1
|
Green CR, Kolar MJ, McGregor GH, Nelson AT, Wallace M, Metallo CM. Quantifying acyl-chain diversity in isobaric compound lipids containing monomethyl branched-chain fatty acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596332. [PMID: 38853874 PMCID: PMC11160641 DOI: 10.1101/2024.05.28.596332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Compound lipids comprise a diverse group of metabolites present in living systems, and metabolic- and environmentally-driven structural distinctions across this family is increasingly linked to biological function. However, methods for deconvoluting these often isobaric lipid species are lacking or require specialized instrumentation. Notably, acyl-chain diversity within cells may be influenced by nutritional states, metabolic dysregulation, or genetic alterations. Therefore, a reliable, validated method of quantifying structurally similar even-, odd-, and branched-chain acyl groups within intact compound lipids will be invaluable for gaining molecular insights into their biological functions. Here we demonstrate the chromatographic resolution of isobaric lipids containing distinct combinations of straight-chain and branched-chain acyl groups via ultra-high-pressure liquid chromatography (UHPLC)-mass spectrometry (MS) using a C30 liquid chromatography column. Using metabolically-engineered adipocytes lacking branched-keto acid dehydrogenase A (Bckdha), we validate this approach through a combination of fatty acid supplementation and metabolic tracing using monomethyl branched-chain fatty acids and valine. We observe resolution of numerous isobaric triacylglycerols and other compound lipids, demonstrating the resolving utility of this method. This approach strengthens our ability to quantify and characterize the inherent diversity of acyl chains across the lipidome.
Collapse
Affiliation(s)
- CR Green
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010N. Torrey Pines Rd., La Jolla, 92037, CA, USA
| | - MJ Kolar
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010N. Torrey Pines Rd., La Jolla, 92037, CA, USA
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - GH McGregor
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010N. Torrey Pines Rd., La Jolla, 92037, CA, USA
| | - AT Nelson
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642
| | - M Wallace
- School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - CM Metallo
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010N. Torrey Pines Rd., La Jolla, 92037, CA, USA
| |
Collapse
|
2
|
Ball AB, Jones AE, Nguyễn KB, Rios A, Marx N, Hsieh WY, Yang K, Desousa BR, Kim KK, Veliova M, del Mundo ZM, Shirihai OS, Benincá C, Stiles L, Bensinger SJ, Divakaruni AS. Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593451. [PMID: 38798678 PMCID: PMC11118427 DOI: 10.1101/2024.05.10.593451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Pro-inflammatory macrophage activation is a hallmark example of how mitochondria serve as signaling organelles. Upon classical macrophage activation, oxidative phosphorylation sharply decreases and mitochondria are repurposed to accumulate signals that amplify effector function. However, evidence is conflicting as to whether this collapse in respiration is essential or largely dispensable. Here we systematically examine this question and show that reduced oxidative phosphorylation is not required for pro-inflammatory macrophage activation. Only stimuli that engage both MyD88- and TRIF-linked pathways decrease mitochondrial respiration, and different pro-inflammatory stimuli have varying effects on other bioenergetic parameters. Additionally, pharmacologic and genetic models of electron transport chain inhibition show no direct link between respiration and pro-inflammatory activation. Studies in mouse and human macrophages also reveal accumulation of the signaling metabolites succinate and itaconate can occur independently of characteristic breaks in the TCA cycle. Finally, in vivo activation of peritoneal macrophages further demonstrates that a pro-inflammatory response can be elicited without reductions to oxidative phosphorylation. Taken together, the results suggest the conventional model of mitochondrial reprogramming upon macrophage activation is incomplete.
Collapse
Affiliation(s)
- Andréa B. Ball
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kaitlyn B. Nguyễn
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy Rios
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nico Marx
- Institute of Integrative Cell Biology and Physiology, Bioenergetics and Mitochondrial Dynamics Section, University of Münster, Schloßplatz 5, D-49078 Münster, Germany
| | - Wei Yuan Hsieh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Krista Yang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brandon R. Desousa
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristen K.O. Kim
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michaela Veliova
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zena Marie del Mundo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Orian S. Shirihai
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cristiane Benincá
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Linsey Stiles
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, 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
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
3
|
Shannon CE, Bakewell T, Fourcaudot MJ, Ayala I, Romero G, Asmis M, Lima LCF, Wallace M, Norton L. Sex-dependent adipose glucose partitioning by the mitochondrial pyruvate carrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593540. [PMID: 38798427 PMCID: PMC11118482 DOI: 10.1101/2024.05.11.593540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Objective The mitochondrial pyruvate carrier (MPC) occupies a critical node in intermediary metabolism, prompting interest in its utility as a therapeutic target for the treatment of obesity and cardiometabolic disease. Dysregulated nutrient metabolism in adipose tissue is a prominent feature of obesity pathophysiology, yet the functional role of adipose MPC has not been explored. We investigated whether the MPC shapes the adaptation of adipose tissue to dietary stress in female and male mice. Methods The impact of pharmacological and genetic disruption of the MPC on mitochondrial pathways of triglyceride assembly (lipogenesis and glyceroneogenesis) was assessed in 3T3L1 adipocytes and murine adipose explants, combined with analyses of adipose MPC expression in metabolically compromised humans. Whole-body and adipose-specific glucose metabolism were subsequently investigated in male and female mice lacking adipocyte MPC1 (Mpc1AD-/-) and fed either standard chow, high-fat western style, or high-sucrose lipid restricted diets for 24 weeks, using a combination of radiolabeled tracers and GC/MS metabolomics. Results Treatment with UK5099 or siMPC1 impaired the synthesis of lipids and glycerol-3-phosphate from pyruvate and blunted triglyceride accumulation in 3T3L1 adipocytes, whilst MPC expression in human adipose tissue was negatively correlated with indices of whole-body and adipose tissue metabolic dysfunction. Mature adipose explants from Mpc1AD-/- mice were intrinsically incapable of incorporating pyruvate into triglycerides. In vivo, MPC deletion restricted the incorporation of circulating glucose into adipose triglycerides, but only in female mice fed a zero fat diet, and this associated with sex-specific reductions in tricarboxylic acid cycle pool sizes and compensatory transcriptional changes in lipogenic and glycerol metabolism pathways. However, whole-body adiposity and metabolic health were preserved in Mpc1AD-/- mice regardless of sex, even under conditions of zero dietary fat. Conclusion These findings highlight the greater capacity for mitochondrially driven triglyceride assembly in adipose from female versus male mice and expose a reliance upon MPC-gated metabolism for glucose partitioning in female adipose under conditions of dietary lipid restriction.
Collapse
Affiliation(s)
- Christopher E Shannon
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Terry Bakewell
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Marcel J Fourcaudot
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Iriscilla Ayala
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Giovanna Romero
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Mara Asmis
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Leandro C Freitas Lima
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Martina Wallace
- UCD Conway Institute, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Luke Norton
- Diabetes Division, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| |
Collapse
|
4
|
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
|
5
|
Andreyev AY, Yang H, Doulias PT, Dolatabadi N, Zhang X, Luevanos M, Blanco M, Baal C, Putra I, Nakamura T, Ischiropoulos H, Tannenbaum SR, Lipton SA. Metabolic Bypass Rescues Aberrant S-nitrosylation-Induced TCA Cycle Inhibition and Synapse Loss in Alzheimer's Disease Human Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306469. [PMID: 38235614 PMCID: PMC10966553 DOI: 10.1002/advs.202306469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/29/2023] [Indexed: 01/19/2024]
Abstract
In Alzheimer's disease (AD), dysfunctional mitochondrial metabolism is associated with synaptic loss, the major pathological correlate of cognitive decline. Mechanistic insight for this relationship, however, is still lacking. Here, comparing isogenic wild-type and AD mutant human induced pluripotent stem cell (hiPSC)-derived cerebrocortical neurons (hiN), evidence is found for compromised mitochondrial energy in AD using the Seahorse platform to analyze glycolysis and oxidative phosphorylation (OXPHOS). Isotope-labeled metabolic flux experiments revealed a major block in activity in the tricarboxylic acid (TCA) cycle at the α-ketoglutarate dehydrogenase (αKGDH)/succinyl coenzyme-A synthetase step, metabolizing α-ketoglutarate to succinate. Associated with this block, aberrant protein S-nitrosylation of αKGDH subunits inhibited their enzyme function. This aberrant S-nitrosylation is documented not only in AD-hiN but also in postmortem human AD brains versus controls, as assessed by two separate unbiased mass spectrometry platforms using both SNOTRAP identification of S-nitrosothiols and chemoselective-enrichment of S-nitrosoproteins. Treatment with dimethyl succinate, a cell-permeable derivative of a TCA substrate downstream to the block, resulted in partial rescue of mitochondrial bioenergetic function as well as reversal of synapse loss in AD-hiN. These findings have therapeutic implications that rescue of mitochondrial energy metabolism can ameliorate synaptic loss in hiPSC-based models of AD.
