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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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2
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Sousa BG, Mebus-Antunes NC, Fernandes-Siqueira LO, Caruso MB, Saraiva GN, Carvalho CF, Neves-Martins TC, Galina A, Zingali RB, Zeidler JD, Da Poian AT. Dengue virus non-structural protein 3 inhibits mitochondrial respiration by impairing complex I function. mSphere 2024; 9:e0040624. [PMID: 38980068 PMCID: PMC11288018 DOI: 10.1128/msphere.00406-24] [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: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024] Open
Abstract
Dengue virus (DENV) infection is known to affect host cell metabolism, but the molecular players involved are still poorly known. Using a proteomics approach, we identified six DENV proteins associated with mitochondria isolated from infected hepatocytes, and most of the peptides identified were from NS3. We also found an at least twofold decrease of several electron transport system (ETS) host proteins. Thus, we investigated whether NS3 could modulate the ETS function by incubating recombinant DENV NS3 constructs in mitochondria isolated from mouse liver. We found that NS3pro (NS3 protease domain), but not the correspondent catalytically inactive mutant (NS3proS135A), impairs complex I (CI)-dependent NADH:ubiquinone oxidoreductase activity, but not the activities of complexes II, III, IV, or V. Accordingly, using high-resolution respirometry, we found that both NS3pro and full-length NS3 decrease the respiratory rates associated with malate/pyruvate oxidation in mitochondria. The NS3-induced impairment in mitochondrial respiration occurs without altering either leak respiration or mitochondria's capacity to maintain membrane potential, suggesting that NS3 does not deeply affect mitochondrial integrity. Remarkably, CI activity is also inhibited in DENV-infected cells, supporting that the NS3 effects observed in isolated mitochondria may be relevant in the context of the infection. Finally, in silico analyses revealed the presence of potential NS3 cleavage sites in 17 subunits of mouse CI and 16 subunits of human CI, most of them located on the CI surface, suggesting that CI is prone to undergo proteolysis by NS3. Our findings suggest that DENV NS3 can modulate mitochondrial bioenergetics by directly affecting CI function. IMPORTANCE Dengue virus (DENV) infection is a major public health problem worldwide, affecting about 400 million people yearly. Despite its importance, many molecular aspects of dengue pathogenesis remain poorly known. For several years, our group has been investigating DENV-induced metabolic alterations in the host cells, focusing on the bioenergetics of mitochondrial respiration. The results of the present study reveal that the DENV non-structural protein 3 (NS3) is found in the mitochondria of infected cells, impairing mitochondrial respiration by directly targeting one of the components of the electron transport system, the respiratory complex I (CI). NS3 acts as the viral protease during the DENV replication cycle, and its proteolytic activity seems necessary for inhibiting CI function. Our findings uncover new nuances of DENV-induced metabolic alterations, highlighting NS3 as an important player in the modulation of mitochondria function during infection.
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Affiliation(s)
- Bruna G. Sousa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nathane C. Mebus-Antunes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Marjolly B. Caruso
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Georgia N. Saraiva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clara F. Carvalho
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais C. Neves-Martins
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Antonio Galina
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B. Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julianna D. Zeidler
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Kalarikkal M, Saikia R, Oliveira L, Bhorkar Y, Lonare A, Varshney P, Dhamale P, Majumdar A, Joseph J. Nup358 restricts ER-mitochondria connectivity by modulating mTORC2/Akt/GSK3β signalling. EMBO Rep 2024:10.1038/s44319-024-00204-8. [PMID: 39026009 DOI: 10.1038/s44319-024-00204-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
ER-mitochondria contact sites (ERMCSs) regulate processes, including calcium homoeostasis, energy metabolism and autophagy. Previously, it was shown that during growth factor signalling, mTORC2/Akt gets recruited to and stabilizes ERMCSs. Independent studies showed that GSK3β, a well-known Akt substrate, reduces ER-mitochondria connectivity by disrupting the VAPB-PTPIP51 tethering complex. However, the mechanisms that regulate ERMCSs are incompletely understood. Here we find that annulate lamellae (AL), relatively unexplored subdomains of ER enriched with a subset of nucleoporins, are present at ERMCSs. Depletion of Nup358, an AL-resident nucleoporin, results in enhanced mTORC2/Akt activation, GSK3β inhibition and increased ERMCSs. Depletion of Rictor, a mTORC2-specific subunit, or exogenous expression of GSK3β, was sufficient to reverse the ERMCS-phenotype in Nup358-deficient cells. We show that growth factor-mediated activation of mTORC2 requires the VAPB-PTPIP51 complex, whereas, Nup358's association with this tether restricts mTORC2/Akt signalling and ER-mitochondria connectivity. Expression of a Nup358 fragment that is sufficient for interaction with the VAPB-PTPIP51 complex suppresses mTORC2/Akt activation and disrupts ERMCSs. Collectively, our study uncovers a novel role for Nup358 in controlling ERMCSs by modulating the mTORC2/Akt/GSK3β axis.
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Affiliation(s)
- Misha Kalarikkal
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Rimpi Saikia
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Lizanne Oliveira
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Yashashree Bhorkar
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Akshay Lonare
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Pallavi Varshney
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Prathamesh Dhamale
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Amitabha Majumdar
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India
| | - Jomon Joseph
- National Centre for Cell Science, S.P. Pune University Campus, Pune, Maharashtra, 411007, India.
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Makrakis D, Dambri OA, Hafid AS. Design of Bio-Optical Transceiver for In Vivo Biomedical Sensor Applications. SENSORS (BASEL, SWITZERLAND) 2024; 24:2584. [PMID: 38676201 PMCID: PMC11054665 DOI: 10.3390/s24082584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
This paper presents an enhanced version of our previously developed bio-optical transceiver, presenting a significant advancement in nanosensor technology. Using self-assembled polymers, this nanodevice is capable of electron detection while maintaining biocompatibility, an essential feature for in vivo medical biosensors. This enhancement finds significance in the field of infectious disease control, particularly in the early detection of respiratory viruses, including high-threat pathogens such as SARS-CoV-2. The proposed system harnesses bioluminescence by converting electric signaling to visible blue light, effectively opening the path of linking nano-sized mechanisms to larger-scale systems, thereby pushing the boundaries of in vivo biomedical sensing. The performance evaluation of our technology is analytical and is based on the use of Markov chains, through which we assess the bit error probability. The calculated improvements indicate that this technology qualifies as a forerunner in terms of supporting the communication needs of smaller, safer, and more efficient manufactured sensor technologies for in vivo medical applications.
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Affiliation(s)
- Dimitrios Makrakis
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | | | - Abdelhakim Senhaji Hafid
- Department of Computer Science and Operations Research, University of Montreal, Montreal, QC H3T 1J4, Canada;
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5
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Sanchez-Lopez I, Orantos-Aguilera Y, Pozo-Guisado E, Alvarez-Barrientos A, Lilla S, Zanivan S, Lachaud C, Martin-Romero FJ. STIM1 translocation to the nucleus protects cells from DNA damage. Nucleic Acids Res 2024; 52:2389-2415. [PMID: 38224453 PMCID: PMC10954485 DOI: 10.1093/nar/gkae001] [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: 03/31/2023] [Revised: 10/30/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024] Open
Abstract
DNA damage represents a challenge for cells, as this damage must be eliminated to preserve cell viability and the transmission of genetic information. To reduce or eliminate unscheduled chemical modifications in genomic DNA, an extensive signaling network, known as the DNA damage response (DDR) pathway, ensures this repair. In this work, and by means of a proteomic analysis aimed at studying the STIM1 protein interactome, we have found that STIM1 is closely related to the protection from endogenous DNA damage, replicative stress, as well as to the response to interstrand crosslinks (ICLs). Here we show that STIM1 has a nuclear localization signal that mediates its translocation to the nucleus, and that this translocation and the association of STIM1 to chromatin increases in response to mitomycin-C (MMC), an ICL-inducing agent. Consequently, STIM1-deficient cell lines show higher levels of basal DNA damage, replicative stress, and increased sensitivity to MMC. We show that STIM1 normalizes FANCD2 protein levels in the nucleus, which explains the increased sensitivity of STIM1-KO cells to MMC. This study not only unveils a previously unknown nuclear function for the endoplasmic reticulum protein STIM1 but also expands our understanding of the genes involved in DNA repair.
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Affiliation(s)
- Irene Sanchez-Lopez
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Universidad de Extremadura, Badajoz 06006, Spain
- Institute of Molecular Pathology Biomarkers, Universidad de Extremadura, Badajoz 06006, Spain
| | - Yolanda Orantos-Aguilera
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Universidad de Extremadura, Badajoz 06006, Spain
- Institute of Molecular Pathology Biomarkers, Universidad de Extremadura, Badajoz 06006, Spain
| | - Eulalia Pozo-Guisado
- Institute of Molecular Pathology Biomarkers, Universidad de Extremadura, Badajoz 06006, Spain
- Department of Cell Biology, School of Medicine, Universidad de Extremadura, Badajoz 06006, Spain
| | | | - Sergio Lilla
- CRUK Scotland Institute, Switchback Road, Glasgow G61 1BD, UK
| | - Sara Zanivan
- CRUK Scotland Institute, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Christophe Lachaud
- Cancer Research Centre of Marseille, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli Calmettes, CRCM, Marseille, France
- OPALE Carnot Institute, Paris, France
| | - Francisco Javier Martin-Romero
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Universidad de Extremadura, Badajoz 06006, Spain
- Institute of Molecular Pathology Biomarkers, Universidad de Extremadura, Badajoz 06006, Spain
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Hung YH, Kim Y, Mitchell SB, Thorn TL, Aydemir TB. Absence of Slc39a14/Zip14 in mouse pancreatic beta cells results in hyperinsulinemia. Am J Physiol Endocrinol Metab 2024; 326:E92-E105. [PMID: 38019082 PMCID: PMC11193513 DOI: 10.1152/ajpendo.00117.2023] [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: 04/19/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023]
Abstract
Zinc is an essential component of the insulin protein complex synthesized in β cells. The intracellular compartmentalization and distribution of zinc are controlled by 24 transmembrane zinc transporters belonging to the ZnT or Zrt/Irt-like protein (ZIP) family. Downregulation of SLC39A14/ZIP14 has been reported in pancreatic islets of patients with type 2 diabetes (T2D) as well as mouse models of high-fat diet (HFD)- or db/db-induced obesity. Our previous studies observed mild hyperinsulinemia in mice with whole body knockout of Slc39a14 (Zip14 KO). Based on our current secondary data analysis from an integrative single-cell RNA-seq dataset of human whole pancreatic tissue, SLC39A14 (coding ZIP14) is the only other zinc transporter expressed abundantly in human β cells besides well-known zinc transporter SLC30A8 (coding ZnT8). In the present work, using pancreatic β cell-specific knockout of Slc39a14 (β-Zip14 KO), we investigated the role of SLC39A14/ZIP14-mediated intracellular zinc trafficking in glucose-stimulated insulin secretion and subsequent metabolic responses. Glucose-stimulated insulin secretion, zinc concentrations, and cellular localization of ZIP14 were assessed using in vivo, ex vivo, and in vitro assays using β-Zip14 KO, isolated islets, and murine cell line MIN6. Metabolic evaluations were done on both chow- and HFD-fed mice using time-domain nuclear magnetic resonance and a comprehensive laboratory animal monitoring system. ZIP14 localizes on the endoplasmic reticulum regulating intracellular zinc trafficking in β cells and serves as a negative regulator of glucose-stimulated insulin secretion. Deletion of Zip14 resulted in greater glucose-stimulated insulin secretion, increased energy expenditure, and shifted energy metabolism toward fatty acid utilization. HFD caused β-Zip14 KO mice to develop greater islet hyperplasia, compensatory hyperinsulinemia, and mild insulin resistance and hyperglycemia. This study provided new insights into the contribution of metal transporter ZIP14-mediated intracellular zinc trafficking in glucose-stimulated insulin secretion and subsequent metabolic responses.NEW & NOTEWORTHY Metal transporter SLC39A14/ZIP14 is downregulated in pancreatic islets of patients with T2D and mouse models of HFD- or db/db-induced obesity. However, the function of ZIP14-mediated intracellular zinc trafficking in β cells is unknown. Our analyses revealed that SLC39A14 is the only Zn transporter expressed abundantly in human β cells besides SLC30A8. Within the β cells, ZIP14 is localized on the endoplasmic reticulum and serves as a negative regulator of insulin secretion, providing a potential therapeutic target for T2D.
