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Cagalinec M, Mohd A, Borecka S, Bultynck G, Choubey V, Yanovsky-Dagan S, Ezer S, Gasperikova D, Harel T, Jurkovicova D, Kaasik A, Liévens JC, Maurice T, Peviani M, Richard EM, Skoda J, Skopkova M, Tarot P, Van Gorp R, Zvejniece L, Delprat B. Improving mitochondria-associated endoplasmic reticulum membranes integrity as converging therapeutic strategy for rare neurodegenerative diseases and cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2025; 1872:119954. [PMID: 40216201 DOI: 10.1016/j.bbamcr.2025.119954] [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: 11/28/2024] [Revised: 03/04/2025] [Accepted: 04/06/2025] [Indexed: 04/26/2025]
Abstract
Membrane contact sites harbor a distinct set of proteins with varying biological functions, thereby emerging as hubs for localized signaling nanodomains underlying adequate cell function. Here, we will focus on mitochondria-associated endoplasmic reticulum membranes (MAMs), which serve as hotspots for Ca2+ signaling, redox regulation, lipid exchange, mitochondrial quality and unfolded protein response pathway. A network of MAM-resident proteins contributes to the structural integrity and adequate function of MAMs. Beyond endoplasmic reticulum (ER)-mitochondrial tethering proteins, MAMs contain several multi-protein complexes that mediate the transfer of or are influenced by Ca2+, reactive oxygen species and lipids. Particularly, IP3 receptors, intracellular Ca2+-release channels, and Sigma-1 receptors (S1Rs), ligand-operated chaperones, serve as important platforms that recruit different accessory proteins and intersect with these local signaling processes. Furthermore, many of these proteins are directly implicated in pathophysiological conditions, where their dysregulation or mutation is not only causing diseases such as cancer and neurodegeneration, but also rare genetic diseases, for example familial Parkinson's disease (PINK1, Parkin, DJ-1), familial Amyotrophic lateral sclerosis (TDP43), Wolfram syndrome1/2 (WFS1 and CISD2), Harel-Yoon syndrome (ATAD3A). In this review, we will discuss the current state-of-the-art regarding the molecular components, protein platforms and signaling networks underlying MAM integrity and function in cell function and how their dysregulation impacts MAMs, thereby driving pathogenesis and/or impacting disease burden. We will highlight how these insights can generate novel, potentially therapeutically relevant, strategies to tackle disease outcomes by improving the integrity of MAMs and the signaling processes occurring at these membrane contact sites.
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Affiliation(s)
- Michal Cagalinec
- Department of Cellular Cardiology, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Adnan Mohd
- Department of Cellular Cardiology, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Silvia Borecka
- Department of Metabolic Diseases, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Geert Bultynck
- KU Leuven, Cellular and Molecular Medicine, Laboratory of Molecular & Cellular Signaling, Campus Gasthuisberg ON-1, Leuven, Belgium
| | - Vinay Choubey
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | | | - Shlomit Ezer
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University Medical Center, Jerusalem, Israel
| | - Daniela Gasperikova
- Department of Metabolic Diseases, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Jurkovicova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Allen Kaasik
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | | | - Tangui Maurice
- MMDN, University of Montpellier, EPHE, INSERM, Montpellier, France
| | - Marco Peviani
- Cellular and Molecular Neuropharmacology Lab., Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Jan Skoda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Martina Skopkova
- Department of Metabolic Diseases, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Pauline Tarot
- MMDN, University of Montpellier, EPHE, INSERM, Montpellier, France
| | - Robbe Van Gorp
- KU Leuven, Cellular and Molecular Medicine, Laboratory of Molecular & Cellular Signaling, Campus Gasthuisberg ON-1, Leuven, Belgium
| | | | - Benjamin Delprat
- MMDN, University of Montpellier, EPHE, INSERM, Montpellier, France.
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2
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Brügel M, Kiesel AS, Haack TB, Peralta S. Mutations in mitochondrial ATAD3 gene and disease, lessons from in vivo models. Front Neurosci 2024; 18:1496142. [PMID: 39605788 PMCID: PMC11599198 DOI: 10.3389/fnins.2024.1496142] [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: 09/13/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024] Open
Abstract
Pathogenic variants in the ATAD3 gene cluster have been associated with different neurodevelopmental disorders showing clinical symptoms like global developmental delay, muscular hypotonia, cardiomyopathy, congenital cataracts, and cerebellar atrophy. ATAD3A encodes for a mitochondrial ATPase whose function is unclear and has been considered one of the five most common nuclear genes associated with mitochondrial diseases in childhood. However, the mechanism causing ATAD3-associated disorders is still unknown. In vivo models have been used to identify ATAD3 function. Here we summarize the features of mouse models with ATAD3 loss of function and Drosophila models overexpressing pathogenic ATAD3 variants. We discuss how these models have contributed to our understanding of ATAD3 function and the pathomechanism of the ATAD3-associated disease.
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Affiliation(s)
| | | | | | - Susana Peralta
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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3
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Goel D, Kumar S. Advancements in unravelling the fundamental function of the ATAD3 protein in multicellular organisms. Adv Biol Regul 2024; 93:101041. [PMID: 38909398 DOI: 10.1016/j.jbior.2024.101041] [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: 05/17/2024] [Revised: 06/05/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
ATPase family AAA domain containing protein 3, commonly known as ATAD3 is a versatile mitochondrial protein that is involved in a large number of pathways. ATAD3 is a transmembrane protein that spans both the inner mitochondrial membrane and outer mitochondrial membrane. It, therefore, functions as a connecting link between the mitochondrial lumen and endoplasmic reticulum facilitating their cross-talk. ATAD3 contains an N-terminal domain which is amphipathic in nature and is inserted into the membranous space of the mitochondria, while the C-terminal domain is present towards the lumen of the mitochondria and contains the ATPase domain. ATAD3 is known to be involved in mitochondrial biogenesis, cholesterol transport, hormone synthesis, apoptosis and several other pathways. It has also been implicated to be involved in cancer and many neurological disorders making it an interesting target for extensive studies. This review aims to provide an updated comprehensive account of the role of ATAD3 in the mitochondria especially in lipid transport, mitochondrial-endoplasmic reticulum interactions, cancer and inhibition of mitophagy.
