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Riols F, Witting M, Haid M. Differential Mobility Spectrometry-Based Cardiolipin Analysis. Methods Mol Biol 2025; 2855:373-385. [PMID: 39354319 DOI: 10.1007/978-1-0716-4116-3_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Cardiolipins (CL) are special lipids in many respects. First of all, CL are composed of four fatty acids linked by two phosphatidic acids, which provide CL a unique molecular structure. Secondly, in eukaryotic cells they are specific to a single organelle, mitochondria, where they are also synthetized. CL are one of the most abundant lipid classes in mitochondria, mainly localized in the inner membrane. They are key determinants of mitochondrial health and homeostasis by modulating membrane integrity and fluidity, mitochondrial shapes, and metabolic pathways. Disturbances in mitochondrial CL composition can lead to tissue malfunction and diseases. It is therefore important to develop analytical tools to study the mitochondrial lipidome, and more particularly the CL. The method described here allows the quantification of cardiolipins at the sum composition level in isolated mitochondria or in liver tissue by flow injection analysis coupled to differential mobility spectrometry (FIA-DMS), also known as DMS-based shotgun lipidomics.
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Affiliation(s)
- Fabien Riols
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany.
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2
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Feola K, Venable AH, Broomfield T, Villegas M, Fu X, Burgess S, Huen SC. Hepatic ketogenesis is not required for starvation adaptation in mice. Mol Metab 2024; 86:101967. [PMID: 38876267 PMCID: PMC11246062 DOI: 10.1016/j.molmet.2024.101967] [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: 04/17/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
OBJECTIVE In response to bacterial inflammation, anorexia of acute illness is protective and is associated with the induction of fasting metabolic programs such as ketogenesis. Forced feeding during the anorectic period induced by bacterial inflammation is associated with suppressed ketogenesis and increased mortality. As ketogenesis is considered essential in fasting adaptation, we sought to determine the role of ketogenesis in illness-induced anorexia. METHODS A mouse model of inducible hepatic specific deletion of the rate limiting enzyme for ketogenesis (HMG-CoA synthase 2, Hmgcs2) was used to investigate the role of ketogenesis in endotoxemia, a model of bacterial inflammation, and in prolonged starvation. RESULTS Mice deficient of hepatic Hmgcs2 failed to develop ketosis during endotoxemia and during prolonged fasting. Surprisingly, hepatic HMGCS2 deficiency and the lack of ketosis did not affect survival, glycemia, or body temperature in response to endotoxemia. Mice with hepatic ketogenic deficiency also did not exhibit any defects in starvation adaptation and were able to maintain blood glucose, body temperature, and lean mass compared to littermate wild-type controls. Mice with hepatic HMGCS2 deficiency exhibited higher levels of plasma acetate levels in response to fasting. CONCLUSIONS Circulating hepatic-derived ketones do not provide protection against endotoxemia, suggesting that alternative mechanisms drive the increased mortality from forced feeding during illness-induced anorexia. Hepatic ketones are also dispensable for surviving prolonged starvation in the absence of inflammation. Our study challenges the notion that hepatic ketogenesis is required to maintain blood glucose and preserve lean mass during starvation, raising the possibility of extrahepatic ketogenesis and use of alternative fuels as potential means of metabolic compensation.
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Affiliation(s)
- Kyle Feola
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrea H Venable
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatyana Broomfield
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Morgan Villegas
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaorong Fu
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shawn Burgess
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sarah C Huen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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3
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Wang X, Menezes CJ, Jia Y, Xiao Y, Venigalla SSK, Cai F, Hsieh MH, Gu W, Du L, Sudderth J, Kim D, Shelton SD, Llamas CB, Lin YH, Zhu M, Merchant S, Bezwada D, Kelekar S, Zacharias LG, Mathews TP, Hoxhaj G, Wynn RM, Tambar UK, DeBerardinis RJ, Zhu H, Mishra P. Metabolic inflexibility promotes mitochondrial health during liver regeneration. Science 2024; 384:eadj4301. [PMID: 38870309 PMCID: PMC11232486 DOI: 10.1126/science.adj4301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024]
Abstract
Mitochondria are critical for proper organ function and mechanisms to promote mitochondrial health during regeneration would benefit tissue homeostasis. We report that during liver regeneration, proliferation is suppressed in electron transport chain (ETC)-dysfunctional hepatocytes due to an inability to generate acetyl-CoA from peripheral fatty acids through mitochondrial β-oxidation. Alternative modes for acetyl-CoA production from pyruvate or acetate are suppressed in the setting of ETC dysfunction. This metabolic inflexibility forces a dependence on ETC-functional mitochondria and restoring acetyl-CoA production from pyruvate is sufficient to allow ETC-dysfunctional hepatocytes to proliferate. We propose that metabolic inflexibility within hepatocytes can be advantageous by limiting the expansion of ETC-dysfunctional cells.
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Affiliation(s)
- Xun Wang
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cameron J Menezes
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuemeng Jia
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Xiao
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Feng Cai
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meng-Hsiung Hsieh
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen Gu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Liming Du
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessica Sudderth
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dohun Kim
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D Shelton
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Claire B Llamas
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Hsuan Lin
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Salma Merchant
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Divya Bezwada
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sherwin Kelekar
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gerta Hoxhaj
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Uttam K Tambar
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Departments of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Ward NP, Yoon SJ, Flynn T, Sherwood AM, Olley MA, Madej J, DeNicola GM. Mitochondrial respiratory function is preserved under cysteine starvation via glutathione catabolism in NSCLC. Nat Commun 2024; 15:4244. [PMID: 38762605 PMCID: PMC11102494 DOI: 10.1038/s41467-024-48695-2] [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: 05/05/2023] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
Cysteine metabolism occurs across cellular compartments to support diverse biological functions and prevent the induction of ferroptosis. Though the disruption of cytosolic cysteine metabolism is implicated in this form of cell death, it is unknown whether the substantial cysteine metabolism resident within the mitochondria is similarly pertinent to ferroptosis. Here, we show that despite the rapid depletion of intracellular cysteine upon loss of extracellular cystine, cysteine-dependent synthesis of Fe-S clusters persists in the mitochondria of lung cancer cells. This promotes a retention of respiratory function and a maintenance of the mitochondrial redox state. Under these limiting conditions, we find that glutathione catabolism by CHAC1 supports the mitochondrial cysteine pool to sustain the function of the Fe-S proteins critical to oxidative metabolism. We find that disrupting Fe-S cluster synthesis under cysteine restriction protects against the induction of ferroptosis, suggesting that the preservation of mitochondrial function is antagonistic to survival under starved conditions. Overall, our findings implicate mitochondrial cysteine metabolism in the induction of ferroptosis and reveal a mechanism of mitochondrial resilience in response to nutrient stress.
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Affiliation(s)
- Nathan P Ward
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Sang Jun Yoon
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Tyce Flynn
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Amanda M Sherwood
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Maddison A Olley
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Juliana Madej
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Gina M DeNicola
- Department of Metabolism & Physiology, Moffitt Cancer Center, Tampa, FL, USA.
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Sprenger HG, Mittenbühler MJ, Sun Y, Van Vranken JG, Schindler S, Jayaraj A, Khetarpal SA, Vargas-Castillo A, Puszynska AM, Spinelli JB, Armani A, Kunchok T, Ryback B, Seo HS, Song K, Sebastian L, O'Young C, Braithwaite C, Dhe-Paganon S, Burger N, Mills EL, Gygi SP, Arthanari H, Chouchani ET, Sabatini DM, Spiegelman BM. Ergothioneine boosts mitochondrial respiration and exercise performance via direct activation of MPST. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588849. [PMID: 38645260 PMCID: PMC11030429 DOI: 10.1101/2024.04.10.588849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Ergothioneine (EGT) is a diet-derived, atypical amino acid that accumulates to high levels in human tissues. Reduced EGT levels have been linked to age-related disorders, including neurodegenerative and cardiovascular diseases, while EGT supplementation is protective in a broad range of disease and aging models in mice. Despite these promising data, the direct and physiologically relevant molecular target of EGT has remained elusive. Here we use a systematic approach to identify how mitochondria remodel their metabolome in response to exercise training. From this data, we find that EGT accumulates in muscle mitochondria upon exercise training. Proteome-wide thermal stability studies identify 3-mercaptopyruvate sulfurtransferase (MPST) as a direct molecular target of EGT; EGT binds to and activates MPST, thereby boosting mitochondrial respiration and exercise training performance in mice. Together, these data identify the first physiologically relevant EGT target and establish the EGT-MPST axis as a molecular mechanism for regulating mitochondrial function and exercise performance.
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Liu D, Webber HC, Bian F, Xu Y, Prakash M, Feng X, Yang M, Yang H, You IJ, Li L, Liu L, Liu P, Huang H, Chang CY, Liu L, Shah SH, Torre AL, Welsbie DS, Sun Y, Duan X, Goldberg JL, Braun M, Lansky Z, Hu Y. Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587832. [PMID: 38617277 PMCID: PMC11014509 DOI: 10.1101/2024.04.02.587832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Optineurin (OPTN) mutations are linked to amyotrophic lateral sclerosis (ALS) and normal tension glaucoma (NTG), but a relevant animal model is lacking, and the molecular mechanisms underlying neurodegeneration are unknown. We found that OPTN C-terminus truncation (OPTN∆C) causes late-onset neurodegeneration of retinal ganglion cells (RGCs), optic nerve (ON), and spinal cord motor neurons, preceded by a striking decrease of axonal mitochondria. Surprisingly, we discover that OPTN directly interacts with both microtubules and the mitochondrial transport complex TRAK1/KIF5B, stabilizing them for proper anterograde axonal mitochondrial transport, in a C-terminus dependent manner. Encouragingly, overexpressing OPTN/TRAK1/KIF5B reverses not only OPTN truncation-induced, but also ocular hypertension-induced neurodegeneration, and promotes striking ON regeneration. Therefore, in addition to generating new animal models for NTG and ALS, our results establish OPTN as a novel facilitator of the microtubule-dependent mitochondrial transport necessary for adequate axonal mitochondria delivery, and its loss as the likely molecular mechanism of neurodegeneration.