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Affiliation(s)
- Yu-Han Hung
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
- Department of College of Veterinary Medicine, Cornell University, Ithaca, New York, United States
| | - Yongeun Kim
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Samuel Blake Mitchell
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Trista Lee Thorn
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Tolunay Beker Aydemir
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
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Hu J, Liu Y, Du Y, Peng X, Liu Z. Cellular organelles as drug carriers for disease treatment. J Control Release 2023; 363:114-135. [PMID: 37742846 DOI: 10.1016/j.jconrel.2023.09.038] [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: 04/24/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Organelles not only constitute the basic structure of the cell but also are important in maintaining the normal physiological activities of the cell. With the development of biomimetic nanoscience, researchers have developed technologies to use organelles as drug carriers for disease treatment. Compared with traditional drug carriers, organelle drug carriers have the advantages of good biocompatibility, high drug loading efficiency, and modifiability, and the surface biomarkers of organelles can also participate in intracellular signal transduction to enhance intracellular and intercellular communication, and assist in enhancing the therapeutic effect of drugs. Among different types of organelles, extracellular vesicles, lipid droplets, lysosomes, and mitochondria have been used as drug carriers. This review briefly reviews the biogenesis, isolation methods, and drug-loading methods of four types of organelles, and systematically summarizes the research progress in using organelles as drug-delivery systems for disease treatment. Finally, the challenges faced by organelle-based drug delivery systems are discussed. Although the organelle-based drug delivery systems still face challenges before they can achieve clinical translation, they offer a new direction and vision for the development of next-generation drug carriers.
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Affiliation(s)
- Jiaxin Hu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Yimin Du
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Xingxing Peng
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan Province, PR China.
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8
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Milane LS, Dolare S, Ren G, Amiji M. Combination Organelle Mitochondrial Endoplasmic Reticulum Therapy (COMET) for Multidrug Resistant Breast Cancer. J Control Release 2023; 363:435-451. [PMID: 37717658 DOI: 10.1016/j.jconrel.2023.09.023] [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: 03/15/2023] [Revised: 07/21/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
It is time for the story of mitochondria and intracellular communication in multidrug resistant cancer to be rewritten. Herein we characterize the extent and cellular advantages of mitochondrial network fusion in multidrug resistant (MDR) breast cancer and have designed a novel nanomedicine that disrupts mitochondrial network fusion and systematically manipulates organelle fusion and function. Combination Organelle Mitochondrial Endoplasmic reticulum Therapy (COMET) is an innovative translational nanomedicine for treating MDR triple negative breast cancer (TNBC) that has superior safety and equivalent efficacy to the current standard of care (paclitaxel). Our study has demonstrated that the increased mitochondrial networks in MDR TNBC contribute to apoptotic resistance and network fusion is mediated by mitofusin2 (MFN2) on the outer mitochondrial membrane. COMET consists of three components; Mitochondrial Network Disrupting (MiND) nanoparticles (NPs) that are loaded with an anti-MFN2 peptide, tunicamycin, and Bam7. The therapeutic rationale of COMET is to reduce the apoptotic threshold in MDR cells with MiND NPs, followed by inducing the endoplasmic reticulum mediated unfolded protein response (UPR) by stressing MDR cells with tunicamycin, and finally, directly inducing mitochondrial apoptosis with Bam7 which is a specific bcl-2 Bax activator. MiND NPs are PEGylated liposomes with the 21 amino acid (2577.98 MW) anti-MFN2 peptide compartmentalized in the aqueous core. Hypoxia (0.5% oxygen) was used to create MDR derivatives of MDA-MB-231 cells and BT-549 cells. Mitochondrial networks were quantified using 3D analysis of 60× live cell images acquired with a Keyence BZ-X710 microscope and MiND NPs effectively fragmented mitochondrial networks in drug sensitive and MDR TNBC cells. The IC50 values, combination index, and dose reduction index derived from dose response studies demonstrate that MiND NPs decrease the apoptotic threshold of both drug sensitive and MDR TNBC cells and COMET is a synergistic drug combination. Complex V (ATP synthase) extracted from bovine cardiac mitochondria was used to assess the effect of MiND NPs on OXPHOS; both MiND NPs and anti-MFN2 peptide solution significantly decrease the activity of mitochondrial complex V and decrease the capacity of OXPHOS. A BacMam viral vector based fluorescent biosensor was used to quantify the unfolded protein response (UPR) at the level of the endoplasmic reticulum and tunicamycin specifically induces the UPR in drug sensitive and MDR TNBC cells. A caspase 3 colorimetric assay demonstrated that the synergistic triple drug combination of COMET increases the ability of Bam7 to specifically induce apoptosis. Dose limiting toxicity and off target effects are a significant challenge for current chemotherapy regimens including paclitaxel. COMET has significantly lower cytotoxicity than paclitaxel in human embryonic kidney epithelial cells and has the potential to fulfill the clinical need for safer cancer therapeutics. COMET is a promising early stage translational nanomedicine for treating MDR TNBC. Manipulating intracellular communication and organelle fusion is a novel approach to treating MDR cancer. The data from this study has rewritten the story of mitochondria, organelle fusion, and intracellular communication and by targeting this intersection, COMET is an exciting new chapter in cancer therapeutics that could transform the clinical outcome of MDR TNBC.
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Affiliation(s)
- Lara Scheherazade Milane
- Northeastern University, Department of Pharmaceutical Sciences, 360 Huntington Ave, Boston, MA 02116, United States of America.
| | - Saket Dolare
- Northeastern University, Department of Pharmaceutical Sciences, 360 Huntington Ave, Boston, MA 02116, United States of America
| | - Guangwen Ren
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States of America
| | - Mansoor Amiji
- Northeastern University, Department of Pharmaceutical Sciences, 360 Huntington Ave, Boston, MA 02116, United States of America
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9
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Wang W, Tan J, Liu X, Guo W, Li M, Liu X, Liu Y, Dai W, Hu L, Wang Y, Lu Q, Lee WX, Tang HW, Zhou Q. Cytoplasmic Endonuclease G promotes nonalcoholic fatty liver disease via mTORC2-AKT-ACLY and endoplasmic reticulum stress. Nat Commun 2023; 14:6201. [PMID: 37794041 PMCID: PMC10550995 DOI: 10.1038/s41467-023-41757-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023] Open
Abstract
Endonuclease G (ENDOG), a nuclear-encoded mitochondrial intermembrane space protein, is well known to be translocated into the nucleus during apoptosis. Recent studies have shown that ENDOG might enter the mitochondrial matrix to regulate mitochondrial genome cleavage and replication. However, little is known about the role of ENDOG in the cytosol. Our previous work showed that cytoplasmic ENDOG competitively binds with 14-3-3γ, which released TSC2 to repress mTORC1 signaling and induce autophagy. Here, we demonstrate that cytoplasmic ENDOG could also release Rictor from 14-3-3γ to activate the mTORC2-AKT-ACLY axis, resulting in acetyl-CoA production. Importantly, we observe that ENDOG could translocate to the ER, bind with Bip, and release IRE1a/PERK to activate the endoplasmic reticulum stress response, promoting lipid synthesis. Taken together, we demonstrate that loss of ENDOG suppresses acetyl-CoA production and lipid synthesis, along with reducing endoplasmic reticulum stress, which eventually alleviates high-fat diet-induced nonalcoholic fatty liver disease in female mice.
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Affiliation(s)
- Wenjun Wang
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China.
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Junyang Tan
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xiaomin Liu
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Wenqi Guo
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Mengmeng Li
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xinjie Liu
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Yanyan Liu
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Wenyu Dai
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China
| | - Liubing Hu
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Yimin Wang
- GeneMind Biosciences Company Limited, No. 116, Qingshuihe 1st Road, Luohu District, Shenzhen, Guangdong, 518000, China
| | - Qiuxia Lu
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hong-Wen Tang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Qinghua Zhou
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, Guangdong, 523067, China.
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, Guangdong, 510632, China.
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510632, China.
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10
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Leiro M, Ventura R, Rojo-Querol N, Hernández-Alvarez MI. Endoplasmic Reticulum Isolation: An Optimized Approach into Cells and Mouse Liver Fractionation. Bio Protoc 2023; 13:e4803. [PMID: 37719073 PMCID: PMC10501922 DOI: 10.21769/bioprotoc.4803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 09/19/2023] Open
Abstract
The subfractionation of the endoplasmic reticulum (ER) is a widely used technique in cell biology. However, current protocols present limitations such as low yield, the use of large number of dishes, and contamination with other organelles. Here, we describe an improved method for ER subfractionation that solves other reported methods' main limitations of being time consuming and requiring less starting material. Our protocol involves a combination of different centrifugations and special buffer incubations as well as a fine-tuned method for homogenization followed by western blotting to confirm the purity of the fractions. This protocol contains a method to extract clean ER samples from cells using only five (150 mm) dishes instead of over 50 plates needed in other protocols. In addition, in this article we not only propose a new cell fractionation approach but also an optimized method to isolate pure ER fractions from one mouse liver instead of three, which are commonly used in other protocols. The protocols described here are optimized for time efficiency and designed for seamless execution in any laboratory, eliminating the need for special/patented reagents. Key features • Subcellular fractionation from cells and mouse liver. • Uses only five dishes (150 mm) or one mouse liver to extract highly enriched endoplasmic reticulum without mitochondrial-associated membrane contamination. • These protocols require the use of ultracentrifuges, dounce homogenizers, and/or Teflon Potter Elvehjem. As a result, highly enriched/clean samples are obtained. Graphical overview.
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Affiliation(s)
- Marc Leiro
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raúl Ventura
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Nil Rojo-Querol
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - María Isabel Hernández-Alvarez
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
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11
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Shi TT, Huang Y, Li Y, Dai XL, He YH, Ding JC, Ran T, Shi Y, Yuan Q, Li WJ, Liu W. MAVI1, an endoplasmic reticulum-localized microprotein, suppresses antiviral innate immune response by targeting MAVS on mitochondrion. SCIENCE ADVANCES 2023; 9:eadg7053. [PMID: 37656786 PMCID: PMC10854431 DOI: 10.1126/sciadv.adg7053] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Pattern recognition receptor-mediated innate immunity is critical for host defense against viruses. A growing number of coding and noncoding genes are found to encode microproteins. However, the landscape and functions of microproteins in responsive to virus infection remain uncharacterized. Here, we systematically identified microproteins that are responsive to vesicular stomatitis virus infection. A conserved and endoplasmic reticulum-localized membrane microprotein, MAVI1 (microprotein in antiviral immunity 1), was found to interact with mitochondrion-localized MAVS protein and inhibit MAVS aggregation and type I interferon signaling activation. The importance of MAVI1 was highlighted that viral infection was attenuated and survival rate was increased in Mavi1-knockout mice. A peptide inhibitor targeting the interaction between MAVI1 and MAVS activated the type I interferon signaling to defend viral infection. Our findings uncovered that microproteins play critical roles in regulating antiviral innate immune responses, and targeting microproteins might represent a therapeutic avenue for treating viral infection.