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Affiliation(s)
- Divya Goel
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sudhir Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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4
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Lee-Glover LP, Shutt TE. Mitochondrial quality control pathways sense mitochondrial protein import. Trends Endocrinol Metab 2024; 35:308-320. [PMID: 38103974 DOI: 10.1016/j.tem.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Mitochondrial quality control (MQC) mechanisms are required to maintain a functional proteome, which enables mitochondria to perform a myriad of important cellular functions from oxidative phosphorylation to numerous other metabolic pathways. Mitochondrial protein homeostasis begins with the import of over 1000 nuclear-encoded mitochondrial proteins and the synthesis of 13 mitochondrial DNA-encoded proteins. A network of chaperones and proteases helps to fold new proteins and degrade unnecessary, damaged, or misfolded proteins, whereas more extensive damage can be removed by mitochondrial-derived vesicles (MDVs) or mitochondrial autophagy (mitophagy). Here, focusing on mechanisms in mammalian cells, we review the importance of mitochondrial protein import as a sentinel of mitochondrial function that activates multiple MQC mechanisms when impaired.
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Affiliation(s)
- Laurie P Lee-Glover
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Timothy E Shutt
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta, Canada; Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada; Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada.
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5
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Gaudó P, de Tomás-Mateo E, Garrido-Pérez N, Santana A, Ruiz-Pesini E, Montoya J, Bayona-Bafaluy P. "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane". Free Radic Biol Med 2024; 211:114-126. [PMID: 38092275 DOI: 10.1016/j.freeradbiomed.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial ATAD3A is an ATPase Associated with diverse cellular Activities (AAA) domain containing enzyme, involved in the structural organization of the inner mitochondrial membrane and of increasing importance in childhood disease. In humans, two ATAD3A paralogs arose by gene duplication during evolution: ATAD3B and ATAD3C. Here we investigate the cellular activities of the ATAD3C paralog that has been considered a pseudogene. We detected unique ATAD3C peptides in HEK 293T cells, with expression similar to that in human tissues, and showed that it is an integral membrane protein that exposes its carboxy-terminus to the intermembrane space. Overexpression of ATAD3C, but not of ATAD3A, in fibroblasts caused a decrease in cell proliferation and oxygen consumption rate, and an increase of cellular ROS. This was due to the incorporation of ATAD3C monomers in ATAD3A complex in the mitochondrial membrane reducing its size. Consistent with a negative regulation of ATAD3A function in mitochondrial membrane organization, ATAD3C expression led to increased accumulation of respiratory chain dimeric CIII in the inner membrane, to the detriment to that assembled in respiratory supercomplexes. Our results demonstrate a negative dominant role of the ATAD3C paralog with implications for mitochondrial OXPHOS function and suggest that its expression regulates ATAD3A in the cell.
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Affiliation(s)
- Paula Gaudó
- Biochemistry and Molecular Biology Department. Universidad de Zaragoza, 50009- and 50013, Zaragoza, Spain
| | - Elena de Tomás-Mateo
- Biochemistry and Molecular Biology Department. Universidad de Zaragoza, 50009- and 50013, Zaragoza, Spain
| | - Nuria Garrido-Pérez
- Biochemistry and Molecular Biology Department. Universidad de Zaragoza, 50009- and 50013, Zaragoza, Spain; Institute for Health Research (IIS) de Aragón, 50009, Zaragoza, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), 28029, Madrid, Spain; Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018, Zaragoza, Spain
| | - Alfredo Santana
- Research Institute of Biomedical and Health Sciences (IUIBS), University of Las Palmas de Gran Canaria, 35001, Las Palmas de Gran Canaria, Spain; Clinical Genetics Unit, Complejo Hospitarlario Universitario Insular-Materno Infantil de Las Palamas de Gran Canaria, 35016, Las Palmas de Gran Canaria, Spain
| | - Eduardo Ruiz-Pesini
- Institute for Health Research (IIS) de Aragón, 50009, Zaragoza, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), 28029, Madrid, Spain.
| | - Julio Montoya
- Biochemistry and Molecular Biology Department. Universidad de Zaragoza, 50009- and 50013, Zaragoza, Spain; Institute for Health Research (IIS) de Aragón, 50009, Zaragoza, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), 28029, Madrid, Spain
| | - Pilar Bayona-Bafaluy
- Biochemistry and Molecular Biology Department. Universidad de Zaragoza, 50009- and 50013, Zaragoza, Spain; Institute for Health Research (IIS) de Aragón, 50009, Zaragoza, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), 28029, Madrid, Spain; Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018, Zaragoza, Spain.
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [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: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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7
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Li S, Zhu C, Zhao Q, Zhang ZM, Sun P, Li Z. Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells. ACS Chem Biol 2023; 18:1405-1415. [PMID: 37231651 DOI: 10.1021/acschembio.3c00149] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for the study of protein structure and protein-protein interactions (PPIs). However, the chemical probes used in the CXMS are limited to bidentate reactive warheads, and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonyl ynamide, was developed as a new zero-length cross-linker that can connect high-abundance carboxyl residues (D/E) with lysine (K) to form amide bonds in the absence of any catalyst. Significant improvement in the cross-linking efficiency and specificity in comparison with traditional EDC/NHS was achieved with model proteins, which includes inter- and intramolecular conjugations. The cross-linked structures were validated by X-ray crystallography. Importantly, this coupling reagent can be successfully used to capture interacting proteins in the whole proteome and can be a useful reagent for probing potential protein-protein interactions in situ.