Collapse
Affiliation(s)
- Alexander Y Andreyev
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hongmei Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Pharmacology, Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry and Institute of Biosciences, University Research Center of Ioannina, University of Ioannina, Ioannina, 45110, Greece
| | - Nima Dolatabadi
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xu Zhang
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Melissa Luevanos
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mayra Blanco
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christine Baal
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ivan Putra
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Pharmacology, Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven R Tannenbaum
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Stuart A Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
6
|
Acevedo A, Jones AE, Danna BT, Turner R, Montales KP, Benincá C, Reue K, Shirihai OS, Stiles L, Wallace M, Wang Y, Bertholet AM, Divakaruni AS. The BCKDK inhibitor BT2 is a chemical uncoupler that lowers mitochondrial ROS production and de novo lipogenesis. J Biol Chem 2024; 300:105702. [PMID: 38301896 PMCID: PMC10910128 DOI: 10.1016/j.jbc.2024.105702] [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: 08/15/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Elevated levels of branched chain amino acids (BCAAs) and branched-chain α-ketoacids are associated with cardiovascular and metabolic disease, but the molecular mechanisms underlying a putative causal relationship remain unclear. The branched-chain ketoacid dehydrogenase kinase (BCKDK) inhibitor BT2 (3,6-dichlorobenzo[b]thiophene-2-carboxylic acid) is often used in preclinical models to increase BCAA oxidation and restore steady-state BCAA and branched-chain α-ketoacid levels. BT2 administration is protective in various rodent models of heart failure and metabolic disease, but confoundingly, targeted ablation of Bckdk in specific tissues does not reproduce the beneficial effects conferred by pharmacologic inhibition. Here, we demonstrate that BT2, a lipophilic weak acid, can act as a mitochondrial uncoupler. Measurements of oxygen consumption, mitochondrial membrane potential, and patch-clamp electrophysiology show that BT2 increases proton conductance across the mitochondrial inner membrane independently of its inhibitory effect on BCKDK. BT2 is roughly sixfold less potent than the prototypical uncoupler 2,4-dinitrophenol and phenocopies 2,4-dinitrophenol in lowering de novo lipogenesis and mitochondrial superoxide production. The data suggest that the therapeutic efficacy of BT2 may be attributable to the well-documented effects of mitochondrial uncoupling in alleviating cardiovascular and metabolic disease.
Collapse
Affiliation(s)
- Aracely Acevedo
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA
| | - Bezawit T Danna
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA
| | - Rory Turner
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Katrina P Montales
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Cristiane Benincá
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Orian S Shirihai
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Linsey Stiles
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Martina Wallace
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Yibin Wang
- DukeNUS School of Medicine, Signature Research Program in Cardiovascular and Metabolic Diseases, Singapore, Singapore
| | - Ambre M Bertholet
- Department of Physiology, University of California, Los Angeles, Los Angeles, California, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA.
| |
Collapse
|
7
|
Kuhlmann-Hogan A, Cordes T, Xu Z, Kuna RS, Traina KA, Robles-Oteiza C, Ayeni D, Kwong EM, Levy S, Globig AM, Nobari MM, Cheng GZ, Leibel SL, Homer RJ, Shaw RJ, Metallo CM, Politi K, Kaech SM. EGFR-driven lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth. Cancer Discov 2024; 14:733526. [PMID: 38241033 DOI: 10.1158/2159-8290.cd-23-0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/15/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
The limited efficacy of currently approved immunotherapies in EGFR-driven lung adenocarcinoma (LUAD) underscores the need to better understand alternative mechanisms governing local immunosuppression to fuel novel therapies. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophage (TA-AM) proliferation which supports tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF-PPARγ signaling and inhibition of airway GM-CSF or PPARγ in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPARγ in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases proinflammatory immune responses. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how cancer cells can metabolically co-opt TA-AMs through GM-CSF-PPARγ signaling to provide nutrients that promote oncogenic signaling and growth.
Collapse
Affiliation(s)
| | - Thekla Cordes
- Technische Universität Braunschweig, Braunschweig, Germany
| | - Ziyan Xu
- Salk Institute for Biological Studies
| | - Ramya S Kuna
- Salk Institute for Biological Studies, La Jolla, Ca, United States
| | | | | | | | - Elizabeth M Kwong
- University of California San Diego Medical Center, La Jolla, CA, United States
| | - Stellar Levy
- Yale School of Medicine, New Haven, CT, United States
| | | | | | - George Z Cheng
- University of California San Diego Medical Center, La Jolla, CA, United States
| | - Sandra L Leibel
- University of California - San Diego School of Medicine, La Jolla, CA, United States
| | | | - Reuben J Shaw
- Salk Institute for Biological Studies, La Jolla, CA, United States
| | | | | | - Susan M Kaech
- Salk Institute for Biological Studies, La Jolla, CA, United States
| |
Collapse
|
8
|
Crowell PD, Giafaglione JM, Jones AE, Nunley NM, Hashimoto T, Delcourt AML, Petcherski A, Agrawal R, Bernard MJ, Diaz JA, Heering KY, Huang RR, Low JY, Matulionis N, Navone NM, Ye H, Zoubeidi A, Christofk HR, Rettig MB, Reiter RE, Haffner MC, Boutros PC, Shirihai OS, Divakaruni AS, Goldstein AS. MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. Cell Rep 2023; 42:113221. [PMID: 37815914 DOI: 10.1016/j.celrep.2023.113221] [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: 02/13/2023] [Revised: 08/17/2023] [Accepted: 09/20/2023] [Indexed: 10/12/2023] Open
Abstract
Advanced prostate cancers are treated with therapies targeting the androgen receptor (AR) signaling pathway. While many tumors initially respond to AR inhibition, nearly all develop resistance. It is critical to understand how prostate tumor cells respond to AR inhibition in order to exploit therapy-induced phenotypes prior to the outgrowth of treatment-resistant disease. Here, we comprehensively characterize the effects of AR blockade on prostate cancer metabolism using transcriptomics, metabolomics, and bioenergetics approaches. The metabolic response to AR inhibition is defined by reduced glycolysis, robust elongation of mitochondria, and increased reliance on mitochondrial oxidative metabolism. We establish DRP1 activity and MYC signaling as mediators of AR-blockade-induced metabolic phenotypes. Rescuing DRP1 phosphorylation after AR inhibition restores mitochondrial fission, while rescuing MYC restores glycolytic activity and prevents sensitivity to complex I inhibition. Our study provides insight into the regulation of treatment-induced metabolic phenotypes and vulnerabilities in prostate cancer.
Collapse
Affiliation(s)
- Preston D Crowell
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jenna M Giafaglione
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas M Nunley
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Takao Hashimoto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amelie M L Delcourt
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anton Petcherski
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Raag Agrawal
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew J Bernard
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Johnny A Diaz
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kylie Y Heering
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rong Rong Huang
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nora M Navone
- Department of GU Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huihui Ye
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amina Zoubeidi
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Heather R Christofk
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B Rettig
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert E Reiter
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Paul C Boutros
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Orian S Shirihai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Clinical Biochemistry, School of Medicine, Ben Gurion University of The Negev, Beer-Sheva, Israel
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew S Goldstein
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
9
|
Doulias PT, Yang H, Andreyev AY, Dolatabadi N, Scott H, K Raspur C, Patel PR, Nakamura T, Tannenbaum SR, Ischiropoulos H, Lipton SA. S-Nitrosylation-mediated dysfunction of TCA cycle enzymes in synucleinopathy studied in postmortem human brains and hiPSC-derived neurons. Cell Chem Biol 2023; 30:965-975.e6. [PMID: 37478858 PMCID: PMC10530441 DOI: 10.1016/j.chembiol.2023.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/16/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
A causal relationship between mitochondrial metabolic dysfunction and neurodegeneration has been implicated in synucleinopathies, including Parkinson disease (PD) and Lewy body dementia (LBD), but underlying mechanisms are not fully understood. Here, using human induced pluripotent stem cell (hiPSC)-derived neurons with mutation in the gene encoding α-synuclein (αSyn), we report the presence of aberrantly S-nitrosylated proteins, including tricarboxylic acid (TCA) cycle enzymes, resulting in activity inhibition assessed by carbon-labeled metabolic flux experiments. This inhibition principally affects α-ketoglutarate dehydrogenase/succinyl coenzyme-A synthetase, metabolizing α-ketoglutarate to succinate. Notably, human LBD brain manifests a similar pattern of aberrantly S-nitrosylated TCA enzymes, indicating the pathophysiological relevance of these results. Inhibition of mitochondrial energy metabolism in neurons is known to compromise dendritic length and synaptic integrity, eventually leading to neuronal cell death. Our evidence indicates that aberrant S-nitrosylation of TCA cycle enzymes contributes to this bioenergetic failure.
Collapse
Affiliation(s)
- Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Departments of Pediatrics and Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry and University Research Center of Ioannina, University of Ioannina, 45110 Ioannina, Greece
| | - Hongmei Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Changchun University of Chinese Medicine, Changchun 130021, China
| | - Alexander Y Andreyev
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nima Dolatabadi
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry Scott
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charlene K Raspur
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Parth R Patel
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tomohiro Nakamura
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Departments of Pediatrics and Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stuart A Lipton
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA.
| |
Collapse
|
10
|
Acevedo A, Jones AE, Danna BT, Turner R, Montales KP, Benincá C, Reue K, Shirihai OS, Stiles L, Wallace M, Wang Y, Bertholet AM, Divakaruni AS. The BCKDK inhibitor BT2 is a chemical uncoupler that lowers mitochondrial ROS production and de novo lipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553413. [PMID: 37645724 PMCID: PMC10461965 DOI: 10.1101/2023.08.15.553413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Elevated levels of branched chain amino acids (BCAAs) and branched-chain α-ketoacids (BCKAs) are associated with cardiovascular and metabolic disease, but the molecular mechanisms underlying a putative causal relationship remain unclear. The branched-chain ketoacid dehydrogenase kinase (BCKDK) inhibitor BT2 is often used in preclinical models to increase BCAA oxidation and restore steady-state BCAA and BCKA levels. BT2 administration is protective in various rodent models of heart failure and metabolic disease, but confoundingly, targeted ablation of Bckdk in specific tissues does not reproduce the beneficial effects conferred by pharmacologic inhibition. Here we demonstrate that BT2, a lipophilic weak acid, can act as a mitochondrial uncoupler. Measurements of oxygen consumption, mitochondrial membrane potential, and patch-clamp electrophysiology show BT2 increases proton conductance across the mitochondrial inner membrane independently of its inhibitory effect on BCKDK. BT2 is roughly five-fold less potent than the prototypical uncoupler 2,4-dinitrophenol (DNP), and phenocopies DNP in lowering de novo lipogenesis and mitochondrial superoxide production. The data suggest the therapeutic efficacy of BT2 may be attributable to the well-documented effects of mitochondrial uncoupling in alleviating cardiovascular and metabolic disease.