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Affiliation(s)
- Tao-tao Shi
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ying Huang
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ying Li
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Xiang-long Dai
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Yao-hui He
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Jian-cheng Ding
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ting Ran
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), KaiYuan Road, Guangzhou, Guangdong 510530, China
| | - Yang Shi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen-juan Li
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
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12
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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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13
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Sarmento MJ, Llorente A, Petan T, Khnykin D, Popa I, Nikolac Perkovic M, Konjevod M, Jaganjac M. The expanding organelle lipidomes: current knowledge and challenges. Cell Mol Life Sci 2023; 80:237. [PMID: 37530856 PMCID: PMC10397142 DOI: 10.1007/s00018-023-04889-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lipids in cell membranes and subcellular compartments play essential roles in numerous cellular processes, such as energy production, cell signaling and inflammation. A specific organelle lipidome is characterized by lipid synthesis and metabolism, intracellular trafficking, and lipid homeostasis in the organelle. Over the years, considerable effort has been directed to the identification of the lipid fingerprints of cellular organelles. However, these fingerprints are not fully characterized due to the large variety and structural complexity of lipids and the great variability in the abundance of different lipid species. The process becomes even more challenging when considering that the lipidome differs in health and disease contexts. This review summarizes the information available on the lipid composition of mammalian cell organelles, particularly the lipidome of the nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus, plasma membrane and organelles in the endocytic pathway. The lipid compositions of extracellular vesicles and lamellar bodies are also described. In addition, several examples of subcellular lipidome dynamics under physiological and pathological conditions are presented. Finally, challenges in mapping organelle lipidomes are discussed.
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Affiliation(s)
- Maria J Sarmento
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167, Oslo, Norway
- Faculty of Medicine, Centre for Cancer Cell Reprogramming, University of Oslo, Montebello, 0379, Oslo, Norway
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Iuliana Popa
- Pharmacy Department, Bâtiment Henri Moissan, University Paris-Saclay, 17 Avenue des Sciences, 91400, Orsay, France
| | | | - Marcela Konjevod
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Morana Jaganjac
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia.
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14
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Yi J, Wang L, Du J, Wang M, Shen H, Liu Z, Qin Y, Liu J, Hu G, Xiao R, Ding J, Chen X, Wang H, Huang H, Ouyang G, Liu W. ER-localized JmjC domain-containing protein JMJD8 targets STING to promote immune evasion and tumor growth in breast cancer. Dev Cell 2023; 58:760-778.e6. [PMID: 37054705 DOI: 10.1016/j.devcel.2023.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/15/2023] [Accepted: 03/20/2023] [Indexed: 04/15/2023]
Abstract
The STING-mediated type I interferon (IFN) signaling pathway has been shown to play critical roles in antitumor immunity. Here, we demonstrate that an endoplasmic reticulum (ER)-localized JmjC domain-containing protein, JMJD8, inhibits STING-induced type I IFN responses to promote immune evasion and breast tumorigenesis. Mechanistically, JMJD8 competes with TBK1 for binding with STING, blocking STING-TBK1 complex formation and restricting type I IFN and IFN-stimulated gene (ISG) expression as well as immune cell infiltration. JMJD8 knockdown improves the efficacy of chemotherapy and immune checkpoint therapy in treating both human and mouse breast cancer cell-derived implanted tumors. The clinical relevance is highlighted in that JMJD8 is highly expressed in human breast tumor samples, and its expression is inversely correlated with that of type I IFN and ISGs as well as immune cell infiltration. Overall, our study found that JMJD8 regulates type I IFN responses, and targeting JMJD8 triggers antitumor immunity.
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Affiliation(s)
- Jia Yi
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Lei Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jiao Du
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Mingyue Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Haifeng Shen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Zhiying Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao Qin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jing Liu
- Xiamen University-Amogene Joint R&D Center for Genetic Diagnostics, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Guosheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rongquan Xiao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jiancheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Xiaoyan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Hongjiao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Haihua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Dongxia North Road, Shantou, Guangdong 515041, China
| | - Gaoliang Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
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15
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Mitochondrial Lon-induced mitophagy benefits hypoxic resistance via Ca 2+-dependent FUNDC1 phosphorylation at the ER-mitochondria interface. Cell Death Dis 2023; 14:199. [PMID: 36927870 PMCID: PMC10020552 DOI: 10.1038/s41419-023-05723-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023]
Abstract
During hypoxia, FUNDC1 acts as a mitophagy receptor and accumulates at the ER (endoplasmic reticulum)-mitochondria contact sites (EMC), also called mitochondria-associated membranes (MAM). In mitophagy, the ULK1 complex phosphorylates FUNDC1(S17) at the EMC site. However, how mitochondria sense the stress and send the signal from the inside to the outside of mitochondria to trigger mitophagy is still unclear. Mitochondrial Lon was reported to be localized at the EMC under stress although the function remained unknown. In this study, we explored the mechanism of how mitochondrial sensors of hypoxia trigger and stabilize the FUNDC1-ULK1 complex by Lon in the EMC for cell survival and cancer progression. We demonstrated that Lon is accumulated in the EMC and associated with FUNDC1-ULK1 complex to induce mitophagy via chaperone activity under hypoxia. Intriguingly, we found that Lon-induced mitophagy is through binding with mitochondrial Na+/Ca2+ exchanger (NCLX) to promote FUNDC1-ULK1-mediated mitophagy at the EMC site in vitro and in vivo. Accordingly, our findings highlight a novel mechanism responsible for mitophagy initiation under hypoxia by chaperone Lon in mitochondria through the interaction with FUNDC1-ULK1 complex at the EMC site. These findings provide a direct correlation between Lon and mitophagy on cell survival and cancer progression.
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16
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Ganji R, Paulo JA, Xi Y, Kline I, Zhu J, Clemen CS, Weihl CC, Purdy JG, Gygi SP, Raman M. The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition. Nat Commun 2023; 14:638. [PMID: 36746962 PMCID: PMC9902492 DOI: 10.1038/s41467-023-36298-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
The intimate association between the endoplasmic reticulum (ER) and mitochondrial membranes at ER-Mitochondria contact sites (ERMCS) is a platform for critical cellular processes, particularly lipid synthesis. How contacts are remodeled and the impact of altered contacts on lipid metabolism remains poorly understood. We show that the p97 AAA-ATPase and its adaptor ubiquitin-X domain adaptor 8 (UBXD8) regulate ERMCS. The p97-UBXD8 complex localizes to contacts and its loss increases contacts in a manner that is dependent on p97 catalytic activity. Quantitative proteomics and lipidomics of ERMCS demonstrates alterations in proteins regulating lipid metabolism and a significant change in membrane lipid saturation upon UBXD8 deletion. Loss of p97-UBXD8 increased membrane lipid saturation via SREBP1 and the lipid desaturase SCD1. Aberrant contacts can be rescued by unsaturated fatty acids or overexpression of SCD1. We find that the SREBP1-SCD1 pathway is negatively impacted in the brains of mice with p97 mutations that cause neurodegeneration. We propose that contacts are exquisitely sensitive to alterations to membrane lipid composition and saturation.
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Affiliation(s)
- Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yuecheng Xi
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ian Kline
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jiang Zhu
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
- Ilumina Inc., San Diego, CA, USA
| | - Christoph S Clemen
- Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John G Purdy
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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17
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Sun L, Zhang H, Zhang H, Lou X, Wang Z, Wu Y, Yang X, Chen D, Guo B, Zhang A, Qian F. Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia. Nat Microbiol 2023; 8:107-120. [PMID: 36593296 DOI: 10.1038/s41564-022-01278-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/21/2022] [Indexed: 01/03/2023]
Abstract
Staphylococcus aureus invades cells and persists intracellularly, causing persistent inflammation that is notoriously difficult to treat. Here we investigated host-pathogen interactions underlying intracellular S. aureus infection in macrophages and discovered that the endoplasmic reticulum (ER) is an important cellular compartment for intracellular S. aureus infection. Using CRISPR-Cas9 guide RNA library screening, we determined that the autocrine motility factor receptor (AMFR), an ER-resident E3 ubiquitin ligase, played an essential role in mediating intracellular S. aureus-induced inflammation. AMFR directly interacted with TAK1-binding protein 3 (TAB3) in the ER, inducing K27-linked polyubiquitination of TAB3 on lysine 649 and promoting TAK1 activation. Moreover, the virulence factor γ-haemolysin B (HIgB) of S. aureus bound to the AMFR and regulated TAB3. Our findings highlight an unknown role of AMFR in intracellular S. aureus infection-induced pneumonia and suggest that pharmacological interruption of AMFR-mediated TAB3 signalling cascades and HIgB targeting may prevent invasive staphylococci-mediated pneumonia.
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Affiliation(s)
- Lei Sun
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Haibo Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Huihui Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyi Lou
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiming Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yaxian Wu
- Department of Basic Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xinyi Yang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Daijie Chen
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Beining Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Ao Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Qian
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Pharm-X Center, Research Center for Small Molecule Immunological Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
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18
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Halilovic M, Marx-Blümel L, Marx C, Buder K, Beck JF, Sonnemann J. Assessment of HDAC Inhibitor-Induced Endoplasmic Reticulum (ER) Stress. Methods Mol Biol 2023; 2589:253-268. [PMID: 36255630 DOI: 10.1007/978-1-0716-2788-4_17] [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: 06/16/2023]
Abstract
The endoplasmic reticulum (ER) is a multifunctional cell organelle which is important for the folding and processing of proteins. Different endogenous and exogenous factors can disturb the ER homeostasis, causing ER stress and activating the unfolded protein response (UPR) to remove misfolded proteins and aggregates. ER stress and the UPR are associated with several human diseases, such as diabetes, Alzheimer's or Parkinson's disease, and cancer. Histone deacetylase inhibitors (HDACi) are used to treat cancer and were shown to induce ER stress/to modulate the UPR, although the exact mechanism is not fully understood and needs further research. Several approaches to monitoring ER stress exist. Here we describe methods including qPCR, Western blot, transmission electron microscopy, and fluorescence microscopy to analyze changes in mRNA and protein expression levels as well as defects in ER structures after HDAC inhibitor-induced ER stress.
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Affiliation(s)
- Melisa Halilovic
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Lisa Marx-Blümel
- Department of Pediatric Hematology and Oncology, Children's Clinic, Jena University Hospital, Jena, Germany
- Research Center Lobeda, Jena University Hospital, Jena, Germany
| | - Christian Marx
- Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul Ehrlich Institute (PEI), Langen, Germany
| | - Katrin Buder
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - James F Beck
- Department of Pediatric Hematology and Oncology, Children's Clinic, Jena University Hospital, Jena, Germany
| | - Jürgen Sonnemann
- Department of Pediatric Hematology and Oncology, Children's Clinic, Jena University Hospital, Jena, Germany.
- Research Center Lobeda, Jena University Hospital, Jena, Germany.