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Affiliation(s)
- Shengrong Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengjun Zhu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Pinghua Sun
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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8
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Skopkova M, Stufkova H, Rambani V, Stranecky V, Brennerova K, Kolnikova M, Pietrzykova M, Karhanek M, Noskova L, Tesarova M, Hansikova H, Gasperikova D. ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability. Orphanet J Rare Dis 2023; 18:92. [PMID: 37095554 PMCID: PMC10127305 DOI: 10.1186/s13023-023-02689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/02/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Pathogenic variants in the ATAD3A gene lead to a heterogenous clinical picture and severity ranging from recessive neonatal-lethal pontocerebellar hypoplasia through milder dominant Harel-Yoon syndrome up to, again, neonatal-lethal but dominant cardiomyopathy. The genetic diagnostics of ATAD3A-related disorders is also challenging due to three paralogous genes in the ATAD3 locus, making it a difficult target for both sequencing and CNV analyses. RESULTS Here we report four individuals from two families with compound heterozygous p.Leu77Val and exon 3-4 deletion in the ATAD3A gene. One of these patients was characterized as having combined OXPHOS deficiency based on decreased complex IV activities, decreased complex IV, I, and V holoenzyme content, as well as decreased levels of COX2 and ATP5A subunits and decreased rate of mitochondrial proteosynthesis. All four reported patients shared a strikingly similar clinical picture to a previously reported patient with the p.Leu77Val variant in combination with a null allele. They presented with a less severe course of the disease and a longer lifespan than in the case of biallelic loss-of-function variants. This consistency of the phenotype in otherwise clinically heterogenous disorder led us to the hypothesis that the severity of the phenotype could depend on the severity of variant impact. To follow this rationale, we reviewed the published cases and sorted the recessive variants according to their impact predicted by their type and the severity of the disease in the patients. CONCLUSION The clinical picture and severity of ATAD3A-related disorders are homogenous in patients sharing the same combinations of variants. This knowledge enables deduction of variant impact severity based on known cases and allows more accurate prognosis estimation, as well as a better understanding of the ATAD3A function.
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Affiliation(s)
- Martina Skopkova
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center SAS, Bratislava, Slovakia
| | - Hana Stufkova
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Vibhuti Rambani
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center SAS, Bratislava, Slovakia
| | - Viktor Stranecky
- Research Unit for Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Katarina Brennerova
- Department of Paediatrics, Medical Faculty of Comenius University, National Institute of Children's Diseases, Bratislava, Slovakia
| | - Miriam Kolnikova
- Department of Paediatric Neurology, Medical Faculty of Comenius University, National Institute of Children's Diseases, Bratislava, Slovakia
| | - Michaela Pietrzykova
- Department of Clinical Genetics, Institute of Medical Biology, Genetics and Clinical Genetics, Medical Faculty of Comenius University, University Hospital in Bratislava, Bratislava, Slovakia
| | - Miloslav Karhanek
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center SAS, Bratislava, Slovakia
| | - Lenka Noskova
- Research Unit for Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marketa Tesarova
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Hana Hansikova
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Daniela Gasperikova
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center SAS, Bratislava, Slovakia.
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9
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Sankaran H, Negi S, McShane LM, Zhao Y, Krushkal J. Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products. BMC Cancer 2022; 22:512. [PMID: 35525914 PMCID: PMC9077913 DOI: 10.1186/s12885-022-09580-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/20/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Indian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel. METHODS We examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database. RESULTS Hierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E. CONCLUSION These findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products.
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Affiliation(s)
- Hari Sankaran
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Simarjeet Negi
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD, 20850, USA
| | - Lisa M McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD, 20850, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD, 20850, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD, 20850, USA.
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10
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Lang L, Loveless R, Dou J, Lam T, Chen A, Wang F, Sun L, Juarez J, Qin ZS, Saba NF, Shay C, Teng Y. ATAD3A mediates activation of RAS-independent mitochondrial ERK1/2 signaling, favoring head and neck cancer development. J Exp Clin Cancer Res 2022; 41:43. [PMID: 35093151 PMCID: PMC8800319 DOI: 10.1186/s13046-022-02274-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Targeting mitochondrial oncoproteins presents a new concept in the development of effective cancer therapeutics. ATAD3A is a nuclear-encoded mitochondrial enzyme contributing to mitochondrial dynamics, cholesterol metabolism, and signal transduction. However, its impact and underlying regulatory mechanisms in cancers remain ill-defined. METHODS We used head and neck squamous cell carcinoma (HNSCC) as a research platform and achieved gene depletion by lentiviral shRNA and CRISPR/Cas9. Molecular alterations were examined by RNA-sequencing, phospho-kinase profiling, Western blotting, RT-qPCR, immunohistochemistry, and immunoprecipitation. Cancer cell growth was assessed by MTT, colony formation, soft agar, and 3D cultures. The therapeutic efficacy in tumor development was evaluated in orthotopic tongue tumor NSG mice. RESULTS ATAD3A is highly expressed in HNSCC tissues and cell lines. Loss of ATAD3A expression suppresses HNSCC cell growth and elicits tumor regression in orthotopic tumor-bearing mice, whereas gain of ATAD3A expression produces the opposite effects. From a mechanistic perspective, the tumor suppression induced by the overexpression of the Walker A dead mutant of ATAD3A (K358) produces a potent dominant-negative effect due to defective ATP-binding. Moreover, ATAD3A binds to ERK1/2 in the mitochondria of HNSCC cells in the presence of VDAC1, and this interaction is essential for the activation of mitochondrial ERK1/2 signaling. Most importantly, the ATAD3A-ERK1/2 signaling axis drives HNSCC development in a RAS-independent fashion and, thus, tumor suppression is more effectively achieved when ATAD3A knockout is combined with RAS inhibitor treatment. CONCLUSIONS These findings highlight the novel function of ATAD3A in regulating mitochondrial ERK1/2 activation that favors HNSCC development. Combined targeting of ATAD3A and RAS signaling may potentiate anticancer activity for HNSCC therapeutics.
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Affiliation(s)
- Liwei Lang
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Juan Dou
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA, 30322, USA
| | - Tiffany Lam
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Alex Chen
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Fang Wang
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Li Sun
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Jakeline Juarez
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Zhaohui Steve Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA, 30322, USA
| | - Chloe Shay
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory, University, Atlanta, GA, 30322, USA
| | - Yong Teng
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA.
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA, 30322, USA.