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Affiliation(s)
- Dong Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hannah C. Webber
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Fuyun Bian
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yangfan Xu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Manjari Prakash
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Xue Feng
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Ming Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hang Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - In-Jee You
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liang Li
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liping Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Pingting Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Haoliang Huang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Chien-Yi Chang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Liang Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sahil H Shah
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA; USA
| | - Derek S. Welsbie
- Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA; USA
| | - Yang Sun
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA; USA
| | - Jeffrey Louis Goldberg
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marcus Braun
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Yang Hu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
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Pegoraro C, Domingo-Ortí I, Conejos-Sánchez I, Vicent MJ. Unlocking the Mitochondria for Nanomedicine-based Treatments: Overcoming Biological Barriers, Improving Designs, and Selecting Verification Techniques. Adv Drug Deliv Rev 2024; 207:115195. [PMID: 38325562 DOI: 10.1016/j.addr.2024.115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Enhanced targeting approaches will support the treatment of diseases associated with dysfunctional mitochondria, which play critical roles in energy generation and cell survival. Obstacles to mitochondria-specific targeting include the presence of distinct biological barriers and the need to pass through (or avoid) various cell internalization mechanisms. A range of studies have reported the design of mitochondrially-targeted nanomedicines that navigate the complex routes required to influence mitochondrial function; nonetheless, a significant journey lies ahead before mitochondrially-targeted nanomedicines become suitable for clinical use. Moving swiftly forward will require safety studies, in vivo assays confirming effectiveness, and methodologies to validate mitochondria-targeted nanomedicines' subcellular location/activity. From a nanomedicine standpoint, we describe the biological routes involved (from administration to arrival within the mitochondria), the features influencing rational design, and the techniques used to identify/validate successful targeting. Overall, rationally-designed mitochondria-targeted-based nanomedicines hold great promise for precise subcellular therapeutic delivery.
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Affiliation(s)
- Camilla Pegoraro
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inés Domingo-Ortí
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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8
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Chi HM, Davies MR, Garcia SM, Montenegro C, Sharma S, Lizarraga M, Wang Z, Nuthalapati P, Kim HT, Liu X, Feeley BT. Defining Endogenous Mitochondrial Transfer in Muscle After Rotator Cuff Injury. Am J Sports Med 2024; 52:451-460. [PMID: 38174367 DOI: 10.1177/03635465231214225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
BACKGROUND Rotator cuff muscle degeneration leads to poor clinical outcomes for patients with rotator cuff tears. Fibroadipogenic progenitors (FAPs) are resident muscle stem cells with the ability to differentiate into fibroblasts as well as white and beige adipose tissue. Induction of the beige adipose phenotype in FAPs has been shown to improve muscle quality after rotator cuff tears, but the mechanisms of how FAPs exert their beneficial effects have not been fully elucidated. PURPOSE To study the horizontal transfer of mitochondria from FAPs to myogenic cells and examine the effects of β-agonism on this novel process. STUDY DESIGN Controlled laboratory study. METHODS In mice that had undergone a massive rotator cuff tear, single-cell RNA sequencing was performed on isolated FAPs for genes associated with mitochondrial biogenesis and transfer. Murine FAPs were isolated by fluorescence-activated cell sorting and treated with a β-agonist versus control. FAPs were stained with mitochondrial dyes and cocultured with recipient C2C12 myoblasts, and the rate of transfer was measured after 24 hours by flow cytometry. PdgfraCreERT/MitoTag mice were generated to study the effects of a rotator cuff injury on mitochondrial transfer. PdgfraCreERT/tdTomato mice were likewise generated to perform lineage tracing of PDGFRA+ cells in this injury model. Both populations of transgenic mice underwent tendon transection and denervation surgery, and MitoTag-labeled mitochondria from Pdgfra+ FAPs were visualized by fluorescent microscopy, spinning disk confocal microscopy, and 2-photon microscopy; overall mitochondrial quantity was compared between mice treated with β-agonists and dimethyl sulfoxide. RESULTS Single-cell RNA sequencing in mice that underwent rotator cuff tear demonstrated an association between transcriptional markers of adipogenic differentiation and genes associated with mitochondrial biogenesis. In vitro cocultures of murine FAPs with C2C12 cells revealed that treatment of cells with a β-agonist increased mitochondrial transfer compared to control conditions (17.8% ± 9.9% to 99.6% ± 0.13% P < .0001). Rotator cuff injury in PdgfraCreERT/MitoTag mice resulted in a robust increase in MitoTag signal in adjacent myofibers compared with uninjured mice. No accumulation of tdTomato signal from PDGFRA+ cells was seen in injured fibers at 6 weeks after injury, suggesting that FAPs do not fuse with injured muscle fibers but rather contribute their mitochondria. CONCLUSION The authors have described a novel process of endogenous mitochondrial transfer that can occur within the injured rotator cuff between FAPs and myogenic cells. This process may be leveraged therapeutically with β-agonist treatment and represents an exciting target for improving translational therapies available for rotator cuff muscle degeneration. CLINICAL RELEVANCE Promoting endogenous mitochondrial transfer may represent a novel translational strategy to address muscle degeneration after rotator cuff tears.
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Affiliation(s)
- Hannah M Chi
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael R Davies
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
| | - Steven M Garcia
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
| | - Cristhian Montenegro
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Sankalp Sharma
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Miguel Lizarraga
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Zili Wang
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Prashant Nuthalapati
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Hubert T Kim
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Xuhui Liu
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
| | - Brian T Feeley
- Department of Orthopaedic Surgery, University of California, San Francisco, California, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, California, USA
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9
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Park I, Kim KE, Kim J, Kim AK, Bae S, Jung M, Choi J, Mishra PK, Kim TM, Kwak C, Kang MG, Yoo CM, Mun JY, Liu KH, Lee KS, Kim JS, Suh JM, Rhee HW. Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis. Nat Chem Biol 2024; 20:221-233. [PMID: 37884807 PMCID: PMC10830421 DOI: 10.1038/s41589-023-01452-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/17/2023] [Indexed: 10/28/2023]
Abstract
Targeting proximity-labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice (MAX-Tg) expressing a mitochondrial matrix-targeted ascorbate peroxidase. Comparative analysis of matrix proteomes from the muscle tissues showed differential enrichment of mitochondrial proteins. We found that reticulon 4-interacting protein 1 (RTN4IP1), also known as optic atrophy-10, is enriched in the mitochondrial matrix of muscle tissues and is an NADPH oxidoreductase. Interactome analysis and in vitro enzymatic assays revealed an essential role for RTN4IP1 in coenzyme Q (CoQ) biosynthesis by regulating the O-methylation activity of COQ3. Rtn4ip1-knockout myoblasts had markedly decreased CoQ9 levels and impaired cellular respiration. Furthermore, muscle-specific knockdown of dRtn4ip1 in flies resulted in impaired muscle function, which was reversed by dietary supplementation with soluble CoQ. Collectively, these results demonstrate that RTN4IP1 is a mitochondrial NAD(P)H oxidoreductase essential for supporting mitochondrial respiration activity in the muscle tissue.
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Affiliation(s)
- Isaac Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Kwang-Eun Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
| | - Ae-Kyeong Kim
- Metabolism and Neurophysiology Research Group, KRIBB, Daejeon, Republic of Korea
| | - Subin Bae
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jinhyuk Choi
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | | | - Taek-Min Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Chang-Mo Yoo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Kwang-Hyeon Liu
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Korea
| | - Kyu-Sun Lee
- Metabolism and Neurophysiology Research Group, KRIBB, Daejeon, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, Korea.
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.
| | - Jae Myoung Suh
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
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10
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Hansen FM, Kremer LS, Karayel O, Bludau I, Larsson NG, Kühl I, Mann M. Mitochondrial phosphoproteomes are functionally specialized across tissues. Life Sci Alliance 2024; 7:e202302147. [PMID: 37984987 PMCID: PMC10662294 DOI: 10.26508/lsa.202302147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Mitochondria are essential organelles whose dysfunction causes human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondrial fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Increasing evidence suggests that phosphorylation may play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. Building on recent advances in mass spectrometry (MS)-based proteomics, we here quantitatively profile mitochondrial tissue proteomes along with their matching phosphoproteomes. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and performed high-resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue-specific mitochondrial proteins (mitophos.de). Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on dynamin-related protein 1 responsible for its mitochondrial recruitment and fission initiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.
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Affiliation(s)
- Fynn M Hansen
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laura S Kremer
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ozge Karayel
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Isabell Bludau
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nils-Göran Larsson
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell, UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthias Mann
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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11
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 PMCID: PMC11378943 DOI: 10.1038/s41580-023-00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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12
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Nusir A, Sinclair P, Kabbani N. Mitochondrial Proteomes in Neural Cells: A Systematic Review. Biomolecules 2023; 13:1638. [PMID: 38002320 PMCID: PMC10669788 DOI: 10.3390/biom13111638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins represent a functional subcellular protein network (mtProteome) that is encoded by mitochondrial and nuclear genomes and significantly varies between cell types and conditions. In neurons, the high metabolic demand and differential energy requirements at the synapses are met by specific modifications to the mtProteome, resulting in alterations in the expression and functional properties of the proteins involved in energy production and quality control, including fission and fusion. The composition of mtProteomes also impacts the localization of mitochondria in axons and dendrites with a growing number of neurodegenerative diseases associated with changes in mitochondrial proteins. This review summarizes the findings on the composition and properties of mtProteomes important for mitochondrial energy production, calcium and lipid signaling, and quality control in neural cells. We highlight strategies in mass spectrometry (MS) proteomic analysis of mtProteomes from cultured cells and tissue. The research into mtProteome composition and function provides opportunities in biomarker discovery and drug development for the treatment of metabolic and neurodegenerative disease.