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19
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Arjona SP, Allen CNS, Santerre M, Gross S, Soboloff J, Booze R, Sawaya BE. Disruption of Mitochondrial-associated ER membranes by HIV-1 tat protein contributes to premature brain aging. CNS Neurosci Ther 2022; 29:365-377. [PMID: 36419337 PMCID: PMC9804058 DOI: 10.1111/cns.14011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/04/2022] [Accepted: 10/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Mitochondrial-associated ER membranes (MAMs) control many cellular functions, including calcium and lipid exchange, intracellular trafficking, and mitochondrial biogenesis. The disruption of these functions contributes to neurocognitive disorders, such as spatial memory impairment and premature brain aging. Using neuronal cells, we demonstrated that HIV-1 Tat protein deregulates the mitochondria. METHODS& RESULTS To determine the mechanisms, we used a neuronal cell line and showed that Tat-induced changes in expression and interactions of both MAM-associated proteins and MAM tethering proteins. The addition of HIV-1 Tat protein alters expression levels of PTPIP51 and VAPB proteins in the MAM fraction but not the whole cell. Phosphorylation of PTPIP51 protein regulates its subcellular localization and function. We demonstrated that the Tat protein promotes PTPIP51 phosphorylation on tyrosine residues and prevents its binding to VAPB. Treatment of the cells with a kinase inhibitor restores the PTPIP51-VAPB interaction and overcomes the effect of Tat. CONCLUSION These results suggest that Tat disrupts the MAM, through the induction of PTPIP51 phosphorylation, leading to ROS accumulation, mitochondrial stress, and altered movement. Hence, we concluded that interfering in the MAM-associated cellular pathways contributes to spatial memory impairment and premature brain aging often observed in HIV-1-infected patients.
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Affiliation(s)
- Sterling P. Arjona
- Molecular Studies of Neurodegenerative Diseases Lab, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Charles N. S. Allen
- Molecular Studies of Neurodegenerative Diseases Lab, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Maryline Santerre
- Molecular Studies of Neurodegenerative Diseases Lab, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Scott Gross
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Jonathan Soboloff
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Rosemarie Booze
- Program of Behavioral Neuroscience, Department of PsychologyUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Bassel E. Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA,Department of Cancer and Cellular BiologyLewis Katz School of Medicine, Temple UniversityPhiladelphiaPennsylvaniaUSA,Department of Neural SciencesLewis Katz School of Medicine, Temple UniversityPhiladelphiaPennsylvaniaUSA
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20
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Shi C, Wang Y, Wu M, Chen Y, Liu F, Shen Z, Wang Y, Xie S, Shen Y, Sang L, Zhang Z, Gao Z, Yang L, Qu L, Yang Z, He X, Guo Y, Pan C, Che J, Ju H, Liu J, Cai Z, Yan Q, Yu L, Wang L, Dong X, Xu P, Shao J, Liu Y, Li X, Wang W, Zhou R, Zhou T, Lin A. Promoting anti-tumor immunity by targeting TMUB1 to modulate PD-L1 polyubiquitination and glycosylation. Nat Commun 2022; 13:6951. [PMID: 36376293 PMCID: PMC9663433 DOI: 10.1038/s41467-022-34346-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Immune checkpoint blockade therapies targeting the PD-L1/PD-1 axis have demonstrated clear clinical benefits. Improved understanding of the underlying regulatory mechanisms might contribute new insights into immunotherapy. Here, we identify transmembrane and ubiquitin-like domain-containing protein 1 (TMUB1) as a modulator of PD-L1 post-translational modifications in tumor cells. Mechanistically, TMUB1 competes with HECT, UBA and WWE domain-containing protein 1 (HUWE1), a E3 ubiquitin ligase, to interact with PD-L1 and inhibit its polyubiquitination at K281 in the endoplasmic reticulum. Moreover, TMUB1 enhances PD-L1 N-glycosylation and stability by recruiting STT3A, thereby promoting PD-L1 maturation and tumor immune evasion. TMUB1 protein levels correlate with PD-L1 expression in human tumor tissue, with high expression being associated with poor patient survival rates. A synthetic peptide engineered to compete with TMUB1 significantly promotes antitumor immunity and suppresses tumor growth in mice. These findings identify TMUB1 as a promising immunotherapeutic target.
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Affiliation(s)
- Chengyu Shi
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China
| | - Ying Wang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China
| | - Minjie Wu
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China
| | - Yu Chen
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China
| | - Fangzhou Liu
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China
| | - Zheyuan Shen
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, Zhejiang 310016 China ,grid.13402.340000 0004 1759 700XHangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Yiran Wang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Shaofang Xie
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang 310024 China
| | - Yingying Shen
- grid.13402.340000 0004 1759 700XInstitute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China
| | - Lingjie Sang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Zhen Zhang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Zerui Gao
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Luojia Yang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Lei Qu
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Zuozhen Yang
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Xinyu He
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Yu Guo
- grid.13402.340000 0004 1759 700XHangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Chenghao Pan
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, Zhejiang 310016 China ,grid.13402.340000 0004 1759 700XHangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Jinxin Che
- grid.13402.340000 0004 1759 700XHangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Huaiqiang Ju
- grid.12981.330000 0001 2360 039XSun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060 China
| | - Jian Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, Zhejiang 314400 China
| | - Zhijian Cai
- grid.13402.340000 0004 1759 700XInstitute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China
| | - Qingfeng Yan
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Luyang Yu
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Liangjing Wang
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, the Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang China
| | - Xiaowu Dong
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, Zhejiang 310016 China ,grid.13402.340000 0004 1759 700XHangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Pinglong Xu
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Jianzhong Shao
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Yang Liu
- grid.13402.340000 0004 1759 700XInstitute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China
| | - Xu Li
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang 310024 China
| | - Wenqi Wang
- grid.266093.80000 0001 0668 7243Department of Developmental and Cell Biology, University of California, Irvine; Irvine, CA 92697 USA
| | - Ruhong Zhou
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XShanghai Institute for Advanced Study, Zhejiang University, 201203 Shanghai, China ,grid.21729.3f0000000419368729Department of Chemistry, Colombia University, New York City, NY 10027 USA ,grid.13402.340000 0004 1759 700XInstitute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Tianhua Zhou
- grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, the Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang 310009 China
| | - Aifu Lin
- grid.13402.340000 0004 1759 700XMOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, Zhejiang 310058 China ,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XBreast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003 China ,grid.13402.340000 0004 1759 700XInternational School of Medicine, International Institutes of Medicine, The 4th Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang 322000 China ,grid.13402.340000 0004 1759 700XZJU-QILU Joint Research Institute, Hangzhou, Zhejiang 310058 China
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21
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Gómez-Mellado VE, Chang JC, Ho-Mok KS, Bernardino Morcillo C, Kersten RHJ, Oude Elferink RPJ, Verhoeven AJ, Paulusma CC. ATP8B1 Deficiency Results in Elevated Mitochondrial Phosphatidylethanolamine Levels and Increased Mitochondrial Oxidative Phosphorylation in Human Hepatoma Cells. Int J Mol Sci 2022; 23:ijms232012344. [PMID: 36293199 PMCID: PMC9604224 DOI: 10.3390/ijms232012344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/20/2022] Open
Abstract
ATP8B1 is a phospholipid flippase that is deficient in patients with progressive familial intrahepatic cholestasis type 1 (PFIC1). PFIC1 patients suffer from severe liver disease but also present with dyslipidemia, including low plasma cholesterol, of yet unknown etiology. Here we show that ATP8B1 knockdown in HepG2 cells leads to a strong increase in the mitochondrial oxidative phosphorylation (OXPHOS) without a change in glycolysis. The enhanced OXPHOS coincides with elevated low-density lipoprotein receptor protein and increased mitochondrial fragmentation and phosphatidylethanolamine levels. Furthermore, expression of phosphatidylethanolamine N-methyltransferase, an enzyme that catalyzes the conversion of mitochondrial-derived phosphatidylethanolamine to phosphatidylcholine, was reduced in ATP8B1 knockdown cells. We conclude that ATP8B1 deficiency results in elevated mitochondrial PE levels that stimulate mitochondrial OXPHOS. The increased OXPHOS leads to elevated LDLR levels, which provides a possible explanation for the reduced plasma cholesterol levels in PFIC1 disease.
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Affiliation(s)
- Valentina E. Gómez-Mellado
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Jung-Chin Chang
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Kam S. Ho-Mok
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Carmen Bernardino Morcillo
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
| | - Remco H. J. Kersten
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Ronald P. J. Oude Elferink
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Arthur J. Verhoeven
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Coen C. Paulusma
- Amsterdam UMC, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
- Correspondence:
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22
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Spears ME, Lee N, Hwang S, Park SJ, Carlisle AE, Li R, Doshi MB, Armando AM, Gao J, Simin K, Zhu LJ, Greer PL, Quehenberger O, Torres EM, Kim D. De novo sphingolipid biosynthesis necessitates detoxification in cancer cells. Cell Rep 2022; 40:111415. [PMID: 36170811 PMCID: PMC9552870 DOI: 10.1016/j.celrep.2022.111415] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Sphingolipids play important signaling and structural roles in cells. Here, we find that during de novo sphingolipid biosynthesis, a toxic metabolite is formed with critical implications for cancer cell survival. The enzyme catalyzing the first step in this pathway, serine palmitoyltransferase complex (SPT), is upregulated in breast and other cancers. SPT is dispensable for cancer cell proliferation, as sphingolipids can be salvaged from the environment. However, SPT activity introduces a liability as its product, 3-ketodihydrosphingosine (3KDS), is toxic and requires clearance via the downstream enzyme 3-ketodihydrosphingosine reductase (KDSR). In cancer cells, but not normal cells, targeting KDSR induces toxic 3KDS accumulation leading to endoplasmic reticulum (ER) dysfunction and loss of proteostasis. Furthermore, the antitumor effect of KDSR disruption can be enhanced by increasing metabolic input (via high-fat diet) to allow greater 3KDS production. Thus, de novo sphingolipid biosynthesis entails a detoxification requirement in cancer cells that can be therapeutically exploited.
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Affiliation(s)
- Meghan E Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sunyoung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anne E Carlisle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Mihir B Doshi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aaron M Armando
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Jenny Gao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Oswald Quehenberger
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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23
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Tábara LC, Al-Salmi F, Maroofian R, Al-Futaisi AM, Al-Murshedi F, Kennedy J, Day JO, Courtin T, Al-Khayat A, Galedari H, Mazaheri N, Protasoni M, Johnson M, Leslie JS, Salter CG, Rawlins LE, Fasham J, Al-Maawali A, Voutsina N, Charles P, Harrold L, Keren B, Kunji ERS, Vona B, Jelodar G, Sedaghat A, Shariati G, Houlden H, Crosby AH, Prudent J, Baple EL. TMEM63C mutations cause mitochondrial morphology defects and underlie hereditary spastic paraplegia. Brain 2022; 145:3095-3107. [PMID: 35718349 PMCID: PMC9473353 DOI: 10.1093/brain/awac123] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/10/2022] [Accepted: 03/13/2022] [Indexed: 02/02/2023] Open
Abstract
The hereditary spastic paraplegias (HSP) are among the most genetically diverse of all Mendelian disorders. They comprise a large group of neurodegenerative diseases that may be divided into 'pure HSP' in forms of the disease primarily entailing progressive lower-limb weakness and spasticity, and 'complex HSP' when these features are accompanied by other neurological (or non-neurological) clinical signs. Here, we identified biallelic variants in the transmembrane protein 63C (TMEM63C) gene, encoding a predicted osmosensitive calcium-permeable cation channel, in individuals with hereditary spastic paraplegias associated with mild intellectual disability in some, but not all cases. Biochemical and microscopy analyses revealed that TMEM63C is an endoplasmic reticulum-localized protein, which is particularly enriched at mitochondria-endoplasmic reticulum contact sites. Functional in cellula studies indicate a role for TMEM63C in regulating both endoplasmic reticulum and mitochondrial morphologies. Together, these findings identify autosomal recessive TMEM63C variants as a cause of pure and complex HSP and add to the growing evidence of a fundamental pathomolecular role of perturbed mitochondrial-endoplasmic reticulum dynamics in motor neurone degenerative diseases.