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11
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Arguello T, Peralta S, Antonicka H, Gaidosh G, Diaz F, Tu YT, Garcia S, Shiekhattar R, Barrientos A, Moraes CT. ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly. Cell Rep 2021; 37:110139. [PMID: 34936866 PMCID: PMC8785211 DOI: 10.1016/j.celrep.2021.110139] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
The ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary role, we generated a neuronal-specific conditional knockout (Atad3 nKO) mouse model, which developed a severe encephalopathy by 5 months of age. Pre-symptomatic mice showed aberrant mitochondrial cristae morphogenesis in the cortex as early as 2 months. Using a multi-omics approach in the CNS of 2-to-3-month-old mice, we found early alterations in the organelle membrane structure. We also show that human ATAD3A associates with different components of the inner membrane, including OXPHOS complex I, Letm1, and prohibitin complexes. Stochastic Optical Reconstruction Microscopy (STORM) shows that ATAD3A is regularly distributed along the inner mitochondrial membrane, suggesting a critical structural role in inner mitochondrial membrane and its organization, most likely in an ATPase-dependent manner. Arguello et al. show that deletion of the mitochondrial protein ATAD3 in neurons leads to neuronal loss and death. The earliest phenotype is disruption of the mitochondrial inner membrane structure; OXPHOS complexes are affected later. ATAD3 is regularly spaced and has several interactors at the inner membrane, including CI subunits.
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Affiliation(s)
- Tania Arguello
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Susana Peralta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Hana Antonicka
- Department of Human Genetics and Montreal Neurological Institute, McGill University, Montreal, QC H3A 0C7, Canada
| | - Gabriel Gaidosh
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ya-Ting Tu
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sofia Garcia
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antonio Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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12
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Kim M, Schulz V, Brings L, Schoeller T, Kühn K, Vierling E. mTERF18 and ATAD3 are required for mitochondrial nucleoid structure and their disruption confers heat tolerance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 232:2026-2042. [PMID: 34482561 DOI: 10.1111/nph.17717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/23/2021] [Indexed: 05/27/2023]
Abstract
Mitochondria play critical roles in generating ATP through oxidative phosphorylation (OXPHOS) and produce both damaging and signaling reactive oxygen species (ROS). They have reduced genomes that encode essential subunits of the OXPHOS machinery. Mitochondrial Transcription tERmination Factor-related (mTERF) proteins are involved in organelle gene expression, interacting with organellar DNA or RNA. We previously found that mutations in Arabidopsis thaliana mTERF18/SHOT1 enable plants to better tolerate heat and oxidative stresses, presumably due to low ROS production and reduced oxidative damage. Here we discover that shot1 mutants have greatly reduced OXPHOS complexes I and IV and reveal that suppressor of hot1-4 1 (SHOT1) binds DNA and localizes to mitochondrial nucleoids, which are disrupted in shot1. Furthermore, three homologues of animal ATPase family AAA domain-containing protein 3 (ATAD3), which is involved in mitochondrial nucleoid organization, were identified as SHOT1-interacting proteins. Importantly, disrupting ATAD3 function disrupts nucleoids, reduces accumulation of complex I, and enhances heat tolerance, as is seen in shot1 mutants. Our data link nucleoid organization to OXPHOS biogenesis and suggest that the common defects in shot1 mutants and ATAD3-disrupted plants lead to critical changes in mitochondrial metabolism and signaling that result in plant heat tolerance.
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Affiliation(s)
- Minsoo Kim
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Vincent Schulz
- Department of Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, 10099, Berlin, Germany
| | - Lea Brings
- Department of Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, 10099, Berlin, Germany
| | - Theresa Schoeller
- Department of Plant Physiology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Kristina Kühn
- Department of Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, 10099, Berlin, Germany
- Department of Plant Physiology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
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13
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Shu L, Hu C, Xu M, Yu J, He H, Lin J, Sha H, Lu B, Engelender S, Guan M, Song Z. ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA. EMBO J 2021; 40:e106283. [PMID: 33665835 PMCID: PMC8047441 DOI: 10.15252/embj.2020106283] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes several key components of respiratory chain complexes that produce cellular energy through oxidative phosphorylation. mtDNA is vulnerable to damage under various physiological stresses, especially oxidative stress. mtDNA damage leads to mitochondrial dysfunction, and dysfunctional mitochondria can be removed by mitophagy, an essential process in cellular homeostasis. However, how damaged mtDNA is selectively cleared from the cell, and how damaged mtDNA triggers mitophagy, remain mostly unknown. Here, we identified a novel mitophagy receptor, ATAD3B, which is specifically expressed in primates. ATAD3B contains a LIR motif that binds to LC3 and promotes oxidative stress-induced mitophagy in a PINK1-independent manner, thus promoting the clearance of damaged mtDNA induced by oxidative stress. Under normal conditions, ATAD3B hetero-oligomerizes with ATAD3A, thus promoting the targeting of the C-terminal region of ATAD3B to the mitochondrial intermembrane space. Oxidative stress-induced mtDNA damage or mtDNA depletion reduces ATAD3B-ATAD3A hetero-oligomerization and leads to exposure of the ATAD3B C-terminus at the mitochondrial outer membrane and subsequent recruitment of LC3 for initiating mitophagy. Furthermore, ATAD3B is little expressed in m.3243A > G mutated cells and MELAS patient fibroblasts showing endogenous oxidative stress, and ATAD3B re-expression promotes the clearance of m.3243A > G mutated mtDNA. Our findings uncover a new pathway to selectively remove damaged mtDNA and reveal that increasing ATAD3B activity is a potential therapeutic approach for mitochondrial diseases.