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Affiliation(s)
- Aya Nusir
- Interdisciplinary Program in Neuroscience, School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
| | - Patricia Sinclair
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
| | - Nadine Kabbani
- Interdisciplinary Program in Neuroscience, School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
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13
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Anunciado-Koza RVP, Guntur AR, Vary CP, Gartner CA, Nowak M, Koza RA. Purification of functional mouse skeletal muscle mitochondria using percoll density gradient centrifugation. BMC Res Notes 2023; 16:243. [PMID: 37777771 PMCID: PMC10544150 DOI: 10.1186/s13104-023-06519-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/20/2023] [Indexed: 10/02/2023] Open
Abstract
OBJECTIVE Our goal was to isolate purified mitochondria from mouse skeletal muscle using a Percoll density gradient and to assess bioenergetic function and purity via Seahorse Extracellular Flux (XF) Analyses and mass spectrometry. RESULTS Mitochondria isolated from murine quadriceps femoris skeletal muscle using a Percoll density gradient method allowed for minimally contaminated preparations with time from tissue harvest to mitochondrial isolation and quantification in about 3-4 h. Percoll purification from 100 to 200 mg fresh tissue yielded ~ 200-400 ug protein. Mitochondrial bioenergetics evaluated using the Seahorse XFe96 analyzer, a high-throughput respirometry platform, showed optimum mitochondrial input at 500 ng with respiratory control ratio ranging from 3.9 to 7.1 using various substrates demonstrating a high degree of functionality. Furthermore, proteomic analysis of Percoll-enriched mitochondria isolated from skeletal muscle using this method showed significant enrichment of mitochondrial proteins indicating high sample purity. This study established a methodology that ensures sufficient high quality mitochondria for downstream analyses such as mitochondrial bioenergetics and proteomics.
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Affiliation(s)
| | - Anyonya R Guntur
- MaineHealth Institute for Research, 81 Research Drive, Scarborough, ME, United States of America
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States of America
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States of America
| | - Calvin P Vary
- MaineHealth Institute for Research, 81 Research Drive, Scarborough, ME, United States of America
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States of America
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States of America
| | - Carlos A Gartner
- MaineHealth Institute for Research, 81 Research Drive, Scarborough, ME, United States of America
| | - Madeleine Nowak
- MaineHealth Institute for Research, 81 Research Drive, Scarborough, ME, United States of America
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States of America
| | - Robert A Koza
- MaineHealth Institute for Research, 81 Research Drive, Scarborough, ME, United States of America.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States of America.
- Pennington Biomedical Research Center, 6400 Perkins Road, Baton Rouge, LA, United States of America.
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14
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Atkinson KC, Osunde M, Tiwari-Woodruff SK. The complexities of investigating mitochondria dynamics in multiple sclerosis and mouse models of MS. Front Neurosci 2023; 17:1144896. [PMID: 37559701 PMCID: PMC10409489 DOI: 10.3389/fnins.2023.1144896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/23/2023] [Indexed: 08/11/2023] Open
Abstract
Multiple sclerosis (MS) is a demyelinating, degenerating disorder of the central nervous system (CNS) that is accompanied by mitochondria energy production failure. A loss of myelin paired with a deficit in energy production can contribute to further neurodegeneration and disability in patients in MS. Mitochondria are essential organelles that produce adenosine triphosphate (ATP) via oxidative phosphorylation in all cells in the CNS, including neurons, oligodendrocytes, astrocytes, and immune cells. In the context of demyelinating diseases, mitochondria have been shown to alter their morphology and undergo an initial increase in metabolic demand. This is followed by mitochondrial respiratory chain deficiency and abnormalities in mitochondrial transport that contribute to progressive neurodegeneration and irreversible disability. The current methodologies to study mitochondria are limiting and are capable of providing only a partial snapshot of the true mitochondria activity at a particular timepoint during disease. Mitochondrial functional studies are mostly performed in cell culture or whole brain tissue, which prevents understanding of mitochondrial pathology in distinct cell types in vivo. A true understanding of cell-specific mitochondrial pathophysiology of MS in mouse models is required. Cell-specific mitochondria morphology, mitochondria motility, and ATP production studies in animal models of MS will help us understand the role of mitochondria in the normal and diseased CNS. In this review, we present currently used methods to investigate mitochondria function in MS mouse models and discuss the current advantages and caveats with using each technique. In addition, we present recently developed mitochondria transgenic mouse lines expressing Cre under the control of CNS specific promoters to relate mitochondria to disease in vivo.
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Affiliation(s)
| | | | - Seema K. Tiwari-Woodruff
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, United States
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15
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de Mello NP, Fecher C, Pastor AM, Perocchi F, Misgeld T. Ex vivo immunocapture and functional characterization of cell-type-specific mitochondria using MitoTag mice. Nat Protoc 2023:10.1038/s41596-023-00831-w. [PMID: 37328604 DOI: 10.1038/s41596-023-00831-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Mitochondria are key bioenergetic organelles involved in many biosynthetic and signaling pathways. However, their differential contribution to specific functions of cells within complex tissues is difficult to dissect with current methods. The present protocol addresses this need by enabling the ex vivo immunocapture of cell-type-specific mitochondria directly from their tissue context through a MitoTag reporter mouse. While other available methods were developed for bulk mitochondria isolation or more abundant cell-type-specific mitochondria, this protocol was optimized for the selective isolation of functional mitochondria from medium-to-low-abundant cell types in a heterogeneous tissue, such as the central nervous system. The protocol has three major parts: First, mitochondria of a cell type of interest are tagged via an outer mitochondrial membrane eGFP by crossing MitoTag mice to a cell-type-specific Cre-driver line or by delivery of viral vectors for Cre expression. Second, homogenates are prepared from relevant tissues by nitrogen cavitation, from which tagged organelles are immunocaptured using magnetic microbeads. Third, immunocaptured mitochondria are used for downstream assays, e.g., to probe respiratory capacity or calcium handling, revealing cell-type-specific mitochondrial diversity in molecular composition and function. The MitoTag approach enables the identification of marker proteins to label cell-type-specific organelle populations in situ, elucidates cell-type-enriched mitochondrial metabolic and signaling pathways, and reveals functional mitochondrial diversity between adjacent cell types in complex tissues, such as the brain. Apart from establishing the mouse colony (6-8 weeks without import), the immunocapture protocol takes 2 h and functional assays require 1-2 h.
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Affiliation(s)
- Natalia Prudente de Mello
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
| | - Caroline Fecher
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
- Department of Cell Biology & Physiology, School of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Adrian Marti Pastor
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases, Munich, Germany.
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16
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Fasimoye R, Dong W, Nirujogi RS, Rawat ES, Iguchi M, Nyame K, Phung TK, Bagnoli E, Prescott AR, Alessi DR, Abu-Remaileh M. Golgi-IP, a tool for multimodal analysis of Golgi molecular content. Proc Natl Acad Sci U S A 2023; 120:e2219953120. [PMID: 37155866 PMCID: PMC10193996 DOI: 10.1073/pnas.2219953120] [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: 11/22/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
The Golgi is a membrane-bound organelle that is essential for protein and lipid biosynthesis. It represents a central trafficking hub that sorts proteins and lipids to various destinations or for secretion from the cell. The Golgi has emerged as a docking platform for cellular signaling pathways including LRRK2 kinase whose deregulation leads to Parkinson disease. Golgi dysfunction is associated with a broad spectrum of diseases including cancer, neurodegeneration, and cardiovascular diseases. To allow the study of the Golgi at high resolution, we report a rapid Golgi immunoprecipitation technique (Golgi-IP) to isolate intact Golgi mini-stacks for subsequent analysis of their content. By fusing the Golgi-resident protein TMEM115 to three tandem HA epitopes (GolgiTAG), we purified the Golgi using Golgi-IP with minimal contamination from other compartments. We then established an analysis pipeline using liquid chromatography coupled with mass spectrometry to characterize the human Golgi proteome, metabolome, and lipidome. Subcellular proteomics confirmed known Golgi proteins and identified proteins not previously associated with the Golgi. Metabolite profiling established the human Golgi metabolome and revealed the enrichment of uridine-diphosphate (UDP) sugars and their derivatives, which is consistent with their roles in protein and lipid glycosylation. Furthermore, targeted metabolomics validated SLC35A2 as the subcellular transporter for UDP-hexose. Finally, lipidomics analysis showed that phospholipids including phosphatidylcholine, phosphatidylinositol, and phosphatidylserine are the most abundant Golgi lipids and that glycosphingolipids are enriched in this compartment. Altogether, our work establishes a comprehensive molecular map of the human Golgi and provides a powerful method to study the Golgi with high precision in health and disease.
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Affiliation(s)
- Rotimi Fasimoye
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Wentao Dong
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Raja S. Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Eshaan S. Rawat
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Miharu Iguchi
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Kwamina Nyame
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Toan K. Phung
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Enrico Bagnoli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Monther Abu-Remaileh
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
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17
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Schäfer JA, Sutandy FXR, Münch C. Omics-based approaches for the systematic profiling of mitochondrial biology. Mol Cell 2023; 83:911-926. [PMID: 36931258 DOI: 10.1016/j.molcel.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.
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Affiliation(s)
- Jasmin Adriana Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - F X Reymond Sutandy
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany.
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18
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Robertson GL, Riffle S, Patel M, Bodnya C, Marshall A, Beasley HK, Garza-Lopez E, Shao J, Vue Z, Hinton A, Stoll MS, de Wet S, Theart RP, Chakrabarty RP, Loos B, Chandel NS, Mears JA, Gama V. DRP1 mutations associated with EMPF1 encephalopathy alter mitochondrial membrane potential and metabolic programs. J Cell Sci 2023; 136:jcs260370. [PMID: 36763487 PMCID: PMC10657212 DOI: 10.1242/jcs.260370] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/22/2022] [Indexed: 02/11/2023] Open
Abstract
Mitochondria and peroxisomes are dynamic signaling organelles that constantly undergo fission, driven by the large GTPase dynamin-related protein 1 (DRP1; encoded by DNM1L). Patients with de novo heterozygous missense mutations in DNM1L present with encephalopathy due to defective mitochondrial and peroxisomal fission (EMPF1) - a devastating neurodevelopmental disease with no effective treatment. To interrogate the mechanisms by which DRP1 mutations cause cellular dysfunction, we used human-derived fibroblasts from patients who present with EMPF1. In addition to elongated mitochondrial morphology and lack of fission, patient cells display lower coupling efficiency, increased proton leak and upregulation of glycolysis. Mitochondrial hyperfusion also results in aberrant cristae structure and hyperpolarized mitochondrial membrane potential. Peroxisomes show a severely elongated morphology in patient cells, which is associated with reduced respiration when cells are reliant on fatty acid oxidation. Metabolomic analyses revealed impaired methionine cycle and synthesis of pyrimidine nucleotides. Our study provides insight into the role of mitochondrial dynamics in cristae maintenance and the metabolic capacity of the cell, as well as the disease mechanism underlying EMPF1.