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Affiliation(s)
- Luis Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Fatema Al-Salmi
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Reza Maroofian
- UCL Queen Square Institute of Neurology, University College
London, London WC1E 6BT, UK
| | - Amna Mohammed Al-Futaisi
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Joanna Kennedy
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Clinical Genetics, University Hospitals Bristol,
Bristol BS2 8EG, UK
| | - Jacob O Day
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Faculty of Health, University of Plymouth,
Plymouth PL4 8AA, UK
| | - Thomas Courtin
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Aisha Al-Khayat
- Department of Biology, College of Science, Sultan Qaboos
University, Muscat, Oman
| | - Hamid Galedari
- Department of Genetics, Faculty of Science, Shahid Chamran University of
Ahvaz, Ahvaz, Iran
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of
Ahvaz, Ahvaz, Iran
| | - Margherita Protasoni
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Mark Johnson
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Joseph S Leslie
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Claire G Salter
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Lettie E Rawlins
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
| | - James Fasham
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
| | - Almundher Al-Maawali
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Nikol Voutsina
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Perrine Charles
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Laura Harrold
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Boris Keren
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Barbara Vona
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing
Research Centre, Eberhard Karls University Tübingen,
Tübingen, Germany
| | - Gholamreza Jelodar
- Pediatric Neurology, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
| | - Alireza Sedaghat
- Health Research Institute, Diabetes Research Center, Ahvaz Jundishapur
University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Department of Medical Genetic, Faculty of Medicine, Ahvaz Jundishapur,
University of Medical Sciences, Ahvaz, Iran
| | - Henry Houlden
- UCL Queen Square Institute of Neurology, University College
London, London WC1E 6BT, UK
| | - Andrew H Crosby
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Emma L Baple
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
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24
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Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy. Nat Commun 2022; 13:5164. [PMID: 36056001 PMCID: PMC9440083 DOI: 10.1038/s41467-022-32564-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
Mitophagy is essential to maintain mitochondrial function and prevent diseases. It activates upon mitochondria depolarization, which causes PINK1 stabilization on the mitochondrial outer membrane. Strikingly, a number of conditions, including mitochondrial protein misfolding, can induce mitophagy without a loss in membrane potential. The underlying molecular details remain unclear. Here, we report that a loss of mitochondrial protein import, mediated by the pre-sequence translocase-associated motor complex PAM, is sufficient to induce mitophagy in polarized mitochondria. A genome-wide CRISPR/Cas9 screen for mitophagy inducers identifies components of the PAM complex. Protein import defects are able to induce mitophagy without a need for depolarization. Upon mitochondrial protein misfolding, PAM dissociates from the import machinery resulting in decreased protein import and mitophagy induction. Our findings extend the current mitophagy model to explain mitophagy induction upon conditions that do not affect membrane polarization, such as mitochondrial protein misfolding. Mitophagy activation is mediated by mitochondrial depolarization. Here, the authors show that mitochondrial protein misfolding can activate mitophagy in a depolarization-independent manner mediated by a protein import reduction.
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25
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Feehan RP, Coleman CS, Ebanks S, Lang CH, Shantz LM. REDD1 interacts with AIF and regulates mitochondrial reactive oxygen species generation in the keratinocyte response to UVB. Biochem Biophys Res Commun 2022; 616:56-62. [DOI: 10.1016/j.bbrc.2022.05.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/18/2022] [Indexed: 12/20/2022]
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26
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Hémono M, Haller A, Chicher J, Duchêne AM, Ngondo RP. The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. BMC Biol 2022; 20:13. [PMID: 35012549 PMCID: PMC8744257 DOI: 10.1186/s12915-021-01213-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/14/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Mitochondria require thousands of proteins to fulfill their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability, or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals. RESULTS Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain. CONCLUSIONS Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.
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Affiliation(s)
- Mickaële Hémono
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
| | - Alexandre Haller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
| | - Richard Patryk Ngondo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France.
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27
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Mito-TIPTP Increases Mitochondrial Function by Repressing the Rubicon-p22phox Interaction in Colitis-Induced Mice. Antioxidants (Basel) 2021; 10:antiox10121954. [PMID: 34943057 PMCID: PMC8750874 DOI: 10.3390/antiox10121954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
The run/cysteine-rich-domain-containing Beclin1-interacting autophagy protein (Rubicon) is essential for the regulation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase by interacting with p22phox to trigger the production of reactive oxygen species (ROS) in immune cells. In a previous study, we demonstrated that the interaction of Rubicon with p22phox increases cellular ROS levels. The correlation between Rubicon and mitochondrial ROS (mtROS) is poorly understood. Here, we report that Rubicon interacts with p22phox in the outer mitochondrial membrane in macrophages and patients with human ulcerative colitis. Upon lipopolysaccharide (LPS) activation, the binding of Rubicon to p22phox was elevated, and increased not only cellular ROS levels but also mtROS, with an impairment of mitochondrial complex III and mitochondrial biogenesis in macrophages. Furthermore, increased Rubicon decreases mitochondrial metabolic flux in macrophages. Mito-TIPTP, which is a p22phox inhibitor containing a mitochondrial translocation signal, enhances mitochondrial function by inhibiting the association between Rubicon and p22phox in LPS-primed bone-marrow-derived macrophages (BMDMs) treated with adenosine triphosphate (ATP) or dextran sulfate sodium (DSS). Remarkably, Mito-TIPTP exhibited a therapeutic effect by decreasing mtROS in DSS-induced acute or chronic colitis mouse models. Thus, our findings suggest that Mito-TIPTP is a potential therapeutic agent for colitis by inhibiting the interaction between Rubicon and p22phox to recover mitochondrial function.
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28
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Ranjan K, Hedl M, Sinha S, Zhang X, Abraham C. Ubiquitination of ATF6 by disease-associated RNF186 promotes the innate receptor-induced unfolded protein response. J Clin Invest 2021; 131:145472. [PMID: 34623328 DOI: 10.1172/jci145472] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 07/20/2021] [Indexed: 02/05/2023] Open
Abstract
Properly balancing microbial responses by the innate immune system through pattern recognition receptors (PRRs) is critical for intestinal immune homeostasis. Ring finger protein 186 (RNF186) genetic variants are associated with inflammatory bowel disease (IBD). However, functions for the E3 ubiquitin ligase RNF186 are incompletely defined. We found that upon stimulation of the PRR nucleotide-binding oligomerization domain containing 2 (NOD2) in human macrophages, RNF186 localized to the ER, formed a complex with ER stress sensors, ubiquitinated the ER stress sensor activating transcription factor 6 (ATF6), and promoted the unfolded protein response (UPR). These events, in turn, led to downstream signaling, cytokine secretion, and antimicrobial pathway induction. Importantly, RNF186-mediated ubiquitination of K152 on ATF6 was required for these outcomes, highlighting a key role for ATF6 ubiquitination in PRR-initiated functions. Human macrophages transfected with the rare RNF186-A64T IBD risk variant and macrophages from common rs6426833 RNF186 IBD risk carriers demonstrated reduced NOD2-induced outcomes, which were restored by rescuing UPR signaling. Mice deficient in RNF186 or ATF6 demonstrated a reduced UPR in colonic tissues, increased weight loss, and less effective clearance of bacteria with dextran sodium sulfate-induced injury and upon oral challenge with Salmonella Typhimurium. Therefore, we identified that RNF186 was required for PRR-induced, UPR-associated signaling leading to key macrophage functions; defined that RNF186-mediated ubiquitination of ATF6 was essential for these functions; and elucidated how RNF186 IBD risk variants modulated these outcomes.
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Affiliation(s)
- Kishu Ranjan
- Department of Internal Medicine, Section of Digestive Diseases, and
| | - Matija Hedl
- Department of Internal Medicine, Section of Digestive Diseases, and
| | - Saloni Sinha
- Department of Internal Medicine, Section of Digestive Diseases, and
| | - Xuchen Zhang
- Department of Pathology, Yale University, New Haven, Connecticut, USA
| | - Clara Abraham
- Department of Internal Medicine, Section of Digestive Diseases, and
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29
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Chen Q, Coto-Llerena M, Suslov A, Teixeira RD, Fofana I, Nuciforo S, Hofmann M, Thimme R, Hensel N, Lohmann V, Ng CKY, Rosenberger G, Wieland S, Heim MH. Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses. Nat Commun 2021; 12:4882. [PMID: 34385466 PMCID: PMC8360984 DOI: 10.1038/s41467-021-25218-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic variants of the interferon lambda (IFNL) gene locus are strongly associated with spontaneous and IFN treatment-induced clearance of hepatitis C virus (HCV) infections. Individuals with the ancestral IFNL4-dG allele are not able to clear HCV in the acute phase and have more than a 90% probability to develop chronic hepatitis C (CHC). Paradoxically, the IFNL4-dG allele encodes a fully functional IFNλ4 protein with antiviral activity against HCV. Here we describe an effect of IFNλ4 on HCV antigen presentation. Only minor amounts of IFNλ4 are secreted, because the protein is largely retained in the endoplasmic reticulum (ER) where it induces ER stress. Stressed cells are significantly weaker activators of HCV specific CD8+ T cells than unstressed cells. This is not due to reduced MHC I surface presentation or extracellular IFNλ4 effects, since T cell responses are restored by exogenous loading of MHC with HCV antigens. Rather, IFNλ4 induced ER stress impairs HCV antigen processing and/or loading onto the MHC I complex. Our results provide a potential explanation for the IFNλ4-HCV paradox.
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Affiliation(s)
- Qian Chen
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Aleksei Suslov
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Isabel Fofana
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sandro Nuciforo
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Maike Hofmann
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Nina Hensel
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research (CIID), University of Heidelberg, Heidelberg, Germany
| | - Charlotte K Y Ng
- Department for BioMedical Research (DBMR), Oncogenomics Lab, University of Bern, Bern, Switzerland
| | | | - Stefan Wieland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus H Heim
- Department of Biomedicine, University of Basel, Basel, Switzerland. .,Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland.
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30
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Structural and Functional Alterations in Mitochondria-Associated Membranes (MAMs) and in Mitochondria Activate Stress Response Mechanisms in an In Vitro Model of Alzheimer's Disease. Biomedicines 2021; 9:biomedicines9080881. [PMID: 34440085 PMCID: PMC8389659 DOI: 10.3390/biomedicines9080881] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease (AD) is characterized by the accumulation of extracellular plaques composed by amyloid-β (Aβ) and intracellular neurofibrillary tangles of hyperphosphorylated tau. AD-related neurodegenerative mechanisms involve early changes of mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs) and impairment of cellular events modulated by these subcellular domains. In this study, we characterized the structural and functional alterations at MAM, mitochondria, and ER/microsomes in a mouse neuroblastoma cell line (N2A) overexpressing the human amyloid precursor protein (APP) with the familial Swedish mutation (APPswe). Proteins levels were determined by Western blot, ER-mitochondria contacts were quantified by transmission electron microscopy, and Ca2+ homeostasis and mitochondria function were analyzed using fluorescent probes and Seahorse assays. In this in vitro AD model, we found APP accumulated in MAM and mitochondria, and altered levels of proteins implicated in ER-mitochondria tethering, Ca2+ signaling, mitochondrial dynamics, biogenesis and protein import, as well as in the stress response. Moreover, we observed a decreased number of close ER-mitochondria contacts, activation of the ER unfolded protein response, reduced Ca2+ transfer from ER to mitochondria, and impaired mitochondrial function. Together, these results demonstrate that several subcellular alterations occur in AD-like neuronal cells, which supports that the defective ER-mitochondria crosstalk is an important player in AD physiopathology.