Collapse
Affiliation(s)
- Aracely Acevedo
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bezawit T Danna
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rory Turner
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Katrina P Montales
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cristiane Benincá
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Orian S Shirihai
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Linsey Stiles
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Martina Wallace
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Yibin Wang
- DukeNUS School of Medicine, Signature Research Program in Cardiovascular and Metabolic Diseases, 8 College Road, Mail Code 169857, Singapore
| | - Ambre M Bertholet
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Lead contact
| |
Collapse
|
11
|
Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
Collapse
Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
12
|
Nikolka F, Karagöz MS, Nassef MZ, Hiller K, Steinert M, Cordes T. The Virulence Factor Macrophage Infectivity Potentiator (Mip) Influences Branched-Chain Amino Acid Metabolism and Pathogenicity of Legionella pneumophila. Metabolites 2023; 13:834. [PMID: 37512541 PMCID: PMC10386555 DOI: 10.3390/metabo13070834] [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: 04/28/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Legionella pneumophila (Lp) is a common etiological agent of bacterial pneumonia that causes Legionnaires' disease (LD). The bacterial membrane-associated virulence factor macrophage infectivity potentiator (Mip) exhibits peptidyl-prolyl-cis/trans-isomerase (PPIase) activity and contributes to the intra- and extracellular pathogenicity of Lp. Though Mip influences disease outcome, little is known about the metabolic consequences of altered Mip activity during infections. Here, we established a metabolic workflow and applied mass spectrometry approaches to decipher how Mip activity influences metabolism and pathogenicity. Impaired Mip activity in genetically engineered Lp strains decreases intracellular replication in cellular infection assays, confirming the contribution of Mip for Lp pathogenicity. We observed that genetic and chemical alteration of Mip using the PPIase inhibitors rapamycin and FK506 induces metabolic reprogramming in Lp, specifically branched-chain amino acid (BCAA) metabolism. Rapamycin also inhibits PPIase activity of mammalian FK506 binding proteins, and we observed that rapamycin induces a distinct metabolic signature in human macrophages compared to bacteria, suggesting potential involvement of Mip in normal bacteria and in infection. Our metabolic studies link Mip to alterations in BCAA metabolism and may help to decipher novel disease mechanisms associated with LD.
Collapse
Affiliation(s)
- Fabian Nikolka
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Mustafa Safa Karagöz
- Institut für Mikrobiologie, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Mohamed Zakaria Nassef
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Thekla Cordes
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| |
Collapse
|
13
|
Green CR, Bonelli R, Ansell BRE, Tzaridis S, Handzlik MK, McGregor GH, Hart B, Trombley J, Reilly MM, Bernstein PS, Egan C, Fruttiger M, Wallace M, Bahlo M, Friedlander M, Metallo CM, Gantner ML. Divergent amino acid and sphingolipid metabolism in patients with inherited neuro-retinal disease. Mol Metab 2023; 72:101716. [PMID: 36997154 PMCID: PMC10114224 DOI: 10.1016/j.molmet.2023.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
OBJECTIVES The non-essential amino acids serine, glycine, and alanine, as well as diverse sphingolipid species, are implicated in inherited neuro-retinal disorders and are metabolically linked by serine palmitoyltransferase (SPT), a key enzyme in membrane lipid biogenesis. To gain insight into the pathophysiological mechanisms linking these pathways to neuro-retinal diseases we compared patients diagnosed with two metabolically intertwined diseases: macular telangiectasia type II (MacTel), hereditary sensory autonomic neuropathy type 1 (HSAN1), or both. METHODS We performed targeted metabolomic analyses of amino acids and broad sphingolipids in sera from a cohort of MacTel (205), HSAN1 (25) and Control (151) participants. RESULTS MacTel patients exhibited broad alterations of amino acids, including changes in serine, glycine, alanine, glutamate, and branched-chain amino acids reminiscent of diabetes. MacTel patients had elevated 1-deoxysphingolipids but reduced levels of complex sphingolipids in circulation. A mouse model of retinopathy indicates dietary serine and glycine restriction can drive this depletion in complex sphingolipids. HSAN1 patients exhibited elevated serine, lower alanine, and a reduction in canonical ceramides and sphingomyelins compared to controls. Those patients diagnosed with both HSAN1 and MacTel showed the most significant decrease in circulating sphingomyelins. CONCLUSIONS These results highlight metabolic distinctions between MacTel and HSAN1, emphasize the importance of membrane lipids in the progression of MacTel, and suggest distinct therapeutic approaches for these two neurodegenerative diseases.
Collapse
Affiliation(s)
- Courtney R Green
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA
| | - Roberto Bonelli
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Michal K Handzlik
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA
| | - Grace H McGregor
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA
| | - Barbara Hart
- Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | | | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Catherine Egan
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK; University College London Institute of Ophthalmology, London, UK
| | - Marcus Fruttiger
- University College London Institute of Ophthalmology, London, UK
| | | | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Christian M Metallo
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA.
| | | |
Collapse
|
14
|
Kuna RS, Kumar A, Wessendorf-Rodriguez KA, Galvez H, Green CR, McGregor GH, Cordes T, Shaw RJ, Svensson RU, Metallo CM. Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress. SCIENCE ADVANCES 2023; 9:eadf0138. [PMID: 37134162 PMCID: PMC10156121 DOI: 10.1126/sciadv.adf0138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA homeostasis under such stresses is critically important. To this end, we applied 13C isotope tracing cell lines deficient in these mitochondrial [ATP-citrate lyase (ACLY)]-, cytosolic [acetyl-CoA synthetase (ACSS2)]-, and peroxisomal [peroxisomal biogenesis factor 5 (PEX5)]-dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting that alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation in cells lacking ACLY, highlighting a role for inter-organelle cross-talk in supporting cell survival in response to nutrient fluctuations.
Collapse
Affiliation(s)
- Ramya S. Kuna
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Avi Kumar
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karl A. Wessendorf-Rodriguez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hector Galvez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Courtney R. Green
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace H. McGregor
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Reuben J. Shaw
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Christian M. Metallo
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
15
|
Kuhlmann-Hogan A, Cordes T, Xu Z, Traina KA, Robles-Oteíza C, Ayeni D, Kwong EM, Levy SR, Nobari M, Cheng GZ, Shaw R, Leibel SL, Metallo CM, Politi K, Kaech SM. EGFR + lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536974. [PMID: 37131637 PMCID: PMC10153136 DOI: 10.1101/2023.04.15.536974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The limited efficacy of currently approved immunotherapies in EGFR-mutant lung adenocarcinoma (LUAD) underscores the need to better understand mechanisms governing local immunosuppression. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophages (TA-AM) to proliferate and support tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF-PPARγ signaling and inhibition of airway GM-CSF or PPARγ in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPARγ in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases T cell effector functions. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how such cancer cells can metabolically co-opt TA-AMs through GM-CSF-PPARγ signaling to provide nutrients that promote oncogenic signaling and growth.
Collapse
|
16
|
Mapping the Metabolic Niche of Citrate Metabolism and SLC13A5. Metabolites 2023; 13:metabo13030331. [PMID: 36984771 PMCID: PMC10054676 DOI: 10.3390/metabo13030331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
The small molecule citrate is a key molecule that is synthesized de novo and involved in diverse biochemical pathways influencing cell metabolism and function. Citrate is highly abundant in the circulation, and cells take up extracellular citrate via the sodium-dependent plasma membrane transporter NaCT encoded by the SLC13A5 gene. Citrate is critical to maintaining metabolic homeostasis and impaired NaCT activity is implicated in metabolic disorders. Though citrate is one of the best known and most studied metabolites in humans, little is known about the consequences of altered citrate uptake and metabolism. Here, we review recent findings on SLC13A5, NaCT, and citrate metabolism and discuss the effects on metabolic homeostasis and SLC13A5-dependent phenotypes. We discuss the “multiple-hit theory” and how stress factors induce metabolic reprogramming that may synergize with impaired NaCT activity to alter cell fate and function. Furthermore, we underline how citrate metabolism and compartmentalization can be quantified by combining mass spectrometry and tracing approaches. We also discuss species-specific differences and potential therapeutic implications of SLC13A5 and NaCT. Understanding the synergistic impact of multiple stress factors on citrate metabolism may help to decipher the disease mechanisms associated with SLC13A5 citrate transport disorders.
Collapse
|
17
|
Handzlik MK, Gengatharan JM, Frizzi KE, McGregor GH, Martino C, Rahman G, Gonzalez A, Moreno AM, Green CR, Guernsey LS, Lin T, Tseng P, Ideguchi Y, Fallon RJ, Chaix A, Panda S, Mali P, Wallace M, Knight R, Gantner ML, Calcutt NA, Metallo CM. Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 2023; 614:118-124. [PMID: 36697822 PMCID: PMC9891999 DOI: 10.1038/s41586-022-05637-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/07/2022] [Indexed: 01/26/2023]
Abstract
Diabetes represents a spectrum of disease in which metabolic dysfunction damages multiple organ systems including liver, kidneys and peripheral nerves1,2. Although the onset and progression of these co-morbidities are linked with insulin resistance, hyperglycaemia and dyslipidaemia3-7, aberrant non-essential amino acid (NEAA) metabolism also contributes to the pathogenesis of diabetes8-10. Serine and glycine are closely related NEAAs whose levels are consistently reduced in patients with metabolic syndrome10-14, but the mechanistic drivers and downstream consequences of this metabotype remain unclear. Low systemic serine and glycine are also emerging as a hallmark of macular and peripheral nerve disorders, correlating with impaired visual acuity and peripheral neuropathy15,16. Here we demonstrate that aberrant serine homeostasis drives serine and glycine deficiencies in diabetic mice, which can be diagnosed with a serine tolerance test that quantifies serine uptake and disposal. Mimicking these metabolic alterations in young mice by dietary serine or glycine restriction together with high fat intake markedly accelerates the onset of small fibre neuropathy while reducing adiposity. Normalization of serine by dietary supplementation and mitigation of dyslipidaemia with myriocin both alleviate neuropathy in diabetic mice, linking serine-associated peripheral neuropathy to sphingolipid metabolism. These findings identify systemic serine deficiency and dyslipidaemia as novel risk factors for peripheral neuropathy that may be exploited therapeutically.