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Affiliation(s)
| | - Stellan Riffle
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Mira Patel
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Caroline Bodnya
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Andrea Marshall
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Heather K. Beasley
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Edgar Garza-Lopez
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA 52246, USA
| | - Zer Vue
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Antentor Hinton
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Maria S. Stoll
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Sholto de Wet
- Stellenbosch University, Department of Physiological Sciences, Matieland, 7602, Stellenbosch, South Africa
| | - Rensu P. Theart
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Ram Prosad Chakrabarty
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Ben Loos
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Navdeep S. Chandel
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
- Northwestern University, Feinberg School of Medicine Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
| | - Jason A. Mears
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Vivian Gama
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Center for Stem Cell Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Brain Institute, Nashville, TN 37232, USA
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19
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Li X, Zhang Y, Xu L, Wang A, Zou Y, Li T, Huang L, Chen W, Liu S, Jiang K, Zhang X, Wang D, Zhang L, Zhang Z, Zhang Z, Chen X, Jia W, Zhao A, Yan X, Zhou H, Zhu L, Ma X, Ju Z, Jia W, Wang C, Loscalzo J, Yang Y, Zhao Y. Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease. Cell Metab 2023; 35:200-211.e9. [PMID: 36309010 PMCID: PMC10560847 DOI: 10.1016/j.cmet.2022.10.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/04/2022] [Accepted: 10/04/2022] [Indexed: 01/07/2023]
Abstract
Despite its central importance in cellular metabolism, many details remain to be determined regarding subcellular lactate metabolism and its regulation in physiology and disease, as there is sensitive spatiotemporal resolution of lactate distribution, and dynamics remains a technical challenge. Here, we develop and characterize an ultrasensitive, highly responsive, ratiometric lactate sensor, named FiLa, enabling the monitoring of subtle lactate fluctuations in living cells and animals. Utilizing FiLa, we demonstrate that lactate is highly enriched in mammalian mitochondria and compile an atlas of subcellular lactate metabolism that reveals lactate as a key hub sensing various metabolic activities. In addition, FiLa sensors also enable direct imaging of elevated lactate levels in diabetic mice and facilitate the establishment of a simple, rapid, and sensitive lactate assay for point-of-care clinical screening. Thus, FiLa sensors provide powerful, broadly applicable tools for defining the spatiotemporal landscape of lactate metabolism in health and disease.
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Affiliation(s)
- Xie Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinan Zhang
- Center for Translational Medicine, The Metabolic Diseases Biobank, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Aoxue Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yejun Zou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Huang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Weicai Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Shuning Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Kun Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xiuze Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Dongmei Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijuan Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zeyi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Jia
- Center for Translational Medicine, The Metabolic Diseases Biobank, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Aihua Zhao
- Center for Translational Medicine, The Metabolic Diseases Biobank, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Xinfeng Yan
- Translational Medical Center for Stem Cell Therapy, Department of Endocrinology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Haimeng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Weiping Jia
- Center for Translational Medicine, The Metabolic Diseases Biobank, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Congrong Wang
- Department of Endocrinology & Metabolism, Shanghai Fourth People's Hospital, Tongji University School of Medicine, Shanghai 200434, China.
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing 100730, China.
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20
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Sidransky E, Chen C, Chen Y. Technological advances expand our knowledge of lysosomal dysfunction in neurodegeneration. Neural Regen Res 2023; 18:539-540. [DOI: 10.4103/1673-5374.346490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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21
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O’Reilly CL, Miller BF, Lewis TL. Exercise and mitochondrial remodeling to prevent age-related neurodegeneration. J Appl Physiol (1985) 2023; 134:181-189. [PMID: 36519568 PMCID: PMC9829476 DOI: 10.1152/japplphysiol.00611.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Healthy brain activity requires precise ion and energy management creating a strong reliance on mitochondrial function. Age-related neurodegeneration leads to a decline in mitochondrial function and increased oxidative stress, with associated declines in mitochondrial mass, respiration capacity, and respiration efficiency. The interdependent processes of mitochondrial protein turnover and mitochondrial dynamics, known together as mitochondrial remodeling, play essential roles in mitochondrial health and therefore brain function. This mini-review describes the role of mitochondria in neurodegeneration and brain health, current practices for assessing both aspects of mitochondrial remodeling, and how exercise mitigates the adverse effects of aging in the brain. Exercise training elicits functional adaptations to improve brain health, and current literature strongly suggests that mitochondrial remodeling plays a vital role in these positive adaptations. Despite substantial implications that the two aspects of mitochondrial remodeling are interdependent, very few investigations have simultaneously measured mitochondrial dynamics and protein synthesis. An improved understanding of the partnership between mitochondrial protein turnover and mitochondrial dynamics will provide a better understanding of their role in both brain health and disease, as well as how they induce protection following exercise.
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Affiliation(s)
- Colleen L. O’Reilly
- 1Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Benjamin F. Miller
- 1Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma,2Oklahoma City Veterans Association, Oklahoma City, Oklahoma
| | - Tommy L. Lewis
- 1Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
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22
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Miyao M, Kawai C, Kotani H, Minami H, Abiru H, Hamayasu H, Eguchi S, Tamaki K. Mitochondrial fission in hepatocytes as a potential therapeutic target for nonalcoholic steatohepatitis. Hepatol Res 2022; 52:1020-1033. [PMID: 36001355 DOI: 10.1111/hepr.13832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 12/12/2022]
Abstract
AIM The mitochondria are highly plastic and dynamic organelles; mitochondrial dysfunction has been reported to play causative roles in diabetes, cardiovascular diseases, and nonalcoholic fatty liver disease (NAFLD). However, the relationship between mitochondrial fission and NAFLD pathogenesis remains unknown. We aimed to investigate whether alterations in mitochondrial fission could play a role in the progression of NAFLD. METHODS Mice were fed a standard diet or choline-deficient, L-amino acid-defined (CDAA) diet with vehicle or mitochondrial division inhibitor-1. RESULTS Substantial enhancement of mitochondrial fission in hepatocytes was triggered by 4 weeks of feeding and was associated with changes reflecting the early stage of human nonalcoholic steatohepatitis (NASH), steatotic change with liver inflammation, and hepatocyte ballooning. Excessive mitochondrial fission inhibition in hepatocytes and lipid metabolism dysregulation in adipose tissue attenuated liver inflammation and fibrogenesis but not steatosis and the systemic pathological changes in the early and chronic fibrotic NASH stages (4- and 12-week CDAA feeding). These beneficial changes due to the suppression of mitochondrial fission against the liver and systemic injuries were associated with decreased autophagic responses and endoplasmic reticulum stress in hepatocytes. Injuries to other liver cells, such as endothelial cells, Kupffer cells, and hepatic stellate cells, were also attenuated by the inhibition of mitochondrial fission in hepatocytes. CONCLUSIONS Taken together, these findings suggest that excessive mitochondrial fission in hepatocytes could play a causative role in NAFLD progression by liver inflammation and fibrogenesis through altered cell cross-talk. This study provides a potential therapeutic target for NAFLD.
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Affiliation(s)
- Masashi Miyao
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chihiro Kawai
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirokazu Kotani
- Department of Forensic Medicine and Sciences, Mie University Graduate School of Medicine, Tsu, Japan
| | - Hirozo Minami
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hitoshi Abiru
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideki Hamayasu
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoru Eguchi
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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23
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Rusilowicz-Jones EV, Brazel AJ, Frigenti F, Urbé S, Clague MJ. Membrane compartmentalisation of the ubiquitin system. Semin Cell Dev Biol 2022; 132:171-184. [PMID: 34895815 DOI: 10.1016/j.semcdb.2021.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022]
Abstract
We now have a comprehensive inventory of ubiquitin system components. Understanding of any system also needs an appreciation of how components are organised together. Quantitative proteomics has provided us with a census of their relative populations in several model cell types. Here, by examining large scale unbiased data sets, we seek to identify and map those components, which principally reside on the major organelles of the endomembrane system. We present the consensus distribution of > 50 ubiquitin modifying enzymes, E2s, E3s and DUBs, that possess transmembrane domains. This analysis reveals that the ER and endosomal compartments have a diverse cast of resident E3s, whilst the Golgi and mitochondria operate with a more restricted palette. We describe key functions of ubiquitylation that are specific to each compartment and relate this to their signature complement of ubiquitin modifying components.
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Affiliation(s)
- Emma V Rusilowicz-Jones
- Dept. of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ailbhe J Brazel
- Dept. of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; Department of Biology, Maynooth University, Maynooth W23 F2K6, Ireland
| | - Francesca Frigenti
- Dept. of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Sylvie Urbé
- Dept. of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
| | - Michael J Clague
- Dept. of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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24
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Vickers SD, Shumar SA, Saporito DC, Kunovac A, Hathaway QA, Mintmier B, King JA, King RD, Rajendran VM, Infante AM, Hollander JM, Leonardi R. NUDT7 regulates total hepatic CoA levels and the composition of the intestinal bile acid pool in male mice fed a Western diet. J Biol Chem 2022; 299:102745. [PMID: 36436558 PMCID: PMC9792899 DOI: 10.1016/j.jbc.2022.102745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Nudix hydrolase 7 (NUDT7) is an enzyme that hydrolyzes CoA species, is highly expressed in the liver, and resides in the peroxisomes. Peroxisomes are organelles where the preferential oxidation of dicarboxylic fatty acids occurs and where the hepatic synthesis of the primary bile acids cholic acid and chenodeoxycholic acid is completed. We previously showed that liver-specific overexpression of NUDT7 affects peroxisomal lipid metabolism but does not prevent the increase in total liver CoA levels that occurs during fasting. We generated Nudt7-/- mice to further characterize the role that peroxisomal (acyl-)CoA degradation plays in the modulation of the size and composition of the acyl-CoA pool and in the regulation of hepatic lipid metabolism. Here, we show that deletion of Nudt7 alters the composition of the hepatic acyl-CoA pool in mice fed a low-fat diet, but only in males fed a Western diet does the lack of NUDT7 activity increase total liver CoA levels. This effect is driven by the male-specific accumulation of medium-chain dicarboxylic acyl-CoAs, which are produced from the β-oxidation of dicarboxylic fatty acids. We also show that, under conditions of elevated synthesis of chenodeoxycholic acid derivatives, Nudt7 deletion promotes the production of tauromuricholic acid, decreasing the hydrophobicity index of the intestinal bile acid pool and increasing fecal cholesterol excretion in male mice. These findings reveal that NUDT7-mediated hydrolysis of acyl-CoA pathway intermediates in liver peroxisomes contributes to the regulation of dicarboxylic fatty acid metabolism and the composition of the bile acid pool.
