we applied these insights to show that perturbing reprogramming of lipid composition can enhance inflammation and promote host defense to bacterial challenge. These studies provide a framework for understanding how inflammatory stimuli reprogram lipid composition of macrophages while providing a knowledge platform to exploit differential lipidomics to influence immunity.
Collapse
Affiliation(s)
- Wei-Yuan Hsieh
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Quan D Zhou
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Autumn G York
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Kevin J Williams
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Philip O Scumpia
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Eliza B Kronenberger
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Xen Ping Hoi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Baolong Su
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Xun Chi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Viet L Bui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Division of Rheumatology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Elvira Khialeeva
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amber Kaplan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Young Min Son
- Department of Immunology, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jie Sun
- Department of Immunology, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Steven J Bensinger
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
9
|
Zhou QD, Chi X, Lee MS, Hsieh WY, Mkrtchyan JJ, Feng AC, He C, York AG, Bui VL, Kronenberger EB, Ferrari A, Xiao X, Daly AE, Tarling EJ, Damoiseaux R, Scumpia PO, Smale ST, Williams KJ, Tontonoz P, Bensinger SJ. Interferon-mediated reprogramming of membrane cholesterol to evade bacterial toxins. Nat Immunol 2020; 21:746-755. [PMID: 32514064 PMCID: PMC7778040 DOI: 10.1038/s41590-020-0695-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/28/2020] [Indexed: 12/21/2022]
Abstract
Plasma membranes of animal cells are enriched for cholesterol. Cholesterol-dependent cytolysins (CDCs) are pore-forming toxins secreted by bacteria that target membrane cholesterol for their effector function. Phagocytes are essential for clearance of CDC-producing bacteria; however, the mechanisms by which these cells evade the deleterious effects of CDCs are largely unknown. Here, we report that interferon (IFN) signals convey resistance to CDC-induced pores on macrophages and neutrophils. We traced IFN-mediated resistance to CDCs to the rapid modulation of a specific pool of cholesterol in the plasma membrane of macrophages without changes to total cholesterol levels. Resistance to CDC-induced pore formation requires the production of the oxysterol 25-hydroxycholesterol (25HC), inhibition of cholesterol synthesis and redistribution of cholesterol to an esterified cholesterol pool. Accordingly, blocking the ability of IFN to reprogram cholesterol metabolism abrogates cellular protection and renders mice more susceptible to CDC-induced tissue damage. These studies illuminate targeted regulation of membrane cholesterol content as a host defense strategy.
Collapse
Affiliation(s)
- Quan D Zhou
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China
| | - Xun Chi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Min Sub Lee
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wei Yuan Hsieh
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan J Mkrtchyan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - An-Chieh Feng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cuiwen He
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Autumn G York
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Viet L Bui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eliza B Kronenberger
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alessandra Ferrari
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xu Xiao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Allison E Daly
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elizabeth J Tarling
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philip O Scumpia
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kevin J Williams
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven J Bensinger
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
10
|
Wallace M, Metallo CM. Tracing insights into de novo lipogenesis in liver and adipose tissues. Semin Cell Dev Biol 2020; 108:65-71. [PMID: 32201132 DOI: 10.1016/j.semcdb.2020.02.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
Lipids play important roles in biology that include structural compartmentation as membranes, energy storage, and regulatory functions as signaling molecules. These molecules can be obtained via the surrounding environment (e.g. diet) or synthesized de novo. Fatty acid synthesis is an energetically demanding process and must therefore be tightly regulated to balance fatty acid availability with the functional and energetic needs of cells and tissues. Here we review key aspects of de novo lipogenesis (DNL) in mammalian systems. We highlight key nodes in the pathway that are used for quantitation of lipogenic fluxes and regulation of fatty acid diversity across tissues. Next, we discuss key aspects of DNL function in the major lipogenic tissues of mammals: liver, white adipose tissue (WAT), and brown adipose tissue (BAT), highlighting recent molecular discoveries that suggest potential roles for tissue specific DNL. Finally, we propose critical questions that will be important to address using the advanced approaches for DNL quantitation described herein.
Collapse
Affiliation(s)
- Martina Wallace
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
11
|
Bravo-Santano N, Ellis JK, Calle Y, Keun HC, Behrends V, Letek M. Intracellular Staphylococcus aureus Elicits the Production of Host Very Long-Chain Saturated Fatty Acids with Antimicrobial Activity. Metabolites 2019; 9:metabo9070148. [PMID: 31330837 PMCID: PMC6680556 DOI: 10.3390/metabo9070148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
As a facultative intracellular pathogen, Staphylococcus aureus is able to invade and proliferate within many types of mammalian cells. Intracellular bacterial replication relies on host nutrient supplies and, therefore, cell metabolism is closely bound to intracellular infection. Here, we investigated how S. aureus invasion affects the host membrane-bound fatty acids. We quantified the relative levels of fatty acids and their labelling pattern after intracellular infection by gas chromatography-mass spectrometry (GC-MS). Interestingly, we observed that the levels of three host fatty acids—docosanoic, eicosanoic and palmitic acids—were significantly increased in response to intracellular S. aureus infection. Accordingly, labelling carbon distribution was also affected in infected cells, in comparison to the uninfected control. In addition, treatment of HeLa cells with these three fatty acids showed a cytoprotective role by directly reducing S. aureus growth.
Collapse
Affiliation(s)
| | - James K Ellis
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W12 0HS, UK
| | - Yolanda Calle
- Health Sciences Research Centre, University of Roehampton, London SW15 4JD, UK
| | - Hector C Keun
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W12 0HS, UK
| | - Volker Behrends
- Health Sciences Research Centre, University of Roehampton, London SW15 4JD, UK.
| | - Michal Letek
- Health Sciences Research Centre, University of Roehampton, London SW15 4JD, UK.
| |
Collapse
|