Collapse
Affiliation(s)
- Michal K Handzlik
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jivani M Gengatharan
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Katie E Frizzi
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Grace H McGregor
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ana M Moreno
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Courtney R Green
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Lucie S Guernsey
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Terry Lin
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Patrick Tseng
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Amandine Chaix
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Martina Wallace
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | | | - Nigel A Calcutt
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christian M Metallo
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
18
|
Perea-Gil I, Seeger T, Bruyneel AAN, Termglinchan V, Monte E, Lim EW, Vadgama N, Furihata T, Gavidia AA, Arthur Ataam J, Bharucha N, Martinez-Amador N, Ameen M, Nair P, Serrano R, Kaur B, Feyen DAM, Diecke S, Snyder MP, Metallo CM, Mercola M, Karakikes I. Serine biosynthesis as a novel therapeutic target for dilated cardiomyopathy. Eur Heart J 2022; 43:3477-3489. [PMID: 35728000 PMCID: PMC9794189 DOI: 10.1093/eurheartj/ehac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
AIMS Genetic dilated cardiomyopathy (DCM) is a leading cause of heart failure. Despite significant progress in understanding the genetic aetiologies of DCM, the molecular mechanisms underlying the pathogenesis of familial DCM remain unknown, translating to a lack of disease-specific therapies. The discovery of novel targets for the treatment of DCM was sought using phenotypic sceening assays in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that recapitulate the disease phenotypes in vitro. METHODS AND RESULTS Using patient-specific iPSCs carrying a pathogenic TNNT2 gene mutation (p.R183W) and CRISPR-based genome editing, a faithful DCM model in vitro was developed. An unbiased phenotypic screening in TNNT2 mutant iPSC-derived cardiomyocytes (iPSC-CMs) with small molecule kinase inhibitors (SMKIs) was performed to identify novel therapeutic targets. Two SMKIs, Gö 6976 and SB 203580, were discovered whose combinatorial treatment rescued contractile dysfunction in DCM iPSC-CMs carrying gene mutations of various ontologies (TNNT2, TTN, LMNA, PLN, TPM1, LAMA2). The combinatorial SMKI treatment upregulated the expression of genes that encode serine, glycine, and one-carbon metabolism enzymes and significantly increased the intracellular levels of glucose-derived serine and glycine in DCM iPSC-CMs. Furthermore, the treatment rescued the mitochondrial respiration defects and increased the levels of the tricarboxylic acid cycle metabolites and ATP in DCM iPSC-CMs. Finally, the rescue of the DCM phenotypes was mediated by the activating transcription factor 4 (ATF4) and its downstream effector genes, phosphoglycerate dehydrogenase (PHGDH), which encodes a critical enzyme of the serine biosynthesis pathway, and Tribbles 3 (TRIB3), a pseudokinase with pleiotropic cellular functions. CONCLUSIONS A phenotypic screening platform using DCM iPSC-CMs was established for therapeutic target discovery. A combination of SMKIs ameliorated contractile and metabolic dysfunction in DCM iPSC-CMs mediated via the ATF4-dependent serine biosynthesis pathway. Together, these findings suggest that modulation of serine biosynthesis signalling may represent a novel genotype-agnostic therapeutic strategy for genetic DCM.
Collapse
Affiliation(s)
- Isaac Perea-Gil
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Timon Seeger
- Department of Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Arne A N Bruyneel
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Vittavat Termglinchan
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Emma Monte
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Takaaki Furihata
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra A Gavidia
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Jennifer Arthur Ataam
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nike Bharucha
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Noel Martinez-Amador
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Mohamed Ameen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Pooja Nair
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Ricardo Serrano
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Balpreet Kaur
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Dries A M Feyen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark Mercola
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
19
|
1-deoxysphingolipid synthesis compromises anchorage-independent growth and plasma membrane endocytosis in cancer cells. J Lipid Res 2022; 63:100281. [PMID: 36115594 DOI: 10.1016/j.jlr.2022.100281] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Serine palmitoyltransferase (SPT) predominantly incorporates serine and fatty acyl-CoAs into diverse sphingolipids that serve as structural components of membranes and signaling molecules within or amongst cells. However, SPT also uses alanine as a substrate in the contexts of low serine availability, alanine accumulation, or disease-causing mutations in hereditary sensory neuropathy type I (HSAN1), resulting in the synthesis and accumulation of 1-deoxysphingolipids. These species promote cytotoxicity in neurons and impact diverse cellular phenotypes, including suppression of anchorage-independent cancer cell growth. While altered serine and alanine levels can promote 1-deoxysphingolipid synthesis, they impact numerous other metabolic pathways important for cancer cells. Here we combined isotope tracing, quantitative metabolomics, and functional studies to better understand the mechanistic drivers of 1-deoxysphingolipid toxicity in cancer cells. We determined that both alanine treatment and SPTLC1C133W expression induce 1-deoxy(dihydro)ceramide synthesis and accumulation but fail to broadly impact intermediary metabolism, abundances of other lipids, or growth of adherent cells. However, we found spheroid culture and soft agar colony formation were compromised when endogenous 1-deoxysphingolipid synthesis was induced via SPTLC1C133W expression. Consistent with these impacts on anchorage-independent cell growth, we observed that 1-deoxysphingolipid synthesis reduced plasma membrane endocytosis. These results highlight a potential role for SPT promiscuity in linking altered amino acid metabolism to plasma membrane endocytosis.
Collapse
|
20
|
Hazim RA, Paniagua AE, Tang L, Yang K, Kim KKO, Stiles L, Divakaruni AS, Williams DS. Vitamin B3, nicotinamide, enhances mitochondrial metabolism to promote differentiation of the retinal pigment epithelium. J Biol Chem 2022; 298:102286. [PMID: 35868562 PMCID: PMC9396405 DOI: 10.1016/j.jbc.2022.102286] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/04/2023] Open
Abstract
In the mammalian retina, a metabolic ecosystem exists in which photoreceptors acquire glucose from the choriocapillaris with the help of the retinal pigment epithelium (RPE). While the photoreceptor cells are primarily glycolytic, exhibiting Warburg-like metabolism, the RPE is reliant on mitochondrial respiration. However, the ways in which mitochondrial metabolism affect RPE cellular functions are not clear. We first used the human RPE cell line, ARPE-19, to examine mitochondrial metabolism in the context of cellular differentiation. We show that nicotinamide induced rapid differentiation of ARPE-19 cells, which was reversed by removal of supplemental nicotinamide. During the nicotinamide-induced differentiation, we observed using quantitative PCR, Western blotting, electron microscopy, and metabolic respiration and tracing assays that (1) mitochondrial gene and protein expression increased, (2) mitochondria became larger with more tightly folded cristae, and (3) mitochondrial metabolism was enhanced. In addition, we show that primary cultures of human fetal RPE cells responded similarly in the presence of nicotinamide. Furthermore, disruption of mitochondrial oxidation of pyruvate attenuated the nicotinamide-induced differentiation of the RPE cells. Together, our results demonstrate a remarkable effect of nicotinamide on RPE metabolism. We also identify mitochondrial respiration as a key contributor to the differentiated state of the RPE and thus to many of the RPE functions that are essential for retinal health and photoreception.
Collapse
Affiliation(s)
- Roni A Hazim
- Department of Ophthalmology and Stein Eye Institute
| | | | - Lisa Tang
- Department of Ophthalmology and Stein Eye Institute
| | - Krista Yang
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Kristen K O Kim
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Linsey Stiles
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095; Department of Medicine, Endocrinology. UCLA David Geffen School of Medicine. Los Angeles, CA, 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - David S Williams
- Department of Ophthalmology and Stein Eye Institute; Department of Neurobiology, David Geffen School of Medicine at UCLA; Molecular Biology Institute; Brain Research Institute, University of California, Los Angeles, CA.
| |
Collapse
|
21
|
Parekh U, McDonald D, Dailamy A, Wu Y, Cordes T, Zhang K, Tipps A, Metallo C, Mali P. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas. iScience 2021; 24:103149. [PMID: 34646987 PMCID: PMC8496177 DOI: 10.1016/j.isci.2021.103149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 11/22/2022] Open
Abstract
Deconstructing tissue-specific effects of genes and variants on proliferation is critical to understanding cellular transformation and systematically selecting cancer therapeutics. This requires scalable methods for multiplexed genetic screens tracking fitness across time, across lineages, and in a suitable niche, since physiological cues influence functional differences. Towards this, we present an approach, coupling single-cell cancer driver screens in teratomas with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serial reinjection. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. Additionally, mutant MEK1 S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful platform for multi-lineage longitudinal study of oncogenesis.