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Affiliation(s)
- Schuyler D Vickers
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Stephanie A Shumar
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Dominique C Saporito
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Breeanna Mintmier
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Judy A King
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, Shreveport, Louisiana, USA
| | - Rachel D King
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Vazhaikkurichi M Rajendran
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Aniello M Infante
- Genomics Core Facility, West Virginia University, Morgantown, West Virginia, USA
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Roberta Leonardi
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA.
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25
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Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell 2022; 185:4654-4673.e28. [PMID: 36334589 PMCID: PMC10040263 DOI: 10.1016/j.cell.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/18/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Brown adipose tissue (BAT) regulates metabolic physiology. However, nearly all mechanistic studies of BAT protein function occur in a single inbred mouse strain, which has limited the understanding of generalizable mechanisms of BAT regulation over physiology. Here, we perform deep quantitative proteomics of BAT across a cohort of 163 genetically defined diversity outbred mice, a model that parallels the genetic and phenotypic variation found in humans. We leverage this diversity to define the functional architecture of the outbred BAT proteome, comprising 10,479 proteins. We assign co-operative functions to 2,578 proteins, enabling systematic discovery of regulators of BAT. We also identify 638 proteins that correlate with protection from, or sensitivity to, at least one parameter of metabolic disease. We use these findings to uncover SFXN5, LETMD1, and ATP1A2 as modulators of BAT thermogenesis or adiposity, and provide OPABAT as a resource for understanding the conserved mechanisms of BAT regulation over metabolic physiology.
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Affiliation(s)
- Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Luiz H M Bozi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yizhi Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher L Riley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mandy Chen
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Evanna L Mills
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Margo P Emont
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Wenfei Sun
- Department of Bioengineering, Stanford University, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, CA 94305, USA
| | - Anita Reddy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan Garrity
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jiani Long
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tobias Becher
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Laura Potano Vitas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Martha Ordonez
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiong Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Weihai Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nhien Tran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yitong Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yang Zhang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yuchen He
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca Deng
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Heiko Schöder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark P Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Linus T Tsai
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Evan D Rosen
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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26
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Advances in measuring cancer cell metabolism with subcellular resolution. Nat Methods 2022; 19:1048-1063. [PMID: 36008629 DOI: 10.1038/s41592-022-01572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
Characterizing metabolism in cancer is crucial for understanding tumor biology and for developing potential therapies. Although most metabolic investigations analyze averaged metabolite levels from all cell compartments, subcellular metabolomics can provide more detailed insight into the biochemical processes associated with the disease. Methodological limitations have historically prevented the wider application of subcellular metabolomics in cancer research. Recently, however, ways to distinguish and identify metabolic pathways within organelles have been developed, including state-of-the-art methods to monitor metabolism in situ (such as mass spectrometry-based imaging, Raman spectroscopy and fluorescence microscopy), to isolate key organelles via new approaches and to use tailored isotope-tracing strategies. Herein, we examine the advantages and limitations of these developments and look to the future of this field of research.
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27
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Lee C, Chen Y, Wang P, Wallace DC, Burke PJ. A Three-Dimensional Printed Inertial Microfluidic Platform for Isolation of Minute Quantities of Vital Mitochondria. Anal Chem 2022; 94:6930-6938. [PMID: 35502898 DOI: 10.1021/acs.analchem.1c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a fast and easy-to-use three-dimensional printed microfluidic platform for mitochondria isolation from cell and tissue lysates based on inertial microfluidics. We present and quantify the quality of the isolated mitochondria by measuring the respiration rate under various conditions. We demonstrate that the technology produces vital mitochondria of equal quality to traditional, but more burdensome, differential centrifugation. We anticipate that the availability of improved tools for studies of bioenergetics to the broader biological community will enable these and other links to be explored in more meaningful ways, leading to further understanding of the links between energy, health, and disease.
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Affiliation(s)
- ChiaHung Lee
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Yumay Chen
- Department of Biological Chemistry, University of California, Irvine, California 92697, United States
| | - Ping Wang
- Department of Diabetes, Endocrinology, and Metabolism, City of Hope National Medical Center, Duarte, California 91010, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and Department of Pediatrics, Division of Human Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Peter J Burke
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States.,Department of Electrical and Engineering and Computer Science, University of California, Irvine, California 92697, United States
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28
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Chen C, Sidransky E, Chen Y. Lyso-IP: Uncovering Pathogenic Mechanisms of Lysosomal Dysfunction. Biomolecules 2022; 12:biom12050616. [PMID: 35625544 PMCID: PMC9138597 DOI: 10.3390/biom12050616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 01/27/2023] Open
Abstract
Lysosomes are ubiquitous membrane-bound organelles found in all eukaryotic cells. Outside of their well-known degradative function, lysosomes are integral in maintaining cellular homeostasis. Growing evidence has shown that lysosomal dysfunction plays an important role not only in the rare group of lysosomal storage diseases but also in a host of others, including common neurodegenerative disorders, such as Alzheimer disease and Parkinson disease. New technological advances have significantly increased our ability to rapidly isolate lysosomes from cells in recent years. The development of the Lyso-IP approach and similar methods now allow for lysosomal purification within ten minutes. Multiple studies using the Lyso-IP approach have revealed novel insights into the pathogenic mechanisms of lysosomal disorders, including Niemann-Pick type C disease, showing the immense potential for this technique. Future applications of rapid lysosomal isolation techniques are likely to greatly enhance our understanding of lysosomal dysfunction in rare and common neurodegeneration causes.
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Affiliation(s)
- Chase Chen
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bld 35A, Room 1E623 35 Convent Drive, MSC 3708, Rockville, MD 20892, USA;
- Aligning Science Across Parkinson’s (ASAP) Collaborative Network, Chevy Chase, MD 20815, USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bld 35A, Room 1E623 35 Convent Drive, MSC 3708, Rockville, MD 20892, USA;
- Aligning Science Across Parkinson’s (ASAP) Collaborative Network, Chevy Chase, MD 20815, USA
- Correspondence: (E.S.); (Y.C.); Tel.: +1-301-496-0373 (E.S. & Y.C.)
| | - Yu Chen
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bld 35A, Room 1E623 35 Convent Drive, MSC 3708, Rockville, MD 20892, USA;
- Aligning Science Across Parkinson’s (ASAP) Collaborative Network, Chevy Chase, MD 20815, USA
- Correspondence: (E.S.); (Y.C.); Tel.: +1-301-496-0373 (E.S. & Y.C.)
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29
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Hammond M, Dorrell RG, Speijer D, Lukeš J. Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. Bioessays 2022; 44:e2100258. [PMID: 35318703 DOI: 10.1002/bies.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
Abstract
Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.
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Affiliation(s)
- Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dave Speijer
- Medical Biochemistry, UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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30
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Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE, Snyder NW. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Mol Cell 2022; 82:447-462.e6. [PMID: 34856123 PMCID: PMC8950487 DOI: 10.1016/j.molcel.2021.11.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 01/22/2023]
Abstract
Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
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Affiliation(s)
- Sophie Trefely
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharina Huber
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Biochemistry, Graz University of Technology, Graz 8010, Austria
| | - Joyce Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay Singh
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mary T Doan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hannah L Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Zhao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimmy P Xu
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth C Bedi
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Eduardo Rame
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Clementina Mesaros
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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31
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Kuhnert F, Weber APM. In Vivo Epitope Tagging of Plant Mitochondria. Methods Mol Biol 2022; 2379:253-264. [PMID: 35188666 DOI: 10.1007/978-1-0716-1791-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a key role in cellular metabolism. Analyses of the genome, the proteome, metabolic, physiological, and biochemical functions of mitochondria frequently require the isolation of intact and functional mitochondria from various plant tissues with sufficient yield. For this purpose, we generated a transgenic Arabidopsis thaliana (Arabidopsis) line which presents a triple hemagglutinin tag on the surface of the outer mitochondrial membrane. The affinity tag enables immunocapture of the organelles in a single step. This chapter gives detailed instructions on how to generate transgenic Arabidopsis lines harboring a ubiquitously expressed 3xHA-sGFP-TOM5 mitochondrial fusion protein that is targeted to the outer mitochondrial membrane and enables purification of the organelles in a single step.
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Affiliation(s)
- Franziska Kuhnert
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany.
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32
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Qin S, Zhang Y, Tian Y, Xu F, Zhang P. Subcellular metabolomics: Isolation, measurement, and applications. J Pharm Biomed Anal 2021; 210:114557. [PMID: 34979492 DOI: 10.1016/j.jpba.2021.114557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/26/2022]
Abstract
Metabolomics, a technique that profiles global small molecules in biological samples, has been a pivotal tool for disease diagnosis and mechanism research. The sample type in metabolomics covers a wide range, including a variety of body fluids, tissues, and cells. However, little attention was paid to the smaller, relatively independent partition systems in cells, namely the organelles. The organelles are specific compartments/places where diverse metabolic activities are happening in an orderly manner. Metabolic disorders of organelles were found to occur in various pathological conditions such as inherited metabolic diseases, diabetes, cancer, and neurodegenerative diseases. However, at the cellular level, the metabolic outcomes of organelles and cytoplasm are superimposed interactively, making it difficult to describe the changes in subcellular compartments. Therefore, characterizing the metabolic pool in the compartmentalized system is of great significance for understanding the role of organelles in physiological functions and diseases. So far, there are very few research articles or reviews related to subcellular metabolomics. In this review, subcellular fractionation and metabolite analysis methods, as well as the application of subcellular metabolomics in the physiological and pathological studies are systematically reviewed, as a practical reference to promote the continued advancement in subcellular metabolomics.