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Affiliation(s)
- Li Shu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - Chao Hu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - Meng Xu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - Jianglong Yu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - He He
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - Jie Lin
- Department of NeurologyHuashan HospitalFudan UniversityShanghaiChina
| | - Hongying Sha
- State Key Laboratory of Medical NeurobiologyInstitute of Brain ScienceShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Bin Lu
- Attardi Institute of Mitochondrial BiomedicineSchool of Life SciencesWenzhou Medical UniversityWenzhouChina
| | - Simone Engelender
- Department of BiochemistryRappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Minxin Guan
- Institute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Zhiyin Song
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
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14
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Yang K, Wu Y. A prognosis-related molecular subtype for early-stage non-small lung cell carcinoma by multi-omics integration analysis. BMC Cancer 2021; 21:128. [PMID: 33549049 PMCID: PMC7866742 DOI: 10.1186/s12885-021-07846-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/27/2021] [Indexed: 12/25/2022] Open
Abstract
Background Early-stage non-small cell lung carcinoma (NSCLC) accounts for more than 80% of lung cancer, which is a kind of cancer with high heterogeneity, so the genetic heterogeneity and molecular subtype should be explored. Methods Partitioning Around Medoid algorithm was used to acquire the molecular subtype for early-stage NSCLC based on prognosis-related mRNAs and methylation sites. Random forest (RF) and support vector machine (SVM) were used to build prediction models for subtypes. Results Six prognosis-related subtypes for early-stage NSCLC, including 4 subtypes for lung squamous cell carcinoma (LUSC) and 2 subtypes for lung adenocarcinoma (LUAD), were identified. There were highly expressed and hypermethylated gene regions for LUSC-C1 and LUAD-C2, highly expressed region for LUAD-C1, and hypermethylated regions for LUSC-C3 and LUSC-C4. Molecular subtypes for LUSC were mainly determined by DNA methylation (14 mRNAs and 362 methylation sites). Molecular subtypes for LUAD were determined by both mRNA and DNA methylation information (143 mRNAs and 458 methylation sites). Ten methylation sites were selected as biomarkers for prediction of LUSC-C1 and LUSC-C3, respectively. Nine genes and 1 methylation site were selected as biomarkers for LUAD subtype prediction. These subtypes can be predicted by the selected biomarkers with RF and SVM models. Conclusions In conclusion, we proposed a prognosis-related molecular subtype for early-stage NSCLC, which can provide important information for personalized therapy of patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07846-0.
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Affiliation(s)
- Kai Yang
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518055, China
| | - Ying Wu
- Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, 510080, China.
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15
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Zhu Z, Fu H, Wang S, Yu X, You Q, Shi M, Dai C, Wang G, Cha W, Wang W. Whole-exome sequencing identifies prognostic mutational signatures in gastric cancer. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1484. [PMID: 33313229 PMCID: PMC7729362 DOI: 10.21037/atm-20-6620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Gastric cancer (GC) is a heterogeneous disease, and is a leading cause of cancer deaths in Eastern Asia. Genomic analysis, such as whole-exome sequencing (WES), can help identify key genetic alterations leading to the malignancy and diversity of GC, and may help identify new drug targets. Methods We identified genomic alterations in a cohort of 38 GC patients, including 26 metastatic and 12 non-metastatic patients. We analyzed the association between novel gene mutations and copy number variations (CNVs) with tumor metastasis and patient survival. Results A number of significantly mutated genes in somatic and germline cells were identified. Among them, ATAD3B somatic mutation, a potential biomarker of immunotherapy in stomach cancers, was associated with better patient survival (P=0.0939) and metastasis (P=0.074). POLE germline variation was correlated with shorter overall survival (OS; P=0.0100). Novel CNVs were also identified and can potentially be used as biomarkers. These included 9p24.1 deletion (P=0.0376) and 16p11.2 amplification (P=0.0066), which were both associated with shorter OS. CNVs of several genes including MMP9, PTPN1, and SS18L1 were found to be significantly related to metastasis (P<0.05). Conclusions We characterized the mutational landscape of 38 GC patients and discovered several potential new predictive markers of survival and metastasis in GC.
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Affiliation(s)
- Zhenxin Zhu
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hongbing Fu
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Xinxin Yu
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Qing You
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Mengyao Shi
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Guan Wang
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Wei Cha
- Dental Department, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weimin Wang
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
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16
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Lang L, Loveless R, Teng Y. Emerging Links between Control of Mitochondrial Protein ATAD3A and Cancer. Int J Mol Sci 2020; 21:E7917. [PMID: 33113782 PMCID: PMC7663417 DOI: 10.3390/ijms21217917] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022] Open
Abstract
Spanning from the mitochondria's outer surface to the inner membrane, the nuclear-encoded protein ATAD3A maintains vital roles in regulating mitochondrial dynamics, homeostasis, metabolism, and interactions with the endoplasmic reticulum. Recently, elevated levels of ATAD3A have been reported in several types of cancer and to be tightly correlated with cancer development and progression, including increased cancer cell potential of proliferation, metastasis, and resistance to chemotherapy and radiotherapy. In the current review, we reveal ATAD3A as the link between mitochondrial functions and cancer biology and the accumulating evidence presenting ATAD3A as an attractive target for the development of novel cancer therapy to inhibit aberrant cancer metabolism and progression.
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Affiliation(s)
- Liwei Lang
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, GA 30912, USA; (L.L.); (R.L.)
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, GA 30912, USA; (L.L.); (R.L.)
| | - Yong Teng
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, GA 30912, USA; (L.L.); (R.L.)
- Georgia Cancer Center, Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medical Laboratory, Imaging and Radiologic Sciences, College of Allied Health, Augusta University, Augusta, GA 30912, USA
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17
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Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M, Lake NJ, Tregoning S, Jabbari JS, Lucattini A, Nitta KR, Ohtake A, Murayama K, Amor DJ, McGillivray G, Wong FY, van der Knaap MS, Jeroen Vermeulen R, Wiltshire EJ, Fletcher JM, Lewis B, Baynam G, Ellaway C, Balasubramaniam S, Bhattacharya K, Freckmann ML, Arbuckle S, Rodriguez M, Taft RJ, Sadedin S, Cowley MJ, Minoche AE, Calvo SE, Mootha VK, Ryan MT, Okazaki Y, Stroud DA, Simons C, Christodoulou J, Thorburn DR. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. MED 2020; 2:49-73. [PMID: 33575671 DOI: 10.1016/j.medj.2020.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.