Collapse
Affiliation(s)
- Udit Parekh
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, USA
| | - Daniella McDonald
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, USA
| | - Amir Dailamy
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Yan Wu
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Thekla Cordes
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Ann Tipps
- School of Medicine, University of California San Diego, San Diego, USA
| | - Christian Metallo
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Salk Institute of Biological Studies, La Jolla, USA
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, San Diego, USA
| |
Collapse
|
22
|
Lim EW, Handzlik MK, Trefts E, Gengatharan JM, Pondevida CM, Shaw RJ, Metallo CM. Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in PolgD257A mice. SCIENCE ADVANCES 2021; 7:eabj4077. [PMID: 34652935 PMCID: PMC8519573 DOI: 10.1126/sciadv.abj4077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/24/2021] [Indexed: 05/03/2023]
Abstract
Mitochondria are central to metabolic homeostasis, and progressive mitochondrial defects have diverse metabolic consequences that could drive distinct pathophysiological states. Here, we comprehensively characterized metabolic alterations in PolgD257A mice. Plasma alanine increased markedly with time, with other organic acids accumulating to a lesser extent. These changes were reflective of increased Cori and Cahill cycling in PolgD257A mice and subsequent hypoglycemia, which did not occur during normal mouse aging. Tracing with [15N]ammonium further supported this shift in amino acid metabolism with mild impairment of the urea cycle. We also measured alterations in the lipidome, observing a reduction in canonical lipids and accumulation of 1-deoxysphingolipids, which are synthesized from alanine via promiscuous serine palmitoyltransferase activity and correlate with peripheral neuropathy. Consistent with this metabolic link, PolgD257A mice exhibited thermal hypoalgesia. These results highlight the longitudinal changes that occur in intermediary metabolism upon mitochondrial impairment and identify a contributing mechanism to mitochondria-associated neuropathy.
Collapse
Affiliation(s)
- Esther W. Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Michal K. Handzlik
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Elijah Trefts
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Jivani M. Gengatharan
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Carlos M. Pondevida
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Reuben J. Shaw
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Christian M. Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| |
Collapse
|
23
|
Kumar A, Cordes T, Thalacker-Mercer AE, Pajor AM, Murphy AN, Metallo CM. NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions. Cell Rep 2021; 36:109701. [PMID: 34525352 PMCID: PMC8500708 DOI: 10.1016/j.celrep.2021.109701] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 01/11/2023] Open
Abstract
Citrate lies at a critical node of metabolism, linking tricarboxylic acid metabolism and lipogenesis via acetyl-coenzyme A. Recent studies have observed that deficiency of the sodium-dependent citrate transporter (NaCT), encoded by SLC13A5, dysregulates hepatic metabolism and drives pediatric epilepsy. To examine how NaCT contributes to citrate metabolism in cells relevant to the pathophysiology of these diseases, we apply 13C isotope tracing to SLC13A5-deficient hepatocellular carcinoma (HCC) cells and primary rat cortical neurons. Exogenous citrate appreciably contributes to intermediary metabolism only under hypoxic conditions. In the absence of glutamine, citrate supplementation increases de novo lipogenesis and growth of HCC cells. Knockout of SLC13A5 in Huh7 cells compromises citrate uptake and catabolism. Citrate supplementation rescues Huh7 cell viability in response to glutamine deprivation or Zn2+ treatment, and NaCT deficiency mitigates these effects. Collectively, these findings demonstrate that NaCT-mediated citrate uptake is metabolically important under nutrient-limited conditions and may facilitate resistance to metal toxicity.
Collapse
Affiliation(s)
- Avi Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna E Thalacker-Mercer
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anne N Murphy
- Department of Pharmacology, 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 92037, USA.
| |
Collapse
|
24
|
Yebra M, Bhargava S, Kumar A, Burgoyne AM, Tang CM, Yoon H, Banerjee S, Aguilera J, Cordes T, Sheth V, Noh S, Ustoy R, Li S, Advani SJ, Corless CL, Heinrich MC, Kurzrock R, Lippman SM, Fanta PT, Harismendy O, Metallo C, Sicklick JK. Establishment of Patient-Derived Succinate Dehydrogenase-Deficient Gastrointestinal Stromal Tumor Models for Predicting Therapeutic Response. Clin Cancer Res 2021; 28:187-200. [PMID: 34426440 DOI: 10.1158/1078-0432.ccr-21-2092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract, with mutant succinate dehydrogenase (SDH) subunits (A-D) comprising less than 7.5% (i.e., 150-200/year) of new cases annually in the United States. Contrary to GISTs harboring KIT or PDGFRA mutations, SDH-mutant GISTs affect adolescents/young adults, often metastasize, and are frequently resistant to tyrosine kinase inhibitors (TKI). Lack of human models for any SDH-mutant tumors, including GIST, has limited molecular characterization and drug discovery. EXPERIMENTAL DESIGN We describe methods for establishing novel patient-derived SDH-mutant (mSDH) GIST models and interrogated the efficacy of temozolomide on these tumor models in vitro and in clinical trials of patients with mSDH GIST. RESULTS Molecular and metabolic characterization of our patient-derived mSDH GIST models revealed that these models recapitulate the transcriptional and metabolic hallmarks of parent tumors and SDH deficiency. We further demonstrate that temozolomide elicits DNA damage and apoptosis in our mSDH GIST models. Translating our in vitro discovery to the clinic, a cohort of patients with SDH-mutant GIST treated with temozolomide (n = 5) demonstrated a 40% objective response rate and 100% disease control rate, suggesting that temozolomide represents a promising therapy for this subset of GIST. CONCLUSIONS We report the first methods to establish patient-derived mSDH tumor models, which can be readily employed for understanding patient-specific tumor biology and treatment strategies. We also demonstrate that temozolomide is effective in patients with mSDH GIST who are refractory to existing chemotherapeutic drugs (namely, TKIs) in clinic for GISTs, bringing a promising treatment option for these patients to clinic.
Collapse
Affiliation(s)
- Mayra Yebra
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Shruti Bhargava
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Avi Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Adam M Burgoyne
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Hematology Oncology, University of California San Diego, San Diego, California
| | - Chih-Min Tang
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Hyunho Yoon
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Sudeep Banerjee
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Joseph Aguilera
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Radiation Medicine and Applied Sciences, University of California San Diego, San Diego, California
| | - Thekla Cordes
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Vipul Sheth
- Department of Radiology, Stanford University, Palo Alto, Stanford, California
| | - Sangkyu Noh
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Rowan Ustoy
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Sam Li
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Sunil J Advani
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Radiation Medicine and Applied Sciences, University of California San Diego, San Diego, California
| | | | - Michael C Heinrich
- Hematology/Medical Oncology, Portland VA Health Care System and OHSU Knight Cancer Institute, Portland, Oregon
| | - Razelle Kurzrock
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Hematology Oncology, University of California San Diego, San Diego, California.,Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| | - Scott M Lippman
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Hematology Oncology, University of California San Diego, San Diego, California.,Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| | - Paul T Fanta
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Hematology Oncology, University of California San Diego, San Diego, California.,Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| | - Olivier Harismendy
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Biomedical Informatics, University of California San Diego, San Diego, California
| | - Christian Metallo
- Moores Cancer Center, University of California San Diego, La Jolla, California.,Department of Bioengineering, University of California San Diego, La Jolla, California.,Diabetes and Endocrinology Research Center, University of California San Diego, La Jolla, California.,Institute of Engineering in Medicine, University of California San Diego, La Jolla, California
| | - Jason K Sicklick
- Moores Cancer Center, University of California San Diego, La Jolla, California. .,Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California.,Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| |
Collapse
|
25
|
Ravi A, Palamiuc L, Loughran RM, Triscott J, Arora GK, Kumar A, Tieu V, Pauli C, Reist M, Lew RJ, Houlihan SL, Fellmann C, Metallo C, Rubin MA, Emerling BM. PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay. Dev Cell 2021; 56:1661-1676.e10. [PMID: 33984270 DOI: 10.1016/j.devcel.2021.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/29/2021] [Accepted: 04/21/2021] [Indexed: 12/16/2022]
Abstract
PI5P4Ks are a class of phosphoinositide kinases that phosphorylate PI-5-P to PI-4,5-P2. Distinct localization of phosphoinositides is fundamental for a multitude of cellular functions. Here, we identify a role for peroxisomal PI-4,5-P2 generated by the PI5P4Ks in maintaining energy balance. We demonstrate that PI-4,5-P2 regulates peroxisomal fatty acid oxidation by mediating trafficking of lipid droplets to peroxisomes, which is essential for sustaining mitochondrial metabolism. Using fluorescent-tagged lipids and metabolite tracing, we show that loss of the PI5P4Ks significantly impairs lipid uptake and β-oxidation in the mitochondria. Further, loss of PI5P4Ks results in dramatic alterations in mitochondrial structural and functional integrity, which under nutrient deprivation is further exacerbated, causing cell death. Notably, inhibition of the PI5P4Ks in cancer cells and mouse tumor models leads to decreased cell viability and tumor growth, respectively. Together, these studies reveal an unexplored role for PI5P4Ks in preserving metabolic homeostasis, which is necessary for tumorigenesis.
Collapse
Affiliation(s)
- Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ryan M Loughran
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Joanna Triscott
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Avi Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivian Tieu
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Chantal Pauli
- Institute of Pathology and Molecular Pathology, University Hospital Zürich and the University of Zurich (UZH), Zurich 8006, Switzerland
| | - Matthias Reist
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Rachel J Lew
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Shauna L Houlihan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christof Fellmann
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christian Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark A Rubin
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
26
|
Su H, Yang F, Fu R, Li X, French R, Mose E, Pu X, Trinh B, Kumar A, Liu J, Antonucci L, Todoric J, Liu Y, Hu Y, Diaz-Meco MT, Moscat J, Metallo CM, Lowy AM, Sun B, Karin M. Cancer cells escape autophagy inhibition via NRF2-induced macropinocytosis. Cancer Cell 2021; 39:678-693.e11. [PMID: 33740421 PMCID: PMC8119368 DOI: 10.1016/j.ccell.2021.02.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/17/2020] [Accepted: 02/19/2021] [Indexed: 12/29/2022]
Abstract
Many cancers, including pancreatic ductal adenocarcinoma (PDAC), depend on autophagy-mediated scavenging and recycling of intracellular macromolecules, suggesting that autophagy blockade should cause tumor starvation and regression. However, until now autophagy-inhibiting monotherapies have not demonstrated potent anti-cancer activity. We now show that autophagy blockade prompts established PDAC to upregulate and utilize an alternative nutrient procurement pathway: macropinocytosis (MP) that allows tumor cells to extract nutrients from extracellular sources and use them for energy generation. The autophagy to MP switch, which may be evolutionarily conserved and not cancer cell restricted, depends on activation of transcription factor NRF2 by the autophagy adaptor p62/SQSTM1. NRF2 activation by oncogenic mutations, hypoxia, and oxidative stress also results in MP upregulation. Inhibition of MP in autophagy-compromised PDAC elicits dramatic metabolic decline and regression of transplanted and autochthonous tumors, suggesting the therapeutic promise of combining autophagy and MP inhibitors in the clinic.