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Affiliation(s)
- Siyuan Qin
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yuxin Zhang
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, PR China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
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33
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van der Walt G, Lindeque JZ, Mason S, Louw R. Sub-Cellular Metabolomics Contributes Mitochondria-Specific Metabolic Insights to a Mouse Model of Leigh Syndrome. Metabolites 2021; 11:metabo11100658. [PMID: 34677373 PMCID: PMC8537744 DOI: 10.3390/metabo11100658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
Direct injury of mitochondrial respiratory chain (RC) complex I by Ndufs4 subunit mutations results in complex I deficiency (CID) and a progressive encephalomyopathy, known as Leigh syndrome. While mitochondrial, cytosolic and multi-organelle pathways are known to be involved in the neuromuscular LS pathogenesis, compartment-specific metabolomics has, to date, not been applied to murine models of CID. We thus hypothesized that sub-cellular metabolomics would be able to contribute organelle-specific insights to known Ndufs4 metabolic perturbations. To that end, whole brains and skeletal muscle from late-stage Ndufs4 mice and age/sex-matched controls were harvested for mitochondrial and cytosolic isolation. Untargeted 1H-NMR and semi-targeted LC-MS/MS metabolomics was applied to the resulting cell fractions, whereafter important variables (VIPs) were selected by univariate statistics. A predominant increase in multiple targeted amino acids was observed in whole-brain samples, with a more prominent effect at the mitochondrial level. Similar pathways were implicated in the muscle tissue, showing a greater depletion of core metabolites with a compartment-specific distribution, however. The altered metabolites expectedly implicate altered redox homeostasis, alternate RC fueling, one-carbon metabolism, urea cycling and dysregulated proteostasis to different degrees in the analyzed tissues. A first application of EDTA-chelated magnesium and calcium measurement by NMR also revealed tissue- and compartment-specific alterations, implicating stress response-related calcium redistribution between neural cell compartments, as well as whole-cell muscle magnesium depletion. Altogether, these results confirm the ability of compartment-specific metabolomics to capture known alterations related to Ndufs4 KO and CID while proving its worth in elucidating metabolic compartmentalization in said pathways that went undetected in the diluted whole-cell samples previously studied.
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34
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Jayashankar V, Selwan E, Hancock SE, Verlande A, Goodson MO, Eckenstein KH, Milinkeviciute G, Hoover BM, Chen B, Fleischman AG, Cramer KS, Hanessian S, Masri S, Turner N, Edinger AL. Drug-like sphingolipid SH-BC-893 opposes ceramide-induced mitochondrial fission and corrects diet-induced obesity. EMBO Mol Med 2021; 13:e13086. [PMID: 34231322 PMCID: PMC8350895 DOI: 10.15252/emmm.202013086] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ceramide-induced mitochondrial fission drives high-fat diet (HFD)-induced obesity. However, molecules targeting mitochondrial dynamics have shown limited benefits in murine obesity models. Here, we reveal that these compounds are either unable to block ceramide-induced mitochondrial fission or require extended incubation periods to be effective. In contrast, targeting endolysosomal trafficking events important for mitochondrial fission rapidly and robustly prevented ceramide-induced disruptions in mitochondrial form and function. By simultaneously inhibiting ARF6- and PIKfyve-dependent trafficking events, the synthetic sphingolipid SH-BC-893 blocked palmitate- and ceramide-induced mitochondrial fission, preserved mitochondrial function, and prevented ER stress in vitro. Similar benefits were observed in the tissues of HFD-fed mice. Within 4 h of oral administration, SH-BC-893 normalized mitochondrial morphology in the livers and brains of HFD-fed mice, improved mitochondrial function in white adipose tissue, and corrected aberrant plasma leptin and adiponectin levels. As an interventional agent, SH-BC-893 restored normal body weight, glucose disposal, and hepatic lipid levels in mice consuming a HFD. In sum, the sphingolipid analog SH-BC-893 robustly and acutely blocks ceramide-induced mitochondrial dysfunction, correcting diet-induced obesity and its metabolic sequelae.
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Affiliation(s)
- Vaishali Jayashankar
- Department of Developmental and Cell BiologyUniversity of California IrvineIrvineCAUSA
| | - Elizabeth Selwan
- Department of Developmental and Cell BiologyUniversity of California IrvineIrvineCAUSA
| | - Sarah E Hancock
- School of Medical SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Amandine Verlande
- Department of Biological ChemistryUniversity of California IrvineIrvineCAUSA
| | - Maggie O Goodson
- Department of Biological ChemistryUniversity of California IrvineIrvineCAUSA
| | - Kazumi H Eckenstein
- Department of Developmental and Cell BiologyUniversity of California IrvineIrvineCAUSA
| | | | - Brianna M Hoover
- Division of Hematology/OncologyDepartment of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Bin Chen
- Department of ChemistryUniversité de MontréalMontréalQCCanada
| | - Angela G Fleischman
- Division of Hematology/OncologyDepartment of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Karina S Cramer
- Department of Neurobiology and BehaviorUniversity of California IrvineIrvineCAUSA
| | | | - Selma Masri
- Department of Biological ChemistryUniversity of California IrvineIrvineCAUSA
| | - Nigel Turner
- School of Medical SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Aimee L Edinger
- Department of Developmental and Cell BiologyUniversity of California IrvineIrvineCAUSA
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35
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Chang M, Wang Q, Liu X, Shi X, Xu G. Facile Synthesis of Antibody-Coupled Polydopamine-Coated Magnetic Graphene Oxide Composites for Efficient Immunopurification and Metabolomics Analysis of Mitochondria. Anal Chem 2021; 93:11099-11107. [PMID: 34347447 DOI: 10.1021/acs.analchem.1c01101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As a vital hub, a mitochondrion houses metabolic pathways that play important roles in cellular physiology. Aberrant metabolites occurring in mitochondria are closely associated with the emergence and progression of various mitochondria-related diseases. Therefore, a simple and versatile approach to efficiently purify intact mitochondria is urgently needed to precisely and comprehensively characterize the composition and abundance of the mitochondrial metabolome in different physiological and pathological states. In this work, novel immunoaffinitive magnetic composites MagG@PD@Avidin@TOM20 were prepared to achieve highly selective isolation of intact mitochondria from three different hepatocytes (LO2, HepG2, and Huh7). The prepared composites inherit combined merits, including strong magnetic responsiveness, excellent stability, and specific and high affinity between antibody TOM20 and mitochondrial outer membrane protein. These mitochondria attached on MagG@PD@Avidin@TOM20 were characterized by the western blot and fluorescence microscopy to confirm their purity and integrity, which are vital for reliable mitochondrial metabolic analysis. Subsequently, ultrahigh-performance liquid chromatography-high-resolution mass spectrometry-based untargeted metabolomics analysis was conducted to characterize the metabolomes in the immunopurified mitochondria and whole cells. Notably, the metabolite profiles of whole cells and mitochondria including itaconic acid, acetylcarnitine, malic acid, etc., were significantly different. These data underscore the importance of determining metabolites at the mitochondrial level, which would supplement us new knowledge at the subcellular level.
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Affiliation(s)
- Mengmeng Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Encarnación-Rosado J, Kimmelman AC. Harnessing metabolic dependencies in pancreatic cancers. Nat Rev Gastroenterol Hepatol 2021; 18:482-492. [PMID: 33742165 PMCID: PMC8249349 DOI: 10.1038/s41575-021-00431-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with a 5-year survival rate of <10%. The tumour microenvironment (TME) of PDAC is characterized by excessive fibrosis and deposition of extracellular matrix, termed desmoplasia. This unique TME leads to high interstitial pressure, vascular collapse and low nutrient and oxygen diffusion. Together, these factors contribute to the unique biology and therapeutic resistance of this deadly tumour. To thrive in this hostile environment, PDAC cells adapt by using non-canonical metabolic pathways and rely on metabolic scavenging pathways such as autophagy and macropinocytosis. Here, we review the metabolic pathways that PDAC use to support their growth in the setting of an austere TME. Understanding how PDAC tumours rewire their metabolism and use scavenging pathways under environmental stressors might enable the identification of novel therapeutic approaches.
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Affiliation(s)
| | - Alec C Kimmelman
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
- Department of Radiation Oncology, New York University School of Medicine, New York, NY, USA.
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37
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Li H, Uittenbogaard M, Hao L, Chiaramello A. Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics. Metabolites 2021; 11:233. [PMID: 33920115 PMCID: PMC8070181 DOI: 10.3390/metabo11040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are dynamic multitask organelles that function as hubs for many metabolic pathways. They produce most ATP via the oxidative phosphorylation pathway, a critical pathway that the brain relies on its energy need associated with its numerous functions, such as synaptic homeostasis and plasticity. Therefore, mitochondrial dysfunction is a prevalent pathological hallmark of many neurodevelopmental and neurodegenerative disorders resulting in altered neurometabolic coupling. With the advent of mass spectrometry (MS) technology, MS-based metabolomics provides an emerging mechanistic understanding of their global and dynamic metabolic signatures. In this review, we discuss the pathogenetic causes of mitochondrial metabolic disorders and the recent MS-based metabolomic advances on their metabolomic remodeling. We conclude by exploring the MS-based metabolomic functional insights into their biosignatures to improve diagnostic platforms, stratify patients, and design novel targeted therapeutic strategies.