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31
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Cheng LC, Zheng D, Zhang Q, Guvenek A, Cheng H, Tian B. Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum. Cell Rep 2021; 36:109407. [PMID: 34289366 PMCID: PMC8501909 DOI: 10.1016/j.celrep.2021.109407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/17/2021] [Accepted: 06/23/2021] [Indexed: 12/28/2022] Open
Abstract
Transcripts encoding membrane and secreted proteins are known to associate with the endoplasmic reticulum (ER) through translation. Here, using cell fractionation, polysome profiling, and 3' end sequencing, we show that transcripts differ substantially in translation-independent ER association (TiERA). Genes in certain functional groups, such as cell signaling, tend to have significantly higher TiERA potentials than others, suggesting the importance of ER association for their mRNA metabolism, such as localized translation. The TiERA potential of a transcript is determined largely by size, sequence content, and RNA structures. Alternative polyadenylation (APA) isoforms can have distinct TiERA potentials because of changes in transcript features. The widespread 3' UTR lengthening in cell differentiation leads to greater transcript association with the ER, especially for genes that are capable of expressing very long 3' UTRs. Our data also indicate that TiERA is in dynamic competition with translation-dependent ER association, suggesting limited space on the ER for mRNA association.
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Affiliation(s)
- Larry C Cheng
- Program in Gene Expression and Regulation and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, Piscataway, NJ 08854, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Qiang Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Rutgers School of Graduate Studies, Newark, NJ 07103, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Tian
- Program in Gene Expression and Regulation and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, Piscataway, NJ 08854, USA; Rutgers School of Graduate Studies, Newark, NJ 07103, USA.
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32
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Wang N, Wang C, Zhao H, He Y, Lan B, Sun L, Gao Y. The MAMs Structure and Its Role in Cell Death. Cells 2021; 10:cells10030657. [PMID: 33809551 PMCID: PMC7999768 DOI: 10.3390/cells10030657] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
The maintenance of cellular homeostasis involves the participation of multiple organelles. These organelles are associated in space and time, and either cooperate or antagonize each other with regards to cell function. Crosstalk between organelles has become a significant topic in research over recent decades. We believe that signal transduction between organelles, especially the endoplasmic reticulum (ER) and mitochondria, is a factor that can influence the cell fate. As the cellular center for protein folding and modification, the endoplasmic reticulum can influence a range of physiological processes by regulating the quantity and quality of proteins. Mitochondria, as the cellular "energy factory," are also involved in cell death processes. Some researchers regard the ER as the sensor of cellular stress and the mitochondria as an important actuator of the stress response. The scientific community now believe that bidirectional communication between the ER and the mitochondria can influence cell death. Recent studies revealed that the death signals can shuttle between the two organelles. Mitochondria-associated membranes (MAMs) play a vital role in the complex crosstalk between the ER and mitochondria. MAMs are known to play an important role in lipid synthesis, the regulation of Ca2+ homeostasis, the coordination of ER-mitochondrial function, and the transduction of death signals between the ER and the mitochondria. Clarifying the structure and function of MAMs will provide new concepts for studying the pathological mechanisms associated with neurodegenerative diseases, aging, and cancers. Here, we review the recent studies of the structure and function of MAMs and its roles involved in cell death, especially in apoptosis.
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Affiliation(s)
- Nan Wang
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
| | - Chong Wang
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
| | - Hongyang Zhao
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
| | - Yichun He
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
| | - Beiwu Lan
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
| | - Liankun Sun
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130012, China
- Correspondence: (L.S.); (Y.G.)
| | - Yufei Gao
- China Japan Union Hospital, Jilin University, Changchun 130031, China; (N.W.); (C.W.); (H.Z.); (Y.H.); (B.L.)
- Correspondence: (L.S.); (Y.G.)
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33
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Gan ES, Tan HC, Le DHT, Huynh TT, Wills B, Seidah NG, Ooi EE, Yacoub S. Dengue virus induces PCSK9 expression to alter antiviral responses and disease outcomes. J Clin Invest 2021; 130:5223-5234. [PMID: 32644974 PMCID: PMC7524462 DOI: 10.1172/jci137536] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022] Open
Abstract
Dengue virus (DENV) infection requires cholesterol as a proviral factor, although statin treatment did not show antiviral efficacy in patients with dengue. Here, we show that DENV infection manipulated cholesterol metabolism in cells residing in low-oxygen microenvironments (hypoxia) such as in the liver, spleen, and lymph nodes. DENV infection induced expression of proprotein convertase subtilisin/kexin type 9 (PCSK9), which reduces low-density lipoprotein receptor (LDLR) recycling and hence cholesterol uptake. We found that, whereas LDLR uptake would have distributed cholesterol throughout the various cell compartments, de novo cholesterol synthesis enriched this lipid in the endoplasmic reticulum (ER). With cholesterol enrichment in the ER, ER-resident STING and type I IFN (IFN) activation was repressed during DENV infection. Our in vitro findings were further supported by the detection of elevated plasma PCSK9 levels in patients with dengue with high viremia and increased severity of plasma leakage. Our findings therefore suggest that PCSK9 plays a hitherto unrecognized role in dengue pathogenesis and that PCSK9 inhibitors could be a suitable host-directed treatment for patients with dengue.
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Affiliation(s)
| | - Hwee Cheng Tan
- Duke-National University of Singapore Medical School, Singapore
| | - Duyen Huynh Thi Le
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Trieu Trung Huynh
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Bridget Wills
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Nabil G Seidah
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute, Université de Montréal, Montréal, Québec, Canada
| | - Eng Eong Ooi
- Duke-National University of Singapore Medical School, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,SingHealth Duke-National University of Singapore Global Health Institute, Singapore.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore MIT Alliance in Research and Technology, Singapore
| | - Sophie Yacoub
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore MIT Alliance in Research and Technology, Singapore
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34
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Xu J, Taubert S. Beyond Proteostasis: Lipid Metabolism as a New Player in ER Homeostasis. Metabolites 2021; 11:52. [PMID: 33466824 PMCID: PMC7830277 DOI: 10.3390/metabo11010052] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Biological membranes are not only essential barriers that separate cellular and subcellular structures, but also perform other critical functions such as the initiation and propagation of intra- and intercellular signals. Each membrane-delineated organelle has a tightly regulated and custom-made membrane lipid composition that is critical for its normal function. The endoplasmic reticulum (ER) consists of a dynamic membrane network that is required for the synthesis and modification of proteins and lipids. The accumulation of unfolded proteins in the ER lumen activates an adaptive stress response known as the unfolded protein response (UPR-ER). Interestingly, recent findings show that lipid perturbation is also a direct activator of the UPR-ER, independent of protein misfolding. Here, we review proteostasis-independent UPR-ER activation in the genetically tractable model organism Caenorhabditis elegans. We review the current knowledge on the membrane lipid composition of the ER, its impact on organelle function and UPR-ER activation, and its potential role in human metabolic diseases. Further, we summarize the bi-directional interplay between lipid metabolism and the UPR-ER. We discuss recent progress identifying the different respective mechanisms by which disturbed proteostasis and lipid bilayer stress activate the UPR-ER. Finally, we consider how genetic and metabolic disturbances may disrupt ER homeostasis and activate the UPR and discuss how using -omics-type analyses will lead to more comprehensive insights into these processes.
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Affiliation(s)
- Jiaming Xu
- Graduate Program in Cell and Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Healthy Starts Theme, British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Stefan Taubert
- Graduate Program in Cell and Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Healthy Starts Theme, British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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35
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Huang C, Hedl M, Ranjan K, Abraham C. LACC1 Required for NOD2-Induced, ER Stress-Mediated Innate Immune Outcomes in Human Macrophages and LACC1 Risk Variants Modulate These Outcomes. Cell Rep 2020; 29:4525-4539.e4. [PMID: 31875558 DOI: 10.1016/j.celrep.2019.11.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 09/17/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
LACC1 genetic variants are associated with multiple immune-mediated diseases. However, laccase domain containing-1 (LACC1) functions are incompletely defined. We find that upon stimulation of the pattern-recognition receptor (PRR) NOD2, LACC1 localizes to the endoplasmic reticulum (ER) and forms a complex with ER-stress sensors. All three ER-stress branches, PERK, IRE1α, and ATF6, are required for NOD2-induced signaling, cytokines, and antimicrobial pathways in human macrophages. LACC1, and its localization to the ER, is required for these outcomes. Relative to wild-type (WT) LACC1, transfection of the common Val254 and rare Arg284 immune-mediated disease-risk LACC1 variants into HeLa cells and macrophages, as well as macrophages from LACC1 Val254 carriers, shows reduced NOD2-induced ER stress-associated outcomes; these downstream outcomes are restored by rescuing ER stress. Therefore, we identify ER stress to be essential in PRR-induced outcomes in macrophages, define a critical role for LACC1 in these ER stress-dependent events, and elucidate how LACC1 disease-risk variants mediate these outcomes.
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Affiliation(s)
- Chen Huang
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT 06510, USA
| | - Matija Hedl
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT 06510, USA
| | - Kishu Ranjan
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT 06510, USA
| | - Clara Abraham
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT 06510, USA.
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36
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Davoudi M, Moradi-Sardareh H, Emamgholipour S, Nabatchian F, Paknejad M. The possible effect of silver nanoparticles on glyceraldehyde-3-phosphate dehydrogenase activity and formation of amyloid-like aggregates in MCF-7 cell line. IUBMB Life 2020; 72:2214-2224. [PMID: 32819028 DOI: 10.1002/iub.2362] [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: 05/28/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 11/06/2022]
Abstract
Silver nanoparticles (AgNPs) are widely used in medicine, however, the underlying mechanisms of their action on cellular signaling have not been completely determined, and fundamental studies are required to clarify them. We aimed to investigate AgNPs effects on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as both the internal control gene and the redox-sensitive enzyme involved in apoptosis-related pathways and the formation of amyloid aggregates. To achieve this purpose, MCF-7 cells were treated with different concentrations (0, 3, 22, and 200 μg/ml) of AgNPs and then cell viability, generation of reactive oxygen species (ROS), induction of apoptosis, expression of GAPDH gene, the formation of amyloid aggregates, and GAPDH activity were assessed. The results indicated that treatment with AgNPs significantly reduced cell viability and increased apoptosis in a dose-dependent manner. The ROS levels increased at lower concentrations of AgNPs (up to 22 μg/ml) and during short-term exposure (30 min). The level of GAPDH gene expression was significantly upregulated by 1.22, 1.47, and 1.56 fold, in the concentrations of 3, 22, and 200 μg/ml, respectively. The amount of amyloid aggregates was significantly increased in a dose-dependent manner. The results of enzyme activity showed that AgNPs were affected on the activity of GAPDH protein, however, it has fluctuated that could not be interpreted by our limited data. In conclusion, our results suggested that AgNPs could affect the GAPDH gene expression and enzyme activity, therefore the selection of GAPDH as a gene and protein internal control in the (AgNPs)-related studies requires careful consideration. Additionally, AgNPs may cause apoptosis due to the increase in the production of amyloid aggregates.