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Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Alison G Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Daniella H Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - AnneMarie E Welch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.,Division of Genomic Medicine Research, Medical Genomics Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Min Wang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nicole J Lake
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Simone Tregoning
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University Hospital, Saitama, 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flora Y Wong
- Ritchie Centre, Hudson Institute of Medical Research; Department of Paediatrics, Monash University; and Monash Newborn, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Marjo S van der Knaap
- Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands
| | - R Jeroen Vermeulen
- Department of Neurology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | - Esko J Wiltshire
- Department of Paediatrics and Child Health, University of Otago Wellington and Capital and Coast District Health Board, Wellington 6021, New Zealand
| | - Janice M Fletcher
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Barry Lewis
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and King Edward Memorial Hospital for Women Perth, Subiaco, WA 6008, Australia.,Telethon Kids Institute and School of Paediatrics and Child Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | | | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW 2145, Australia
| | - Michael Rodriguez
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Simon Sadedin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Kensington, NSW 2750, Australia; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Lead contact
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18
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Ryl PSJ, Bohlke-Schneider M, Lenz S, Fischer L, Budzinski L, Stuiver M, Mendes MML, Sinn L, O'Reilly FJ, Rappsilber J. In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria. J Proteome Res 2019; 19:327-336. [PMID: 31746214 PMCID: PMC7010328 DOI: 10.1021/acs.jproteome.9b00541] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the popular noncleavable cross-linker disuccinimidyl suberate (DSS) to human mitochondria and identify 5518 distance restraints between protein residues. Each distance restraint on proteins or their interactions provides structural information within mitochondria. Comparing these restraints to protein data bank (PDB)-deposited structures and comparative models reveals novel protein conformations. Our data suggest, among others, substrates and protein flexibility of mitochondrial heat shock proteins. Through this study, we bring forward two central points for the progression of CLMS towards large-scale in situ structural biology: First, clustered conflicts of cross-link data reveal in situ protein conformation states in contrast to error-rich individual conflicts. Second, noncleavable cross-linkers are compatible with proteome-wide studies.
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Affiliation(s)
- Petra S J Ryl
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Michael Bohlke-Schneider
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Swantje Lenz
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Lutz Fischer
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , Edinburgh EH9 3BF , Scotland , United Kingdom
| | - Lisa Budzinski
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Marchel Stuiver
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Marta M L Mendes
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Ludwig Sinn
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , Edinburgh EH9 3BF , Scotland , United Kingdom
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19
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Peralta S, González-Quintana A, Ybarra M, Delmiro A, Pérez-Pérez R, Docampo J, Arenas J, Blázquez A, Ugalde C, Martín MA. Novel ATAD3A recessive mutation associated to fatal cerebellar hypoplasia with multiorgan involvement and mitochondrial structural abnormalities. Mol Genet Metab 2019; 128:452-462. [PMID: 31727539 DOI: 10.1016/j.ymgme.2019.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/24/2022]
Abstract
Lethal neonatal encephalopathies are heterogeneous congenital disorders that can be caused by mitochondrial dysfunction. Biallelic large deletions in the contiguous ATAD3B and ATAD3A genes, encoding mitochondrial inner membrane ATPases of unknown function, as well as compound heterozygous nonsense and missense mutations in the ATAD3A gene have been recently associated with fatal neonatal cerebellar hypoplasia. In this work, whole exome sequencing (WES) identified the novel homozygous variant c.1217 T > G in ATAD3A, predicting a p.(Leu406Arg) substitution, in four siblings from a consanguineous family presenting with fatal neonatal cerebellar hypoplasia, seizures, axial hypotonia, hypertrophic cardiomyopathy, hepatomegaly, congenital cataract, and dysmorphic facies. Biochemical phenotypes of the patients included hyperlactatemia and hypocholesterolemia. Healthy siblings and parents were heterozygous for this variant, which is predicted to introduce a polar chain within the catalytic domain of ATAD3A that shortens its beta-sheet structure, presumably affecting protein stability. Accordingly, patient's fibroblasts with the homozygous variant displayed a specific reduction in ATAD3A protein levels associated with profound ultrastructural alterations of mitochondrial cristae and morphology. Our findings exclude the causative role of ATAD3B on this severe phenotype, expand the phenotypical spectrum of ATAD3A pathogenic variants and emphasize the vital role of ATAD3A in mitochondrial biogenesis.
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Affiliation(s)
- Susana Peralta
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Adrián González-Quintana
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
| | - Marta Ybarra
- Servicio de Neonatología, Hospital Infantil La Paz, 28046 Madrid, Spain
| | - Aitor Delmiro
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
| | - Rafael Pérez-Pérez
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Jorge Docampo
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
| | - Joaquín Arenas
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
| | - Alberto Blázquez
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
| | - Cristina Ugalde
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain.
| | - Miguel A Martín
- Laboratorio de Enfermedades Raras, Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, U723, 28029 Madrid, Spain
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20
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Liu X, Li G, Ai L, Ye Q, Yu T, Yang B. Prognostic value of ATAD3 gene cluster expression in hepatocellular carcinoma. Oncol Lett 2019; 18:1304-1310. [PMID: 31423190 PMCID: PMC6607384 DOI: 10.3892/ol.2019.10454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 04/17/2019] [Indexed: 12/24/2022] Open
Abstract
ATPase family AAA domain-containing protein 3 (ATAD3) is a mitochondrial membrane-bound ATPase that is involved in a number of cellular processes and is linked with the progression of various types of malignancies. In primates, the ATAD3 gene cluster contains ATAD3A, ATAD3B and ATAD3C. The association between ATAD3 gene cluster expression and hepatocellular carcinoma (HCC) remains unknown. Therefore, the present study examined the prognostic significance of ATAD3 gene cluster expression in patients with HCC. Box plots of expression differences between HCC and normal liver tissues for the ATAD3 family genes were obtained from the online tool Gene Expression Profiling Interactive Analysis. Data from 360 patients with HCC in The Cancer Genome Atlas database were analyzed. Kaplan-Meier analysis and a Cox regression model were used to calculate median survival time (MST) and overall survival (OS). ATAD3A and ATAD3B expression levels were higher in HCC compared with normal liver tissues (P<0.05). However, ATAD3C expression was significantly decreased in HCC tissues compared with normal liver tissues (P<0.05). ATAD3A [P=0.017, hazard ratio (HR)=1.54, 95% confidence interval (CI)=1.08-2.20; adjusted P=0.032; adjusted HR=1.52; 95% CI=1.04-2.22] and ATAD3B (P=0.026, HR=1.49, 95% CI=1.05-2.13; adjusted P=0.031, adjusted HR=1.52, 95% CI=1.04-2.21) expression levels were significantly associated with OS. A joint-effects analysis revealed that patients with high ATAD3A and ATAD3B expression had reduced OS rates compared with patients with low ATAD3A and ATAD3B expression (P=0.007, HR=1.77, 95% CI=1.16-2.69; adjusted P=0.013, adjusted HR=1.76, 95% CI=1.13-2.75). In conclusion, ATAD3A and ATAD3B may serve as potential prognostic biomarkers for patients with HCC.