Collapse
Affiliation(s)
- Hua Su
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China
| | - Fei Yang
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China
| | - Rao Fu
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China
| | - Xin Li
- Laboratory of Cancer ImmunoMetabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Randall French
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego Moores Cancer Center, La Jolla, CA 92093, USA
| | - Evangeline Mose
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego Moores Cancer Center, La Jolla, CA 92093, USA
| | - Xiaohong Pu
- Department of Pathology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China
| | - Brittney Trinh
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Avi Kumar
- Institute of Engineering in Medicine, Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Junlai Liu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Laura Antonucci
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jelena Todoric
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Yuan Liu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yinling Hu
- Laboratory of Cancer ImmunoMetabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Christian M Metallo
- Institute of Engineering in Medicine, Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew M Lowy
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego Moores Cancer Center, La Jolla, CA 92093, USA
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China.
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
27
|
Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase. Metabolites 2021; 11:metabo11020117. [PMID: 33670656 PMCID: PMC7922098 DOI: 10.3390/metabo11020117] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/29/2022] Open
Abstract
Itaconate is a small molecule metabolite that is endogenously produced by cis-aconitate decarboxylase-1 (ACOD1) in mammalian cells and influences numerous cellular processes. The metabolic consequences of itaconate in cells are diverse and contribute to its regulatory function. Here, we have applied isotope tracing and mass spectrometry approaches to explore how itaconate impacts various metabolic pathways in cultured cells. Itaconate is a competitive and reversible inhibitor of Complex II/succinate dehydrogenase (SDH) that alters tricarboxylic acid (TCA) cycle metabolism leading to succinate accumulation. Upon activation with coenzyme A (CoA), itaconyl-CoA inhibits adenosylcobalamin-mediated methylmalonyl-CoA (MUT) activity and, thus, indirectly impacts branched-chain amino acid (BCAA) metabolism and fatty acid diversity. Itaconate, therefore, alters the balance of CoA species in mitochondria through its impacts on TCA, amino acid, vitamin B12, and CoA metabolism. Our results highlight the diverse metabolic pathways regulated by itaconate and provide a roadmap to link these metabolites to potential downstream biological functions.
Collapse
|
28
|
Audano M, Pedretti S, Ligorio S, Giavarini F, Caruso D, Mitro N. Investigating metabolism by mass spectrometry: From steady state to dynamic view. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4658. [PMID: 33084147 DOI: 10.1002/jms.4658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Metabolism is the set of life-sustaining reactions in organisms. These biochemical reactions are organized in metabolic pathways, in which one metabolite is converted through a series of steps catalyzed by enzymes in another chemical compound. Metabolic reactions are categorized as catabolic, the breaking down of metabolites to produce energy, and/or anabolic, the synthesis of compounds that consume energy. The balance between catabolism of the preferential fuel substrate and anabolism defines the overall metabolism of a cell or tissue. Metabolomics is a powerful tool to gain new insights contributing to the identification of complex molecular mechanisms in the field of biomedical research, both basic and translational. The enormous potential of this kind of analyses consists of two key aspects: (i) the possibility of performing so-called targeted and untargeted experiments through which it is feasible to verify or formulate a hypothesis, respectively, and (ii) the opportunity to run either steady-state analyses to have snapshots of the metabolome at a given time under different experimental conditions or dynamic analyses through the use of labeled tracers. In this review, we will highlight the most important practical (e.g., different sample extraction approaches) and conceptual steps to consider for metabolomic analysis, describing also the main application contexts in which it is used. In addition, we will provide some insights into the most innovative approaches and progress in the field of data analysis and processing, highlighting how this part is essential for the proper extrapolation and interpretation of data.
Collapse
Affiliation(s)
- Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Simona Ligorio
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Flavio Giavarini
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Donatella Caruso
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| |
Collapse
|
29
|
Gheller BJ, Blum JE, Lim EW, Handzlik MK, Hannah Fong EH, Ko AC, Khanna S, Gheller ME, Bender EL, Alexander MS, Stover PJ, Field MS, Cosgrove BD, Metallo CM, Thalacker-Mercer AE. Extracellular serine and glycine are required for mouse and human skeletal muscle stem and progenitor cell function. Mol Metab 2021; 43:101106. [PMID: 33122122 PMCID: PMC7691553 DOI: 10.1016/j.molmet.2020.101106] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/08/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Skeletal muscle regeneration relies on muscle-specific adult stem cells (MuSCs), MuSC progeny, muscle progenitor cells (MPCs), and a coordinated myogenic program that is influenced by the extracellular environment. Following injury, MPCs undergo a transient and rapid period of population expansion, which is necessary to repair damaged myofibers and restore muscle homeostasis. Certain pathologies (e.g., metabolic diseases and muscle dystrophies) and advanced age are associated with dysregulated muscle regeneration. The availability of serine and glycine, two nutritionally non-essential amino acids, is altered in humans with these pathologies, and these amino acids have been shown to influence the proliferative state of non-muscle cells. Our objective was to determine the role of serine/glycine in MuSC/MPC function. METHODS Primary human MPCs (hMPCs) were used for in vitro experiments, and young (4-6 mo) and old (>20 mo) mice were used for in vivo experiments. Serine/glycine availability was manipulated using specially formulated media in vitro or dietary restriction in vivo followed by downstream metabolic and cell proliferation analyses. RESULTS We identified that serine/glycine are essential for hMPC proliferation. Dietary restriction of serine/glycine in a mouse model of skeletal muscle regeneration lowered the abundance of MuSCs 3 days post-injury. Stable isotope-tracing studies showed that hMPCs rely on extracellular serine/glycine for population expansion because they exhibit a limited capacity for de novo serine/glycine biosynthesis. Restriction of serine/glycine to hMPCs resulted in cell cycle arrest in G0/G1. Extracellular serine/glycine was necessary to support glutathione and global protein synthesis in hMPCs. Using an aged mouse model, we found that reduced serine/glycine availability augmented intermyocellular adipocytes 28 days post-injury. CONCLUSIONS These studies demonstrated that despite an absolute serine/glycine requirement for MuSC/MPC proliferation, de novo synthesis was inadequate to support these demands, making extracellular serine and glycine conditionally essential for efficient skeletal muscle regeneration.
Collapse
Affiliation(s)
- Brandon J Gheller
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Jamie E Blum
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Esther W Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Michal K Handzlik
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Anthony C Ko
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shray Khanna
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Molly E Gheller
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Erica L Bender
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Matthew S Alexander
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL, USA; UAB Center for Exercise Medicine, Birmingham, AL, USA; Civitan International Research Center at the University of Alabama at Birmingham, Birmingham, AL, USA; Department of Genetics at the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Patrick J Stover
- College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Benjamin D Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Anna E Thalacker-Mercer
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; UAB Center for Exercise Medicine, Birmingham, AL, USA; Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, USA.
| |
Collapse
|
30
|
Lim EW, Parker SJ, Metallo CM. Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells. Methods Mol Biol 2020; 2088:51-71. [PMID: 31893370 DOI: 10.1007/978-1-0716-0159-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Oxidation-reduction (redox) reactions are ubiquitous in biology and typically occur in specific subcellular compartments. In cells, the electron transfer between molecules and organelles is commonly facilitated by pyridine nucleotides such as nicotinamide adenine dinucleotide phosphate (NADPH) and nicotinamide adenine dinucleotide (NADH). While often taken for granted, these metabolic reactions are critically important for maintaining redox homeostasis and biochemical potentials across membranes. While 13C tracing and metabolic flux analysis (MFA) have emerged as powerful tools to study intracellular metabolism, this approach is limited when applied to pathways catalyzed in multiple cellular compartments. To address this issue, we and others have applied 2H (deuterium) tracers to observe transfer of labeled hydride anions, which accompanies electron transfer. Furthermore, we have developed a reporter system for indirectly quantifying NADPH enrichment in specific subcellular compartments. Here, we provide a detailed description of 2H tracing applications and the interrogation of mitochondrial versus cytosolic NAD(P)H metabolism in cultured mammalian cells. Specifically, we describe the generation of reporter cell lines that express epitope-tagged R132H-IDH1 or R172K-IDH2 and produce (D)2-hydroxyglutarate in a doxycycline-dependent manner. These tools and methods allow for quantitation of reducing equivalent turnover rates, the directionality of pathways present in multiple compartments, and the estimation of pathway contributions to NADPH pools.
Collapse
Affiliation(s)
- Esther W Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Seth J Parker
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Diabetes and Endocrinology Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
31
|
Veliova M, Ferreira CM, Benador IY, Jones AE, Mahdaviani K, Brownstein AJ, Desousa BR, Acín-Pérez R, Petcherski A, Assali EA, Stiles L, Divakaruni AS, Prentki M, Corkey BE, Liesa M, Oliveira MF, Shirihai OS. Blocking mitochondrial pyruvate import in brown adipocytes induces energy wasting via lipid cycling. EMBO Rep 2020; 21:e49634. [PMID: 33275313 PMCID: PMC7726774 DOI: 10.15252/embr.201949634] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Combined fatty acid esterification and lipolysis, termed lipid cycling, is an ATP‐consuming process that contributes to energy expenditure. Therefore, interventions that stimulate energy expenditure through lipid cycling are of great interest. Here we find that pharmacological and genetic inhibition of the mitochondrial pyruvate carrier (MPC) in brown adipocytes activates lipid cycling and energy expenditure, even in the absence of adrenergic stimulation. We show that the resulting increase in ATP demand elevates mitochondrial respiration coupled to ATP synthesis and fueled by lipid oxidation. We identify that glutamine consumption and the Malate‐Aspartate Shuttle are required for the increase in Energy Expenditure induced by MPC inhibition in Brown Adipocytes (MAShEEBA). We thus demonstrate that energy expenditure through enhanced lipid cycling can be activated in brown adipocytes by decreasing mitochondrial pyruvate availability. We present a new mechanism to increase energy expenditure and fat oxidation in brown adipocytes, which does not require adrenergic stimulation of mitochondrial uncoupling.