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Affiliation(s)
- Maryam Davoudi
- Department of Medical Laboratory, School of Allied Health Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hemen Moradi-Sardareh
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Solaleh Emamgholipour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Nabatchian
- Department of Medical Laboratory, School of Allied Health Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maliheh Paknejad
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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37
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Wang WX, Prajapati P, Nelson PT, Springer JE. The Mitochondria-Associated ER Membranes Are Novel Subcellular Locations Enriched for Inflammatory-Responsive MicroRNAs. Mol Neurobiol 2020; 57:2996-3013. [PMID: 32451872 PMCID: PMC7320068 DOI: 10.1007/s12035-020-01937-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022]
Abstract
The mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs) are specific ER domains that contact the mitochondria and function to facilitate communication between ER and mitochondria. Disruption of contact between the mitochondria and ER is associated with a variety of pathophysiological conditions including neurodegenerative diseases. Considering the many cellular functions of MAMs, we hypothesized that MAMs play an important role in regulating microRNA (miRNA) activity linked to its unique location between mitochondria and ER. Here we present new findings from human and rat brains indicating that the MAMs are subcellular sites enriched for specific miRNAs. We employed subcellular fractionation and TaqMan® RT-qPCR miRNA analysis to quantify miRNA levels in subcellular fractions isolated from male rat brains and six human brain samples. We found that MAMs contain a substantial number of miRNAs and the profile differs significantly from that of cytosolic, mitochondria, or ER. Interestingly, MAMs are particularly enriched in inflammatory-responsive miRNAs, including miR-146a, miR-142-3p, and miR-142-5p in both human and rat brains; miR-223 MAM enrichment was observed only in human brain samples. Further, mitochondrial uncoupling or traumatic brain injury in male rats resulted in the alteration of inflammatory miRNA enrichment in the isolated subcellular fractions. These observations demonstrate that miRNAs are distributed differentially in organelles and may re-distribute between organelles and the cytosol in response to cellular stress and metabolic demands.
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Affiliation(s)
- Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, 800 S. Limestone, Lexington, KY, 40536, USA.
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA.
| | - Paresh Prajapati
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA
- Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, 800 S. Limestone, Lexington, KY, 40536, USA
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Joe E Springer
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA
- Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
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38
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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39
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Nagashima S, Tábara LC, Tilokani L, Paupe V, Anand H, Pogson JH, Zunino R, McBride HM, Prudent J. Golgi-derived PI (4 )P-containing vesicles drive late steps of mitochondrial division. Science 2020; 367:1366-1371. [PMID: 32193326 DOI: 10.1126/science.aax6089] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 12/09/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
Abstract
Mitochondrial plasticity is a key regulator of cell fate decisions. Mitochondrial division involves Dynamin-related protein-1 (Drp1) oligomerization, which constricts membranes at endoplasmic reticulum (ER) contact sites. The mechanisms driving the final steps of mitochondrial division are still unclear. Here, we found that microdomains of phosphatidylinositol 4-phosphate [PI(4)P] on trans-Golgi network (TGN) vesicles were recruited to mitochondria-ER contact sites and could drive mitochondrial division downstream of Drp1. The loss of the small guanosine triphosphatase ADP-ribosylation factor 1 (Arf1) or its effector, phosphatidylinositol 4-kinase IIIβ [PI(4)KIIIβ], in different mammalian cell lines prevented PI(4)P generation and led to a hyperfused and branched mitochondrial network marked with extended mitochondrial constriction sites. Thus, recruitment of TGN-PI(4)P-containing vesicles at mitochondria-ER contact sites may trigger final events leading to mitochondrial scission.
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Affiliation(s)
- Shun Nagashima
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Luis-Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Lisa Tilokani
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Vincent Paupe
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Hanish Anand
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Joe H Pogson
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3B 2B4, Canada
| | - Rodolfo Zunino
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3B 2B4, Canada
| | - Heidi M McBride
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3B 2B4, Canada.
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
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40
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Abstract
Membrane phase behavior in cells permits transient concentration of specific proteins and lipids into dynamic nanoscopic domains. Here, we tested the existence and role of such phase behavior in endoplasmic reticulum (ER) membranes. Employing hypotonic cell swelling, we created large intracellular vesicles (LICVs) from internal organelles. ER LICVs maintained stable interorganelle contacts, with known protein tethers concentrated at the contact sites. Cooled ER LICVs underwent reversible phase separation into microscopically visible domains with different lipid order and membrane fluidity. The phase-separated domains specified sites of contact between the ER and different organelles. The endoplasmic reticulum (ER) is the site of synthesis of secretory and membrane proteins and contacts every organelle of the cell, exchanging lipids and metabolites in a highly regulated manner. How the ER spatially segregates its numerous and diverse functions, including positioning nanoscopic contact sites with other organelles, is unclear. We demonstrate that hypotonic swelling of cells converts the ER and other membrane-bound organelles into micrometer-scale large intracellular vesicles (LICVs) that retain luminal protein content and maintain contact sites with each other through localized organelle tethers. Upon cooling, ER-derived LICVs phase-partition into microscopic domains having different lipid-ordering characteristics, which is reversible upon warming. Ordered ER lipid domains mark contact sites with ER and mitochondria, lipid droplets, endosomes, or plasma membrane, whereas disordered ER lipid domains mark contact sites with lysosomes or peroxisomes. Tethering proteins concentrate at ER–organelle contact sites, allowing time-dependent behavior of lipids and proteins to be studied at these sites. These findings demonstrate that LICVs provide a useful model system for studying the phase behavior and interactive properties of organelles in intact cells.
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41
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Shin H, Cha HJ, Lee MJ, Na K, Park D, Kim CY, Han DH, Kim H, Paik YK. Identification of ALDH6A1 as a Potential Molecular Signature in Hepatocellular Carcinoma via Quantitative Profiling of the Mitochondrial Proteome. J Proteome Res 2020; 19:1684-1695. [PMID: 31985234 DOI: 10.1021/acs.jproteome.9b00846] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Various liver diseases, including hepatocellular carcinoma (HCC), have been linked to mitochondrial dysfunction, reduction of reactive oxygen species (ROS), and elevation of nitric oxide (NO). In this study, we subjected the human liver mitochondrial proteome to extensive quantitative proteomic profiling analysis and molecular characterization to identify potential signatures indicative of cancer cell growth and progression. Sequential proteomic analysis identified 2452 mitochondrial proteins, of which 1464 and 2010 were classified as nontumor and tumor (HCC) mitochondrial proteins, respectively, with 1022 overlaps. Further metabolic mapping of the HCC mitochondrial proteins narrowed our biological characterization to four proteins, namely, ALDH4A1, LRPPRC, ATP5C1, and ALDH6A1. The latter protein, a mitochondrial methylmalonate semialdehyde dehydrogenase (ALDH6A1), was most strongly suppressed in HCC tumor regions (∼10-fold decrease) in contrast to LRPPRC (∼6-fold increase) and was predicted to be present in plasma. Accordingly, we selected ALDH6A1 for functional analysis and engineered Hep3B cells to overexpress this protein, called ALDH6A1-O/E cells. Since ALDH6A1 is predicted to be involved in mitochondrial respiration, we assessed changes in the levels of NO and ROS in the overexpressed cell lines. Surprisingly, in ALDH6A1-O/E cells, NO was decreased nearly 50% but ROS was increased at a similar level, while the former was restored by treatment with S-nitroso-N-acetyl-penicillamine. The lactate levels were also decreased relative to control cells. Propidium iodide and Rhodamine-123 staining suggested that the decrease in NO and increase in ROS in ALDH6A1-O/E cells could be caused by depolarization of the mitochondrial membrane potential (ΔΨ). Taken together, our results suggest that hepatic neoplastic transformation appears to suppress the expression of ALDH6A1, which is accompanied by a respective increase and decrease in NO and ROS in cancer cells. Given the close link between ALDH6A1 suppression and abnormal cancer cell growth, this protein may serve as a potential molecular signature or biomarker of hepatocarcinogenesis and treatment responses.
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Affiliation(s)
- Heon Shin
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun-Jeong Cha
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Min Jung Lee
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Keun Na
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Donha Park
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea.,Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Dai Hoon Han
- Department of Surgery and Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Department of Pathology, College of Medicine, Severance Hospital, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoguen Kim
- Department of Pathology, College of Medicine, Severance Hospital, Yonsei University, Seoul 03722, Republic of Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, Republic of Korea
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42
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Kryvenko V, Wessendorf M, Morty RE, Herold S, Seeger W, Vagin O, Dada LA, Sznajder JI, Vadász I. Hypercapnia Impairs Na,K-ATPase Function by Inducing Endoplasmic Reticulum Retention of the β-Subunit of the Enzyme in Alveolar Epithelial Cells. Int J Mol Sci 2020; 21:E1467. [PMID: 32098115 PMCID: PMC7073107 DOI: 10.3390/ijms21041467] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 01/02/2023] Open
Abstract
Alveolar edema, impaired alveolar fluid clearance, and elevated CO2 levels (hypercapnia) are hallmarks of the acute respiratory distress syndrome (ARDS). This study investigated how hypercapnia affects maturation of the Na,K-ATPase (NKA), a key membrane transporter, and a cell adhesion molecule involved in the resolution of alveolar edema in the endoplasmic reticulum (ER). Exposure of human alveolar epithelial cells to elevated CO2 concentrations caused a significant retention of NKA-β in the ER and, thus, decreased levels of the transporter in the Golgi apparatus. These effects were associated with a marked reduction of the plasma membrane (PM) abundance of the NKA-α/β complex as well as a decreased total and ouabain-sensitive ATPase activity. Furthermore, our study revealed that the ER-retained NKA-β subunits were only partially assembled with NKA α-subunits, which suggests that hypercapnia modifies the ER folding environment. Moreover, we observed that elevated CO2 levels decreased intracellular ATP production and increased ER protein and, particularly, NKA-β oxidation. Treatment with α-ketoglutaric acid (α-KG), which is a metabolite that has been shown to increase ATP levels and rescue mitochondrial function in hypercapnia-exposed cells, attenuated the deleterious effects of elevated CO2 concentrations and restored NKA PM abundance and function. Taken together, our findings provide new insights into the regulation of NKA in alveolar epithelial cells by elevated CO2 levels, which may lead to the development of new therapeutic approaches for patients with ARDS and hypercapnia.
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Affiliation(s)
- Vitalii Kryvenko
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
- The Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
| | - Miriam Wessendorf
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
| | - Rory E. Morty
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
- The Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Susanne Herold
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
- The Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
| | - Werner Seeger
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
- The Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Olga Vagin
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA;
- Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Laura A. Dada
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (L.A.D.); (J.I.S.)
| | - Jacob I. Sznajder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (L.A.D.); (J.I.S.)
| | - István Vadász
- Department of Internal Medicine, Justus Liebig University, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), 35392 Giessen, Germany; (V.K.); (M.W.); (R.E.M.); (S.H.); (W.S.)