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Affiliation(s)
- Haorong Li
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Martine Uittenbogaard
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
| | - Ling Hao
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Anne Chiaramello
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
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38
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Tran DH, Kesavan R, Rion H, Soflaee MH, Solmonson A, Bezwada D, Vu HS, Cai F, Phillips JA, DeBerardinis RJ, Hoxhaj G. Mitochondrial NADP + is essential for proline biosynthesis during cell growth. Nat Metab 2021; 3:571-585. [PMID: 33833463 PMCID: PMC9210447 DOI: 10.1038/s42255-021-00374-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/25/2021] [Indexed: 01/05/2023]
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP+) is vital to produce NADPH, a principal supplier of reducing power for biosynthesis of macromolecules and protection against oxidative stress. NADPH exists in separate pools, in both the cytosol and mitochondria; however, the cellular functions of mitochondrial NADPH are incompletely described. Here, we find that decreasing mitochondrial NADP(H) levels through depletion of NAD kinase 2 (NADK2), an enzyme responsible for production of mitochondrial NADP+, renders cells uniquely proline auxotrophic. Cells with NADK2 deletion fail to synthesize proline, due to mitochondrial NADPH deficiency. We uncover the requirement of mitochondrial NADPH and NADK2 activity for the generation of the pyrroline-5-carboxylate metabolite intermediate as the bottleneck step in the proline biosynthesis pathway. Notably, after NADK2 deletion, proline is required to support nucleotide and protein synthesis, making proline essential for the growth and proliferation of NADK2-deficient cells. Thus, we highlight proline auxotrophy in mammalian cells and discover that mitochondrial NADPH is essential to enable proline biosynthesis.
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Affiliation(s)
- Diem H Tran
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rushendhiran Kesavan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Halie Rion
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mona Hoseini Soflaee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashley Solmonson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Divya Bezwada
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gerta Hoxhaj
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Noterman MF, Chaubey K, Lin-Rahardja K, Rajadhyaksha AM, Pieper AA, Taylor EB. Dual-process brain mitochondria isolation preserves function and clarifies protein composition. Proc Natl Acad Sci U S A 2021; 118:e2019046118. [PMID: 33836587 PMCID: PMC7980376 DOI: 10.1073/pnas.2019046118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The brain requires continuously high energy production to maintain ion gradients and normal function. Mitochondria critically undergird brain energetics, and mitochondrial abnormalities feature prominently in neuropsychiatric disease. However, many unique aspects of brain mitochondria composition and function are poorly understood. Developing improved neuroprotective therapeutics thus requires more comprehensively understanding brain mitochondria, including accurately delineating protein composition and channel-transporter functional networks. However, obtaining pure mitochondria from the brain is especially challenging due to its distinctive lipid and cell structure properties. As a result, conflicting reports on protein localization to brain mitochondria abound. Here we illustrate this problem with the neuropsychiatric disease-associated L-type calcium channel Cav1.2α1 subunit previously observed in crude mitochondria. We applied a dual-process approach to obtain functionally intact versus compositionally pure brain mitochondria. One branch utilizes discontinuous density gradient centrifugation to isolate semipure mitochondria suitable for functional assays but unsuitable for protein localization because of endoplasmic reticulum (ER) contamination. The other branch utilizes self-forming density gradient ultracentrifugation to remove ER and yield ultrapure mitochondria that are suitable for investigating protein localization but functionally compromised. Through this process, we evaluated brain mitochondria protein content and observed the absence of Cav1.2α1 and other previously reported mitochondrial proteins, including the NMDA receptor, ryanodine receptor 1, monocarboxylate transporter 1, excitatory amino acid transporter 1, and glyceraldehyde 3-phosphate dehydrogenase. Conversely, we confirmed mitochondrial localization of several plasma membrane proteins previously reported to also localize to mitochondria. We expect this dual-process isolation procedure will enhance understanding of brain mitochondria in both health and disease.
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Affiliation(s)
- Maria F Noterman
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242
| | - Kalyani Chaubey
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106
| | - Kristi Lin-Rahardja
- Department of Systems Biology and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106
| | - Anjali M Rajadhyaksha
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY 10065
- Pediatric Neurology, Pediatrics, Weill Cornell Medicine of Cornell University, New York, NY 10065
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106;
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY 10065
- Geriatric Research Education and Clinical Centers, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Eric B Taylor
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242;
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242
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Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, Mekhedov SL, Williams KJ, Caicci F, Valle G, Giacomello M, Quiroga AD, Lehner R, Miksis MJ, Toth K, de Aguiar Vallim TQ, Koonin EV, Scorrano L, Pellegrini L. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis. Cell Rep 2021; 34:108873. [PMID: 33730569 DOI: 10.1016/j.celrep.2021.108873] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by sheets of curved rough endoplasmic reticulum closely wrapped around the mitochondria (wrappER). To elucidate the in vivo function of this contact, mouse liver fractions enriched in wrappER-associated mitochondria are analyzed by transcriptomics, proteomics, and lipidomics. The biochemical signature of the wrappER points to a role in the biogenesis of very-low-density lipoproteins (VLDL). Altering wrappER-mitochondria contacts curtails VLDL secretion and increases hepatic fatty acids, lipid droplets, and neutral lipid content. Conversely, acute liver-specific ablation of Mttp, the most upstream regulator of VLDL biogenesis, recapitulates this hepatic dyslipidemia phenotype and promotes remodeling of the wrappER-mitochondria contact. The discovery that liver wrappER-mitochondria contacts participate in VLDL biology suggests an involvement of inter-organelle contacts in systemic lipid homeostasis.
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Affiliation(s)
- Irene Anastasia
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Nicolò Ilacqua
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - Philippe Lemieux
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | | | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Sergei L Mekhedov
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Kevin J Williams
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Giorgio Valle
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ariel D Quiroga
- Instituto de Fisiología Experimental, CONICET, UNR, Rosario, Argentina; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Richard Lehner
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Michael J Miksis
- Department of Engineering Science and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Katalin Toth
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Q de Aguiar Vallim
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Medicine, Division of Cardiology, UCLA, Los Angeles, CA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Luca Scorrano
- Department of Biology, University of Padua, Padua, Italy
| | - Luca Pellegrini
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada.
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41
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Caicedo A, Zambrano K, Sanon S, Gavilanes AWD. Extracellular mitochondria in the cerebrospinal fluid (CSF): Potential types and key roles in central nervous system (CNS) physiology and pathogenesis. Mitochondrion 2021; 58:255-269. [PMID: 33662579 DOI: 10.1016/j.mito.2021.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
The cerebrospinal fluid (CSF) has an important role in the transport of nutrients and signaling molecules to the central nervous and immune systems through its circulation along the brain and spinal cord tissues. The mitochondrial activity in the central nervous system (CNS) is essential in processes such as neuroplasticity, neural differentiation and production of neurotransmitters. Interestingly, extracellular and active mitochondria have been detected in the CSF where they act as a biomarker for the outcome of pathologies such as subarachnoid hemorrhage and delayed cerebral ischemia. Additionally, cell-free-circulating mitochondrial DNA (ccf-mtDNA) has been detected in both the CSF of healthy donors and in that of patients with neurodegenerative diseases. Key questions arise as there is still much debate regarding if ccf-mtDNA detected in CSF is associated with a diversity of active or inactive extracellular mitochondria coexisting in distinct pathologies. Additionally, it is of great scientific and medical importance to identify the role of extracellular mitochondria (active and inactive) in the CSF and the difference between them being damage associated molecular patterns (DAMPs) or factors that promote homeostasis. This review analyzes the different types of extracellular mitochondria, methods for their identification and their presence in CSF. Extracellular mitochondria in the CSF could have an important implication in health and disease, which may lead to the development of medical approaches that utilize mitochondria as therapeutic agents.
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Affiliation(s)
- Andrés Caicedo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Kevin Zambrano
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands; Instituto de Neurociencias, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Serena Sanon
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Cornell University, Ithaca, United States
| | - Antonio W D Gavilanes
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
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Hewton KG, Johal AS, Parker SJ. Transporters at the Interface between Cytosolic and Mitochondrial Amino Acid Metabolism. Metabolites 2021; 11:metabo11020112. [PMID: 33669382 PMCID: PMC7920303 DOI: 10.3390/metabo11020112] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are central organelles that coordinate a vast array of metabolic and biologic functions important for cellular health. Amino acids are intricately linked to the bioenergetic, biosynthetic, and homeostatic function of the mitochondrion and require specific transporters to facilitate their import, export, and exchange across the inner mitochondrial membrane. Here we review key cellular metabolic outputs of eukaryotic mitochondrial amino acid metabolism and discuss both known and unknown transporters involved. Furthermore, we discuss how utilization of compartmentalized amino acid metabolism functions in disease and physiological contexts. We examine how improved methods to study mitochondrial metabolism, define organelle metabolite composition, and visualize cellular gradients allow for a more comprehensive understanding of how transporters facilitate compartmentalized metabolism.
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Affiliation(s)
- Keeley G. Hewton
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
| | - Amritpal S. Johal
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
| | - Seth J. Parker
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V6H 0B3, Canada
- Correspondence: ; Tel.: +1-604-875-3121
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43
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Towards a systems-level understanding of mitochondrial biology. Cell Calcium 2021; 95:102364. [PMID: 33601101 DOI: 10.1016/j.ceca.2021.102364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 11/21/2022]
Abstract
Human mitochondria are complex and highly dynamic biological systems, comprised of over a thousand parts and evolved to fully integrate into the specialized intracellular signaling networks and metabolic requirements of each cell and organ. Over the last two decades, several complementary, top-down computational and experimental approaches have been developed to identify, characterize and modulate the human mitochondrial system, demonstrating the power of integrating classical reductionist and discovery-driven analyses in order to de-orphanize hitherto unknown molecular components of mitochondrial machineries and pathways. To this goal, systematic, multiomics-based surveys of proteome composition, protein networks, and phenotype-to-pathway associations at the tissue, cell and organellar level have been largely exploited to predict the full complement of mitochondrial proteins and their functional interactions, therefore catalyzing data-driven hypotheses. Collectively, these multidisciplinary and integrative research approaches hold the potential to propel our understanding of mitochondrial biology and provide a systems-level framework to unraveling mitochondria-mediated and disease-spanning pathomechanisms.