Collapse
Affiliation(s)
- Michaela Veliova
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Caroline M Ferreira
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ilan Y Benador
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Kiana Mahdaviani
- Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Alexandra J Brownstein
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Molecular Cellular Integrative Physiology, University of California, Los Angeles, CA, USA
| | - Brandon R Desousa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Rebeca Acín-Pérez
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anton Petcherski
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Essam A Assali
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Clinical Biochemistry, School of Medicine, Ben Gurion University of The Negev, Beer-Sheva, Israel
| | - Linsey Stiles
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marc Prentki
- Department of Nutrition, , Université de Montréal, Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Barbara E Corkey
- Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Marc Liesa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marcus F Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Orian S Shirihai
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
32
|
Jones AE, Sheng L, Acevedo A, Veliova M, Shirihai OS, Stiles L, Divakaruni AS. Forces, fluxes, and fuels: tracking mitochondrial metabolism by integrating measurements of membrane potential, respiration, and metabolites. Am J Physiol Cell Physiol 2020; 320:C80-C91. [PMID: 33147057 DOI: 10.1152/ajpcell.00235.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Assessing mitochondrial function in cell-based systems is a central component of metabolism research. However, the selection of an initial measurement technique may be complicated given the range of parameters that can be studied and the need to define the mitochondrial (dys)function of interest. This methods-focused review compares and contrasts the use of mitochondrial membrane potential measurements, plate-based respirometry, and metabolomics and stable isotope tracing. We demonstrate how measurements of 1) cellular substrate preference, 2) respiratory chain activity, 3) cell activation, and 4) mitochondrial biogenesis are enriched by integrating information from multiple methods. This manuscript is meant to serve as a perspective to help choose which technique might be an appropriate initial method to answer a given question, as well as provide a broad "roadmap" for designing follow-up assays to enrich datasets or resolve ambiguous results.
Collapse
Affiliation(s)
- Anthony E Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Li Sheng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Aracely Acevedo
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Michaela Veliova
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California.,Department of Medicine, University of California, Los Angeles, California
| | - Orian S Shirihai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California.,Department of Medicine, University of California, Los Angeles, California
| | - Linsey Stiles
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California.,Department of Medicine, University of California, Los Angeles, California
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| |
Collapse
|
33
|
Chella Krishnan K, Floyd RR, Sabir S, Jayasekera DW, Leon-Mimila PV, Jones AE, Cortez AA, Shravah V, Péterfy M, Stiles L, Canizales-Quinteros S, Divakaruni AS, Huertas-Vazquez A, Lusis AJ. Liver Pyruvate Kinase Promotes NAFLD/NASH in Both Mice and Humans in a Sex-Specific Manner. Cell Mol Gastroenterol Hepatol 2020; 11:389-406. [PMID: 32942044 PMCID: PMC7788245 DOI: 10.1016/j.jcmgh.2020.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The etiology of nonalcoholic fatty liver disease (NAFLD) is poorly understood, with males and certain populations exhibiting markedly increased susceptibility. Using a systems genetics approach involving multi-omic analysis of ∼100 diverse inbred strains of mice, we recently identified several candidate genes driving NAFLD. We investigated the role of one of these, liver pyruvate kinase (L-PK or Pklr), in NAFLD by using patient samples and mouse models. METHODS We examined L-PK expression in mice of both sexes and in a cohort of bariatric surgery patients. We used liver-specific loss- and gain-of-function strategies in independent animal models of diet-induced steatosis and fibrosis. After treatment, we measured several metabolic phenotypes including obesity, insulin resistance, dyslipidemia, liver steatosis, and fibrosis. Liver tissues were used for gene expression and immunoblotting, and liver mitochondria bioenergetics was characterized. RESULTS In both mice and humans, L-PK expression is up-regulated in males via testosterone and is strongly associated with NAFLD severity. In a steatosis model, L-PK silencing in male mice improved glucose tolerance, insulin sensitivity, and lactate/pyruvate tolerance compared with controls. Furthermore, these animals had reduced plasma cholesterol levels and intrahepatic triglyceride accumulation. Conversely, L-PK overexpression in male mice resulted in augmented disease phenotypes. In contrast, female mice overexpressing L-PK were unaffected. Mechanistically, L-PK altered mitochondrial pyruvate flux and its incorporation into citrate, and this, in turn, increased liver triglycerides via up-regulated de novo lipogenesis and increased PNPLA3 levels accompanied by mitochondrial dysfunction. Also, L-PK increased plasma cholesterol levels via increased PCSK9 levels. On the other hand, L-PK silencing reduced de novo lipogenesis and PNPLA3 and PCSK9 levels and improved mitochondrial function. Finally, in fibrosis model, we demonstrate that L-PK silencing in male mice reduced both liver steatosis and fibrosis, accompanied by reduced de novo lipogenesis and improved mitochondrial function. CONCLUSIONS L-PK acts in a male-specific manner in the development of liver steatosis and fibrosis. Because NAFLD/nonalcoholic steatohepatitis exhibit sexual dimorphism, our results have important implications for the development of personalized therapeutics.
Collapse
Affiliation(s)
- Karthickeyan Chella Krishnan
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California,Correspondence Address correspondence to: Karthickeyan Chella Krishnan, PhD, UCLA Department of Medicine/Division of Cardiology, 650 Charles E. Young Drive South, Box 951679, Los Angeles, California 90095-1679. fax: (310) 794-7345, or
| | - Raquel R. Floyd
- Department of Biology, University of California, Los Angeles, California
| | - Simon Sabir
- Department of Psychology, University of California, Los Angeles, California
| | - Dulshan W. Jayasekera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California
| | - Paola V. Leon-Mimila
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California,Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Unidad de Genómica de Poblaciones Aplicada a la Salud, Mexico City, Mexico
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Angel A. Cortez
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Varun Shravah
- Department of Chemistry, University of California, Los Angeles, California
| | - Miklós Péterfy
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California,Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, California
| | - Linsey Stiles
- Department of Medicine/Division of Endocrinology, University of California, Los Angeles, California
| | - Samuel Canizales-Quinteros
- Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Unidad de Genómica de Poblaciones Aplicada a la Salud, Mexico City, Mexico
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California
| | - Adriana Huertas-Vazquez
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California
| | - Aldons J. Lusis
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California,Department of Human Genetics, University of California, Los Angeles, California,Aldons J. Lusis, PhD, UCLA Department of Medicine/Division of Cardiology, 650 Charles E. Young Drive South, Box 951679, Los Angeles, California 90095-1679.
| |
Collapse
|
34
|
Muthusamy T, Cordes T, Handzlik MK, You L, Lim EW, Gengatharan J, Pinto AFM, Badur MG, Kolar MJ, Wallace M, Saghatelian A, Metallo CM. Serine restriction alters sphingolipid diversity to constrain tumour growth. Nature 2020; 586:790-795. [PMID: 32788725 PMCID: PMC7606299 DOI: 10.1038/s41586-020-2609-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
Serine, glycine, and other non-essential amino acids are critical for tumor progression, and strategies to limit their availability are emerging as potential cancer therapies1–3. However, the molecular mechanisms driving this response remain unclear, and the impact on lipid metabolism is relatively unexplored. Serine palmitoyltransferase (SPT) catalyzes the de novo biosynthesis of sphingolipids but also produces non-canonical 1-deoxysphingolipids (doxSLs) when using alanine as a substrate4,5. DoxSLs accumulate in the context of SPTLC1 or SPTLC2 mutations6,7 or low serine availability8,9 to drive neuropathy, and deoxysphinganine (doxSA) has been investigated as an anti-cancer agent10. Here we exploit amino acid metabolism and SPT promiscuity to modulate the endogenous synthesis of toxic doxSLs and slow tumor progression. Anchorage-independent growth reprograms a metabolic network involving serine, alanine, and pyruvate resulting in increased susceptibility to endogenous doxSL synthesis. Targeting the mitochondrial pyruvate carrier (MPC) promotes alanine oxidation to mitigate doxSL synthesis and improves spheroid growth, while direct inhibition of doxSL synthesis drives similar phenotypes. Restriction of dietary serine/glycine potently induces accumulation of doxSLs in xenografts while decreasing tumor growth. Pharmacological modulation of SPT rescues xenograft growth on serine/glycine-restricted diets, while reduction of circulating serine by inhibition of phosphoglycerate dehydrogenase (PHGDH) leads to doxSL accumulation and mitigates tumor growth. SPT promiscuity therefore links serine and mitochondrial alanine metabolism to membrane lipid diversity, which sensitizes tumors to metabolic stress.