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Affiliation(s)
- Xiaoling Liu
- Department of Geriatrics, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Gang Li
- Department of Abdominal Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Liang Ai
- Department of Abdominal Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Qiuwen Ye
- Department of Abdominal Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Burong Yang
- Department of Abdominal Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
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21
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Differentially Expressed Mitochondrial Proteins in Human MCF7 Breast Cancer Cells Resistant to Paclitaxel. Int J Mol Sci 2019; 20:ijms20122986. [PMID: 31248089 PMCID: PMC6628585 DOI: 10.3390/ijms20122986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Identification of novel proteins with changed expression in resistant cancer cells could be helpful in elucidation mechanisms involved in the development of acquired resistance to paclitaxel. In this study, we carried out a 2D-PAGE using the mitochondrial-enriched fraction from paclitaxel-resistant MCF7/PacR cells compared to original paclitaxel-sensitive MCF7 breast cancer cells. Differentially expressed proteins were identified employing mass spectrometry. We found that lysosomal cathepsin D and mitochondrial abhydrolase-domain containing protein 11 (ABHD11) had decreased expression in MCF7/PacR cells. On the other hand, mitochondrial carbamoyl-phosphate synthetase 1 (CPS1) and ATPase family AAA-domain containing protein 3A and 3B (ATAD3A, ATAD3B) were overexpressed in MCF7/PacR cells. Further, we showed that there was no difference in localization of CPS1 in MCF7 and MCF7/PacR cells. We demonstrated a significant increase in the number of CPS1 positive MCF7/PacR cells, using FACS analysis, compared to the number of CPS1 positive MCF7 cells. Silencing of CPS1 expression by specific siRNA had no significant effect on the resistance of MCF7/PacR cells to paclitaxel. To summarize, we identified several novel proteins of a mitochondrial fraction whose role in acquired resistance to paclitaxel in breast cancer cells should be further assessed.
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22
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Zhao Y, Sun X, Hu D, Prosdocimo DA, Hoppel C, Jain MK, Ramachandran R, Qi X. ATAD3A oligomerization causes neurodegeneration by coupling mitochondrial fragmentation and bioenergetics defects. Nat Commun 2019; 10:1371. [PMID: 30914652 PMCID: PMC6435701 DOI: 10.1038/s41467-019-09291-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial fragmentation and bioenergetic failure manifest in Huntington’s disease (HD), a fatal neurodegenerative disease. The factors that couple mitochondrial fusion/fission with bioenergetics and their impacts on neurodegeneration however remain poorly understood. Our proteomic analysis identifies mitochondrial protein ATAD3A as an interactor of mitochondrial fission GTPase, Drp1, in HD. Here we show that, in HD, ATAD3A dimerization due to deacetylation at K135 residue is required for Drp1-mediated mitochondrial fragmentation. Disturbance of ATAD3A steady state impairs mtDNA maintenance by disrupting TFAM/mtDNA binding. Blocking Drp1/ATAD3A interaction with a peptide, DA1, abolishes ATAD3A oligomerization, suppresses mitochondrial fragmentation and mtDNA lesion, and reduces bioenergetic deficits and cell death in HD mouse- and patient-derived cells. DA1 treatment reduces behavioral and neuropathological phenotypes in HD transgenic mice. Our findings demonstrate that ATAD3A plays a key role in neurodegeneration by linking Drp1-induced mitochondrial fragmentation to defective mtDNA maintenance, suggesting that DA1 might be useful for developing HD therapeutics. Huntington’s disease leads to mitochondrial fragmentation and bioenergetic failure, although how the two events are connected is poorly understood. Here, Zhao et al. identify ATAD3A as a molecular linker and show that a peptide inhibitor of ATAD3A oligomerization suppresses HD phenotypes.
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Affiliation(s)
- Yuanyuan Zhao
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Xiaoyan Sun
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Domenick A Prosdocimo
- Case Cardiovascular Research Institute and Harrington Heart and Vascular Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Department of Medicine, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Charles Hoppel
- Center for Mitochondrial Disease, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mukesh K Jain
- Case Cardiovascular Research Institute and Harrington Heart and Vascular Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Department of Medicine, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA. .,Center for Mitochondrial Disease, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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23
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Baudier J. ATAD3 proteins: brokers of a mitochondria-endoplasmic reticulum connection in mammalian cells. Biol Rev Camb Philos Soc 2017; 93:827-844. [PMID: 28941010 DOI: 10.1111/brv.12373] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 12/25/2022]
Abstract
In yeast, a sequence of physical and genetic interactions termed the endoplasmic reticulum (ER)-mitochondria organizing network (ERMIONE) controls mitochondria-ER interactions and mitochondrial biogenesis. Several functions that characterize ERMIONE complexes are conserved in mammalian cells, suggesting that a similar tethering complex must exist in metazoans. Recent studies have identified a new family of nuclear-encoded ATPases associated with diverse cellular activities (AAA+-ATPase) mitochondrial membrane proteins specific to multicellular eukaryotes, called the ATPase family AAA domain-containing protein 3 (ATAD3) proteins (ATAD3A and ATAD3B). These proteins are crucial for normal mitochondrial-ER interactions and lie at the heart of processes underlying mitochondrial biogenesis. ATAD3A orthologues have been studied in flies, worms, and mammals, highlighting the widespread importance of this gene during embryonic development and in adulthood. ATAD3A is a downstream effector of target of rapamycin (TOR) signalling in Drosophila and exhibits typical features of proteins from the ERMIONE-like complex in metazoans. In humans, mutations in the ATAD3A gene represent a new link between altered mitochondrial-ER interaction and recognizable neurological syndromes. The primate-specific ATAD3B protein is a biomarker of pluripotent embryonic stem cells. Through negative regulation of ATAD3A function, ATAD3B supports mitochondrial stemness properties.