- The Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
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43
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Identification of mecciRNAs and their roles in the mitochondrial entry of proteins. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1429-1449. [PMID: 32048164 DOI: 10.1007/s11427-020-1631-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/19/2020] [Indexed: 12/23/2022]
Abstract
Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria. Here, we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by the mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components involved in mitochondrial protein and RNA importation, such as TOM40 and PNPASE, interact with mecciRNAs and regulate protein entry. The expression of mecciRNAs is regulated, and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.
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44
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Prajapati P, Wang WX, Nelson PT, Springer JE. Methodology for Subcellular Fractionation and MicroRNA Examination of Mitochondria, Mitochondria Associated ER Membrane (MAM), ER, and Cytosol from Human Brain. Methods Mol Biol 2020; 2063:139-154. [PMID: 31667768 PMCID: PMC8919243 DOI: 10.1007/978-1-0716-0138-9_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Eukaryotic cell organelles exert unique functions individually but also interact with each other for essential cellular functions. This physical interface between the organelles serves as an important platform for biomolecule trafficking and signaling. Mitochondria are membrane-bound organelles and form a dynamic contact with other organelles. The interactions and communication between mitochondria and endoplasmic reticulum (ER) are facilitated by an ER specific domain, named mitochondria associated ER membrane (MAM). Due to its unique location, the MAM is a "hotspot" for important cell signaling and biochemical processes including calcium homeostasis, lipid synthesis/exchange, inflammasome and autophagosome formation, and mitochondria fission/fusion. Although techniques are available for isolation of organelle fractions including MAM, most utilize animal tissues and cell lines. Here we describe a protocol that is tailored to the isolation of highly purified MAM, mitochondria, ER, and cytosol from human brain. In addition, we include a protocol for the isolation of total RNA and subsequent analysis of microRNAs from these highly purified organelle fractions. Finally, we include a panel of protein markers that are useful for validating the enrichment and purity of each subcellular fraction.
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Affiliation(s)
- Paresh Prajapati
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Wang-Xia Wang
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA.
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA.
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Joe E Springer
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA.
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45
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Abstract
Subcellular proteomics include, in its experimental workflow, steps aimed at purifying organelles. The purity of the subcellular fraction should be assessed before mass spectrometry analysis, in order to confidently conclude the presence of associated specific proteoforms, deepening the knowledge of its biological function. In this chapter, a protocol for isolating endoplasmic reticulum (ER) and purity assessment is reported, and it precedes the proteomic analysis through a gel-free/label-free proteomic approach. Dysfunction of quality-control mechanisms of protein metabolism in ER leads to ER stress. Additionally, ER, which is a calcium-storage organelle, is responsible for signaling and homeostatic function, and calcium homeostasis is required for plant tolerance. With such predominant cell functions, effective protocols to fractionate highly purified ER are needed. Here, isolation methods and purity assessments of ER are described. In addition, a gel-free/label-free proteomic approach of ER is presented.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui, Japan.
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46
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Matheny T, Rao BS, Parker R. Transcriptome-Wide Comparison of Stress Granules and P-Bodies Reveals that Translation Plays a Major Role in RNA Partitioning. Mol Cell Biol 2019; 39:e00313-19. [PMID: 31591142 PMCID: PMC6879202 DOI: 10.1128/mcb.00313-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic cytosol contains multiple RNP granules, including P-bodies and stress granules. Three different methods have been used to describe the transcriptome of stress granules or P-bodies, but how these methods compare and how RNA partitioning occurs between P-bodies and stress granules have not been addressed. Here, we compare the analysis of the stress granule transcriptome based on differential centrifugation with and without subsequent stress granule immunopurification. We find that while differential centrifugation alone gives a first approximation of the stress granule transcriptome, this methodology contains nonspecific transcripts that play a confounding role in the interpretation of results. We also immunopurify and compare the RNAs in stress granules and P-bodies under arsenite stress and compare those results to those for the P-body transcriptome described under nonstress conditions. We find that the P-body transcriptome is dominated by poorly translated mRNAs under nonstress conditions, but during arsenite stress, when translation is globally repressed, the P-body transcriptome is very similar to the stress granule transcriptome. This suggests that translation is a dominant factor in targeting mRNAs into both P-bodies and stress granules, and during stress, when most mRNAs are untranslated, the composition of P-bodies reflects this broader translation repression.
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Affiliation(s)
- Tyler Matheny
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Bhalchandra S Rao
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Howard Hughes Medical Institute, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Howard Hughes Medical Institute, Boulder, Colorado, USA
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Bhatta A, Atianand M, Jiang Z, Crabtree J, Blin J, Fitzgerald KA. A Mitochondrial Micropeptide Is Required for Activation of the Nlrp3 Inflammasome. THE JOURNAL OF IMMUNOLOGY 2019; 204:428-437. [PMID: 31836654 DOI: 10.4049/jimmunol.1900791] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Functional peptides encoded by short open reading frames are emerging as important mediators of fundamental biological processes. In this study, we identified a micropeptide produced from a putative long noncoding RNA (lncRNAs) that is important in controlling innate immunity. By studying lncRNAs in mice macrophages, we identified lncRNA 1810058I24Rik, which was downregulated in both human and murine myeloid cells exposed to LPS as well as other TLR ligands and inflammatory cytokines. Analysis of lncRNA 1810058I24Rik subcellular localization revealed that this transcript was localized in the cytosol, prompting us to evaluate its coding potential. In vitro translation with 35S-labeled methionine resulted in translation of a 47 aa micropeptide. Microscopy and subcellular fractionation studies in macrophages demonstrated endogenous expression of this peptide on the mitochondrion. We thus named this gene mitochondrial micropeptide-47 (Mm47). Crispr-Cas9-mediated deletion of Mm47, as well as small interfering RNA studies in mice primary macrophages, showed that the transcriptional response downstream of TLR4 was intact in cells lacking Mm47. In contrast, Mm47-deficient or knockdown cells were compromised for Nlrp3 inflammasome responses. Activation of Nlrc4 or Aim2 inflammasomes were intact in cells lacking Mm47. This study therefore identifies, to our knowledge, a novel mitochondrial micropeptide Mm47 that is required for the activation of the Nlrp3 inflammasome. This work further highlights the functional activity of short open reading frame-encoded peptides and underscores their importance in innate immunity.
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Affiliation(s)
- Ankit Bhatta
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Maninjay Atianand
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Juliet Crabtree
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Juliana Blin
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
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Accumulation of Cytoplasmic DNA Due to ATM Deficiency Activates the Microglial Viral Response System with Neurotoxic Consequences. J Neurosci 2019; 39:6378-6394. [PMID: 31189575 DOI: 10.1523/jneurosci.0774-19.2019] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/07/2023] Open
Abstract
ATM (ataxia-telangiectasia mutated) is a PI3K-like kinase best known for its role in the DNA damage response (DDR), especially after double-strand breaks. Mutations in the ATM gene result in a condition known as ataxia-telangiectasia (A-T) that is characterized by cancer predisposition, radiosensitivity, neurodegeneration, sterility, and acquired immune deficiency. We show here that the innate immune system is not spared in A-T. ATM-deficient microglia adopt an active phenotype that includes the overproduction of proinflammatory cytokines that are toxic to cultured neurons and likely contribute to A-T neurodegeneration. Causatively, ATM dysfunction results in the accumulation of DNA in the cytoplasm of microglia as well as a variety of other cell types. In microglia, cytoplasmic DNA primes an antiviral response via the DNA sensor, STING (stimulator of interferon genes). The importance of this response pathway is supported by our finding that inhibition of STING blocks the overproduction of neurotoxic cytokines. Cytosolic DNA also activates the AIM2 (absent in melanoma 2) containing inflammasome and induces proteolytic processing of cytokine precursors such as pro-IL-1β. Our study furthers our understanding of neurodegeneration in A-T and highlights the role of cytosolic DNA in the innate immune response.SIGNIFICANCE STATEMENT Conventionally, the immune deficiencies found in ataxia-telangiectasia (A-T) patients are viewed as defects of the B and T cells of the acquired immune system. In this study, we demonstrate the microglia of the innate immune system are also affected and uncover the mechanism by which this occurs. Loss of ATM (ataxia-telangiectasia mutated) activity leads to a slowing of DNA repair and an accumulation of cytoplasmic fragments of genomic DNA. This ectopic DNA induces the antivirus response, which triggers the production of neurotoxic cytokines. This expands our understanding of the neurodegeneration found in A-T and offers potentially new therapeutic options.
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Léger JL, Jougleux JL, Savadogo F, Pichaud N, Boudreau LH. Rapid isolation and purification of functional platelet mitochondria using a discontinuous Percoll gradient. Platelets 2019; 31:258-264. [PMID: 31057000 DOI: 10.1080/09537104.2019.1609666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The isolation of mitochondria is gaining importance in experimental and clinical laboratory settings. The mitochondrion is known as the powerhouse of the cell as it produces the energy to power most cellular functions but is also involved in many cellular processes. Of interest, mitochondria and mitochondrial components (i.e. circular DNA, N-formylated peptides, cardiolipin) have been involved in several human inflammatory pathologies, such as cancer, Alzheimer's disease, Parkinson's disease, and rheumatoid arthritis. Therefore, stringent methods of isolation and purification of mitochondria are of the utmost importance in assessing mitochondrial-related diseases. While several mitochondrial isolation methods have been previously published, these techniques are aimed at yielding mitochondria from cells types other than platelets. In addition, little information is known on the number of platelet-derived microparticles that can contaminate the mitochondrial preparation or even the overall quality and integrity of the mitochondria. In this project, we provide an alternate purification method yielding mitochondria of high purity and integrity from human platelets. Using human platelets, flow cytometry and transmission electron microscopy experiments were performed to demonstrate that the Percoll gradient method yielded significantly purified mitochondria by removing platelet membrane debris. Mitochondrial respiration following the substrate-uncoupler-inhibitor-titration (SUIT) protocol was similar in both the purified and crude mitochondrial extraction methods. Finally, the cytochrome c effect and JC-1 staining did not exhibit a significant difference between the two methods, suggesting that the mitochondrial integrity was not affected. Our study suggests that the Percoll discontinuous gradient purifies viable platelet-derived mitochondria by removing platelet-derived debris, including microparticles, therefore confirming that this isolation method is ideal for studying the downstream effects of intact mitochondria in mitochondrial-related diseases.
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Affiliation(s)
- Jacob L Léger
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, Canada
| | - Jean-Luc Jougleux
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, Canada
| | - Fanta Savadogo
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, Canada
| | - Nicolas Pichaud
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, Canada
| | - Luc H Boudreau
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, Canada
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Pannexin 2 Localizes at ER-Mitochondria Contact Sites. Cancers (Basel) 2019; 11:cancers11030343. [PMID: 30862038 PMCID: PMC6468579 DOI: 10.3390/cancers11030343] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 01/02/2023] Open
Abstract
Endomembrane specialization allows functional compartmentalization but imposes physical constraints to information flow within the cell. However, the evolution of an endomembrane system was associated with the emergence of contact sites facilitating communication between membrane-bound organelles. Contact sites between the endoplasmic reticulum (ER) and mitochondria are highly conserved in terms of their morphological features but show surprising molecular diversity within and across eukaryote species. ER-mitochondria contact sites are thought to regulate key processes in oncogenesis but their molecular composition remains poorly characterized in mammalian cells. In this study, we investigate the localization of pannexin 2 (Panx2), a membrane channel protein showing tumor-suppressing properties in cancer cells. Using a combination of subcellular fractionation, particle tracking in live-cell, and immunogold electron microscopy, we show that Panx2 localizes at ER-mitochondria contact sites in mammalian cells and sensitizes cells to apoptotic stimuli.
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