Collapse
Affiliation(s)
| | - Thekla Cordes
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Michal K Handzlik
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Le You
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jivani Gengatharan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Antonio F M Pinto
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mehmet G Badur
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew J Kolar
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martina Wallace
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. .,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
35
|
Downes DP, Daurio NA, McLaren DG, Carrington P, Previs SF, Williams KB. Impact of Extracellular Fatty Acids and Oxygen Tension on Lipid Synthesis and Assembly in Pancreatic Cancer Cells. ACS Chem Biol 2020; 15:1892-1900. [PMID: 32396332 DOI: 10.1021/acschembio.0c00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid oxidation and biosynthesis are crucial for cell survival, especially for rapidly proliferating cancer cells in a heterogeneous metabolic environment. The storage of high-energy lipid reservoirs competitively advantages the cancer cell over non-neoplastic tissue. Disrupting lipid biosynthetic processes, through modulation of fatty acid (FA) esterification or de novo lipogenesis (DNL), is of interest in drug discovery. Mimicking the in vivo environment in vitro is also vital for testing the efficacy of potential drug compounds. We present here a stable isotope tracer-based approach for examining the impact of exogenous FA and oxygen tension on the pathways that affect lipid biosynthesis, including the rates of metabolic flux. By applying tandem mass spectrometry (MS/MS) analyses to studies using parallel tracers, we characterized the impact of FA bioavailability on the positional enrichment within specific lipids. Our observations suggest that adding bioavailable FA as a carbon source preferentially biases the cellular metabolism away from DNL and toward esterification of free fatty acid pools. Additionally, we have found that this FA addition, under hypoxic conditions, led to a biased increase in the total triglyceride pool (nearly 5-fold, as compared to phospholipids), regardless of the isotope tracer utilized. We discuss the implications of this metabolic flexibility on studies that aim to characterize apparent drug efficacy.
Collapse
Affiliation(s)
- Daniel P. Downes
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Natalie A. Daurio
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - David G. McLaren
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Paul Carrington
- Merck & Co., Inc, 213 East Grand Avenue, South San Francisco, California 94080, United States
| | - Stephen F. Previs
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Katharine B. Williams
- Merck & Co., Inc, 213 East Grand Avenue, South San Francisco, California 94080, United States
| |
Collapse
|
36
|
Henke C, Töllner K, van Dijk RM, Miljanovic N, Cordes T, Twele F, Bröer S, Ziesak V, Rohde M, Hauck SM, Vogel C, Welzel L, Schumann T, Willmes DM, Kurzbach A, El-Agroudy NN, Bornstein SR, Schneider SA, Jordan J, Potschka H, Metallo CM, Köhling R, Birkenfeld AL, Löscher W. Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus. Neurobiol Dis 2020; 143:105018. [PMID: 32682952 DOI: 10.1016/j.nbd.2020.105018] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/08/2020] [Accepted: 07/11/2020] [Indexed: 12/28/2022] Open
Abstract
In addition to tissues such as liver, the plasma membrane sodium-dependent citrate transporter, NaCT (SLC13A5), is highly expressed in brain neurons, but its function is not understood. Loss-of-function mutations in the human SLC13A5 gene have been associated with severe neonatal encephalopathy and pharmacoresistant seizures. The molecular mechanisms of these neurological alterations are not clear. We performed a detailed examination of a Slc13a5 deletion mouse model including video-EEG monitoring, behavioral tests, and electrophysiologic, proteomic, and metabolomic analyses of brain and cerebrospinal fluid. The experiments revealed an increased propensity for epileptic seizures, proepileptogenic neuronal excitability changes in the hippocampus, and significant citrate alterations in the CSF and brain tissue of Slc13a5 deficient mice, which may underlie the neurological abnormalities. These data demonstrate that SLC13A5 is involved in brain citrate regulation and suggest that abnormalities in this regulation can induce seizures. The present study is the first to (i) establish the Slc13a5-knockout mouse model as a helpful tool to study the neuronal functions of NaCT and characterize the molecular mechanisms by which functional deficiency of this citrate transporter causes epilepsy and impairs neuronal function; (ii) evaluate all hypotheses that have previously been suggested on theoretical grounds to explain the neurological phenotype of SLC13A5 mutations; and (iii) indicate that alterations in brain citrate levels result in neuronal network excitability and increased seizure propensity.
Collapse
Affiliation(s)
- Christine Henke
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Kathrin Töllner
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - R Maarten van Dijk
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University, Munich, Germany
| | - Nina Miljanovic
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University, Munich, Germany
| | - Thekla Cordes
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Friederike Twele
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Sonja Bröer
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Vanessa Ziesak
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany
| | - Marco Rohde
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Neuherberg, Germany
| | - Charlotte Vogel
- Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Germany
| | - Lisa Welzel
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; Center for Systems Neuroscience, 30559 Hannover, Germany
| | - Tina Schumann
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Diana M Willmes
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Anica Kurzbach
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Nermeen N El-Agroudy
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Stefan R Bornstein
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany
| | | | - Jens Jordan
- Institute for Aerospace Medicine, German Aerospace Center (DLR) and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany
| | - Heidrun Potschka
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University, Munich, Germany
| | - 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 92037, USA
| | - Rüdiger Köhling
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany
| | - Andreas L Birkenfeld
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Wolfgang Löscher
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; Center for Systems Neuroscience, 30559 Hannover, Germany.
| |
Collapse
|
37
|
Kumar A, Mitchener J, King ZA, Metallo CM. Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data. BMC Bioinformatics 2020; 21:297. [PMID: 32650717 PMCID: PMC7350651 DOI: 10.1186/s12859-020-03632-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/23/2020] [Indexed: 12/23/2022] Open
Abstract
Background Stable isotope tracing has become an invaluable tool for probing the metabolism of biological systems. However, data analysis and visualization from metabolic tracing studies often involve multiple software packages and lack pathway architecture. A deep understanding of the metabolic contexts from such datasets is required for biological interpretation. Currently, there is no single software package that allows researchers to analyze and integrate stable isotope tracing data into annotated or custom-built metabolic networks. Results We built a standalone web-based software, Escher-Trace, for analyzing tracing data and communicating results. Escher-Trace allows users to upload baseline corrected mass spectrometer (MS) tracing data and correct for natural isotope abundance, generate publication quality graphs of metabolite labeling, and present data in the context of annotated metabolic pathways. Here we provide a detailed walk-through of how to incorporate and visualize 13C metabolic tracing data into the Escher-Trace platform. Conclusions Escher-Trace is an open-source software for analysis and interpretation of stable isotope tracing data and is available at https://escher-trace.github.io/.
Collapse
Affiliation(s)
- Avi Kumar
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jack Mitchener
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
38
|
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: 68] [Impact Index Per Article: 17.0] [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
|
39
|
Damiani C, Gaglio D, Sacco E, Alberghina L, Vanoni M. Systems metabolomics: from metabolomic snapshots to design principles. Curr Opin Biotechnol 2020; 63:190-199. [PMID: 32278263 DOI: 10.1016/j.copbio.2020.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Metabolomics is a rapidly expanding technology that finds increasing application in a variety of fields, form metabolic disorders to cancer, from nutrition and wellness to design and optimization of cell factories. The integration of metabolic snapshots with metabolic fluxes, physiological readouts, metabolic models, and knowledge-informed Artificial Intelligence tools, is required to obtain a system-level understanding of metabolism. The emerging power of multi-omic approaches and the development of integrated experimental and computational tools, able to dissect metabolic features at cellular and subcellular resolution, provide unprecedented opportunities for understanding design principles of metabolic (dis)regulation and for the development of precision therapies in multifactorial diseases, such as cancer and neurodegenerative diseases.
Collapse
Affiliation(s)
- Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Daniela Gaglio
- ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy; Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, Milan, Italy
| | - Elena Sacco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy.
| |
Collapse
|
40
|
Cordes T, Lucas A, Divakaruni AS, Murphy AN, Cabrales P, Metallo CM. Itaconate modulates tricarboxylic acid and redox metabolism to mitigate reperfusion injury. Mol Metab 2020; 32:122-135. [PMID: 32029222 PMCID: PMC6961711 DOI: 10.1016/j.molmet.2019.11.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Cerebral ischemia/reperfusion (IR) drives oxidative stress and injurious metabolic processes that lead to redox imbalance, inflammation, and tissue damage. However, the key mediators of reperfusion injury remain unclear, and therefore, there is considerable interest in therapeutically targeting metabolism and the cellular response to oxidative stress. METHODS The objective of this study was to investigate the molecular, metabolic, and physiological impact of itaconate treatment to mitigate reperfusion injuries in in vitro and in vivo model systems. We conducted metabolic flux and bioenergetic studies in response to exogenous itaconate treatment in cultures of primary rat cortical neurons and astrocytes. In addition, we administered itaconate to mouse models of cerebral reperfusion injury with ischemia or traumatic brain injury followed by hemorrhagic shock resuscitation. We quantitatively characterized the metabolite levels, neurological behavior, markers of redox stress, leukocyte adhesion, arterial blood flow, and arteriolar diameter in the brains of the treated/untreated mice. RESULTS We demonstrate that the "immunometabolite" itaconate slowed tricarboxylic acid (TCA) cycle metabolism and buffered redox imbalance via succinate dehydrogenase (SDH) inhibition and induction of anti-oxidative stress response in primary cultures of astrocytes and neurons. The addition of itaconate to reperfusion fluids after mouse cerebral IR injury increased glutathione levels and reduced reactive oxygen/nitrogen species (ROS/RNS) to improve neurological function. Plasma organic acids increased post-reperfusion injury, while administration of itaconate normalized these metabolites. In mouse cranial window models, itaconate significantly improved hemodynamics while reducing leukocyte adhesion. Further, itaconate supplementation increased survival in mice experiencing traumatic brain injury (TBI) and hemorrhagic shock. CONCLUSIONS We hypothesize that itaconate transiently inhibits SDH to gradually "awaken" mitochondrial function upon reperfusion that minimizes ROS and tissue damage. Collectively, our data indicate that itaconate acts as a mitochondrial regulator that controls redox metabolism to improve physiological outcomes associated with IR injury.
Collapse
Affiliation(s)
- Thekla Cordes
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA
| | - Alfredo Lucas
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA
| | - Ajit S Divakaruni
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA
| | - Anne N Murphy
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA
| | - Pedro Cabrales
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 92093 La Jolla, CA, USA.
| |
Collapse
|