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Dixon RA, Sarnala S. Proanthocyanidin Biosynthesis-a Matter of Protection. PLANT PHYSIOLOGY 2020; 184:579-591. [PMID: 32817234 PMCID: PMC7536678 DOI: 10.1104/pp.20.00973] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/11/2020] [Indexed: 05/20/2023]
Abstract
Proanthocyanidins are the second most abundant plant phenolic polymer, but, despite intensive investigation, several aspects of their biosynthesis and functions remain unclear.
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Affiliation(s)
- Richard A Dixon
- Hagler Institute for Advanced Study and Department of Biological Sciences, Texas A&M University, College Station, Texas 77843-3572
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Sai Sarnala
- Texas Academy of Mathematics and Science, University of North Texas, Denton, Texas 76203-5017
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45
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mSphere of Influence: Tweaking Organellar Purification Approaches. mSphere 2020; 5:5/5/e00690-20. [PMID: 32907951 PMCID: PMC7485686 DOI: 10.1128/msphere.00690-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Diego Huet studies the organelles involved in the metabolic adaptations of the apicomplexan parasite Toxoplasma gondii. In this mSphere of Influence article, he reflects on how the paper “Absolute quantification of matrix metabolites reveals the dynamics of mitochondrial metabolism” by Chen et al. (W. W. Chen, E. Freinkman, T. Wang, K. Birsoy, and D. M. Sabatini, Cell 166:1324–1337.e11, 2016, https://doi.org/10.1016/j.cell.2016.07.040) shaped his research by providing an approach for rapidly and specifically isolating mitochondria to probe the metabolism of these organelles. Diego Huet studies the organelles involved in the metabolic adaptations of the apicomplexan parasite Toxoplasma gondii. In this mSphere of Influence article, he reflects on how the paper “Absolute quantification of matrix metabolites reveals the dynamics of mitochondrial metabolism” by Chen et al. (W. W. Chen, E. Freinkman, T. Wang, K. Birsoy, and D. M. Sabatini, Cell 166:1324–1337.e11, 2016, https://doi.org/10.1016/j.cell.2016.07.040) shaped his research by providing an approach for rapidly and specifically isolating mitochondria to probe the metabolism of these organelles.
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46
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Schüler SC, Gebert N, Ori A. Stem cell aging: The upcoming era of proteins and metabolites. Mech Ageing Dev 2020; 190:111288. [DOI: 10.1016/j.mad.2020.111288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
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47
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Motori E, Atanassov I, Kochan SMV, Folz-Donahue K, Sakthivelu V, Giavalisco P, Toni N, Puyal J, Larsson NG. Neuronal metabolic rewiring promotes resilience to neurodegeneration caused by mitochondrial dysfunction. SCIENCE ADVANCES 2020; 6:eaba8271. [PMID: 32923630 PMCID: PMC7455195 DOI: 10.1126/sciadv.aba8271] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/15/2020] [Indexed: 05/03/2023]
Abstract
Neurodegeneration in mitochondrial disorders is considered irreversible because of limited metabolic plasticity in neurons, yet the cell-autonomous implications of mitochondrial dysfunction for neuronal metabolism in vivo are poorly understood. Here, we profiled the cell-specific proteome of Purkinje neurons undergoing progressive OXPHOS deficiency caused by disrupted mitochondrial fusion dynamics. We found that mitochondrial dysfunction triggers a profound rewiring of the proteomic landscape, culminating in the sequential activation of precise metabolic programs preceding cell death. Unexpectedly, we identified a marked induction of pyruvate carboxylase (PCx) and other anaplerotic enzymes involved in replenishing tricarboxylic acid cycle intermediates. Suppression of PCx aggravated oxidative stress and neurodegeneration, showing that anaplerosis is protective in OXPHOS-deficient neurons. Restoration of mitochondrial fusion in end-stage degenerating neurons fully reversed these metabolic hallmarks, thereby preventing cell death. Our findings identify a previously unappreciated pathway conferring resilience to mitochondrial dysfunction and show that neurodegeneration can be reversed even at advanced disease stages.
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Affiliation(s)
- E. Motori
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Corresponding author. , (E.M.); (N.-G.L.)
| | - I. Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - S. M. V. Kochan
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - K. Folz-Donahue
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - V. Sakthivelu
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - P. Giavalisco
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - N. Toni
- Center for Psychiatric Neurosciences, Department of Psychiatry, Lausanne University Hospital, Lausanne University, Lausanne, Switzerland
| | - J. Puyal
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - N.-G. Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Max Planck Institute for Biology of Ageing–Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Corresponding author. , (E.M.); (N.-G.L.)
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Gella A, Prada-Dacasa P, Carrascal M, Urpi A, González-Torres M, Abian J, Sanz E, Quintana A. Mitochondrial Proteome of Affected Glutamatergic Neurons in a Mouse Model of Leigh Syndrome. Front Cell Dev Biol 2020; 8:660. [PMID: 32850799 PMCID: PMC7399339 DOI: 10.3389/fcell.2020.00660] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 07/01/2020] [Indexed: 01/03/2023] Open
Abstract
Defects in mitochondrial function lead to severe neuromuscular orphan pathologies known as mitochondrial disease. Among them, Leigh Syndrome is the most common pediatric presentation, characterized by symmetrical brain lesions, hypotonia, motor and respiratory deficits, and premature death. Mitochondrial diseases are characterized by a marked anatomical and cellular specificity. However, the molecular determinants for this susceptibility are currently unknown, hindering the efforts to find an effective treatment. Due to the complex crosstalk between mitochondria and their supporting cell, strategies to assess the underlying alterations in affected cell types in the context of mitochondrial dysfunction are critical. Here, we developed a novel virus-based tool, the AAV-mitoTag viral vector, to isolate mitochondria from genetically defined cell types. Expression of the AAV-mitoTag in the glutamatergic vestibular neurons of a mouse model of Leigh Syndrome lacking the complex I subunit Ndufs4 allowed us to assess the proteome and acetylome of a subset of susceptible neurons in a well characterized model recapitulating the human disease. Our results show a marked reduction of complex I N-module subunit abundance and an increase in the levels of the assembly factor NDUFA2. Transiently associated non-mitochondrial proteins such as PKCδ, and the complement subcomponent C1Q were also increased in Ndufs4-deficient mitochondria. Furthermore, lack of Ndufs4 induced ATP synthase complex and pyruvate dehydrogenase (PDH) subunit hyperacetylation, leading to decreased PDH activity. We provide novel insight on the pathways involved in mitochondrial disease, which could underlie potential therapeutic approaches for these pathologies.
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Affiliation(s)
- Alejandro Gella
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Patricia Prada-Dacasa
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Montserrat Carrascal
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Andrea Urpi
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Melania González-Torres
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joaquin Abian
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Elisenda Sanz
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Albert Quintana
- Mitochondrial Neuropathology Lab, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
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49
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van der Walt G, Louw R. Novel mitochondrial and cytosolic purification pipeline for compartment-specific metabolomics in mammalian disease model tissues. Metabolomics 2020; 16:78. [PMID: 32577914 DOI: 10.1007/s11306-020-01697-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/13/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mitochondria represent an important milieu for studying the pathogenesis of several major diseases. The need for organelle-level metabolic resolution exists, as mitochondrial/cytosolic metabolites are often diluted beyond detection limits in complex samples. Compartment-specific studies are still hindered by the lack of efficient, cost-effective fractioning methods-applicable to laboratories of all financial/analytical standing. OBJECTIVES We established a novel mitochondrial/cytosolic purification pipeline for complimentary GC-TOF-MS and 1H-NMR metabolomics using robust, commercially available fractionation strategies. METHODS Magnetic based mitochondria isolation kits (MACS) were adapted for this purpose, accompanied by cytosolic filtering. Yield was assessed through the percentage recovery of citrate synthase (CS; a mitochondrial marker), purity by immunoblotting against compartment-specific proteins and integrity interrogated through the respiratory coupling ratio (RCR). The effects of the kit-based buffers on MS/NMR analyses of pure metabolite standards were evaluated. Finally, biological applicability to mammalian disease models was shown using Ndufs4 mouse brain tissue. RESULTS With minor modifications, MACS produced around 60% more mitochondria compared to a differential centrifugation method. Less than 15% of lysosomal LAMP-2 protein was found in the MACS isolates, confirming relative purity-while RCR's above 6 indicate sufficient mitochondrial integrity. The filtering approach effectively depleted mitochondria from the cytosolic fraction, as indicated by negligible Hsp60 and CS levels. Our GC-MS pilot yielded 60-70 features per fraction, while NMR analyses could quantify 6-10 of the most abundant compounds in each fraction. CONCLUSION This study provides a simple and flexible solution for mitochondrial and cytosolic metabolomics in animal model tissues, towards large-scale application of such methodologies in disease research.
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Affiliation(s)
- Gunter van der Walt
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa
| | - Roan Louw
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa.
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50
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Ray GJ, Boydston EA, Shortt E, Wyant GA, Lourido S, Chen WW, Sabatini DM. A PEROXO-Tag Enables Rapid Isolation of Peroxisomes from Human Cells. iScience 2020; 23:101109. [PMID: 32417403 PMCID: PMC7254474 DOI: 10.1016/j.isci.2020.101109] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022] Open
Abstract
Peroxisomes are metabolic organelles that perform a diverse array of critical functions in human physiology. Traditional isolation methods for peroxisomes can take more than 1 h to complete and can be laborious to implement. To address this, we have now extended our prior work on rapid organellar isolation to peroxisomes via the development of a peroxisomally localized 3XHA epitope tag ("PEROXO-Tag") and associated immunoprecipitation ("PEROXO-IP") workflow. Our PEROXO-IP workflow has excellent reproducibility, is easy to implement, and achieves highly rapid (~10 min post homogenization) and specific isolation of human peroxisomes, which we characterize here via proteomic profiling. By offering speed, specificity, reproducibility, and ease of use, the PEROXO-IP workflow should facilitate studies on the biology of peroxisomes.
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Affiliation(s)
- G Jordan Ray
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| | - Elizabeth A Boydston
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Emily Shortt
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Gregory A Wyant
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA.
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA.
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