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Affiliation(s)
- Jacques Baudier
- Aix Marseille Université, CNRS, IBDM, 13284, Marseille Cedex 07, France.,Institut de Biologie du Développement de Marseille-UMR CNRS 7288, 13288, Marseille Cedex 9, France
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24
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Increased AAA-TOB3 correlates with lymph node metastasis and advanced stage of lung adenocarcinoma. Int J Biol Markers 2017. [PMID: 28623644 DOI: 10.5301/ijbm.5000275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND This study was to investigate the differential mitochondrial protein expressions in human lung adenocarcinoma and provide preliminary data for further exploration of the carcinogenic mechanism. METHODS Total proteins of A549 and 16HBE mitochondria were extracted through 2D polyacrylamide gel electrophoresis (2-DE). The differential mitochondria proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and were further confirmed by Western blot, immunoelectron microscopy and immunohistochemistry (IHC) in A549 cells as well as lung adenocarcinoma tissues. RESULTS A total of 41 differentially expressed protein spots were found in A549 mitochondria. Of them, 15 proteins were highly expressed and 26 proteins were lowly expressed in the mitochondria of A549 (by more than 1.5 times). Among the 15 more highly expressed proteins, AAA-TOB3 (by more than 3 times) was highly expressed in the mitochondria of A549 compared with the 16HBE, by LC-MS/MS identification. High electron density and clear circular colloidal gold-marked AAA-TOB3 particles were observed in the A549 cells via immunoelectron microscopy. Besides, AAA-TOB3 was confirmed to be elevated in lung adenocarcinoma by Western blot and IHC. Moreover, increased AAA-TOB3 correlated with lymph node metastasis and advanced stage of lung adenocarcinoma (p<0.05). CONCLUSIONS AAA-TOB3 was highly expressed in lung adenocarcinoma, and the up-regulation of AAA-TOB3 correlated with lymph node metastasis and advanced stage of lung adenocarcinoma, which suggested that it could serve as a potential molecular marker for lung adenocarcinoma.
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25
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Cooper HM, Yang Y, Ylikallio E, Khairullin R, Woldegebriel R, Lin KL, Euro L, Palin E, Wolf A, Trokovic R, Isohanni P, Kaakkola S, Auranen M, Lönnqvist T, Wanrooij S, Tyynismaa H. ATPase-deficient mitochondrial inner membrane protein ATAD3A disturbs mitochondrial dynamics in dominant hereditary spastic paraplegia. Hum Mol Genet 2017; 26:1432-1443. [PMID: 28158749 PMCID: PMC5393146 DOI: 10.1093/hmg/ddx042] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/24/2017] [Indexed: 01/02/2023] Open
Abstract
De novo mutations in ATAD3A (ATPase family AAA-domain containing protein 3A) were recently found to cause a neurological syndrome with developmental delay, hypotonia, spasticity, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. Using whole-exome sequencing, we identified a dominantly inherited heterozygous variant c.1064G > A (p.G355D) in ATAD3A in a mother presenting with hereditary spastic paraplegia (HSP) and axonal neuropathy and her son with dyskinetic cerebral palsy, both with disease onset in childhood. HSP is a clinically and genetically heterogeneous disorder of the upper motor neurons. Symptoms beginning in early childhood may resemble spastic cerebral palsy. The function of ATAD3A, a mitochondrial inner membrane AAA ATPase, is yet undefined. AAA ATPases form hexameric rings, which are catalytically dependent on the co-operation of the subunits. The dominant-negative patient mutation affects the Walker A motif, which is responsible for ATP binding in the AAA module of ATAD3A, and we show that the recombinant mutant ATAD3A protein has a markedly reduced ATPase activity. We further show that overexpression of the mutant ATAD3A fragments the mitochondrial network and induces lysosome mass. Similarly, we observed altered dynamics of the mitochondrial network and increased lysosomes in patient fibroblasts and neurons derived through differentiation of patient-specific induced pluripotent stem cells. These alterations were verified in patient fibroblasts to associate with upregulated basal autophagy through mTOR inactivation, resembling starvation. Mutations in ATAD3A can thus be dominantly inherited and underlie variable neurological phenotypes, including HSP, with intrafamiliar variability. This finding extends the group of mitochondrial inner membrane AAA proteins associated with spasticity.
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Affiliation(s)
- Helen M Cooper
- Åbo Akademi University, Faculty of Natural Sciences and Technology, Turku, Finland
| | - Yang Yang
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Emil Ylikallio
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Rafil Khairullin
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Rosa Woldegebriel
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Kai-Lan Lin
- Åbo Akademi University, Faculty of Natural Sciences and Technology, Turku, Finland
| | - Liliya Euro
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Eino Palin
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
| | - Ras Trokovic
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Child Neurology, Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Seppo Kaakkola
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mari Auranen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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26
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Control of mitochondrial function and cell growth by the atypical cadherin Fat1. Nature 2016; 539:575-578. [PMID: 27828948 DOI: 10.1038/nature20170] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/19/2016] [Indexed: 12/20/2022]
Abstract
Mitochondrial products such as ATP, reactive oxygen species, and aspartate are key regulators of cellular metabolism and growth. Abnormal mitochondrial function compromises integrated growth-related processes such as development and tissue repair, as well as homeostatic mechanisms that counteract ageing and neurodegeneration, cardiovascular disease, and cancer. Physiologic mechanisms that control mitochondrial activity in such settings remain incompletely understood. Here we show that the atypical Fat1 cadherin acts as a molecular 'brake' on mitochondrial respiration that regulates vascular smooth muscle cell (SMC) proliferation after arterial injury. Fragments of Fat1 accumulate in SMC mitochondria, and the Fat1 intracellular domain interacts with multiple mitochondrial proteins, including critical factors associated with the inner mitochondrial membrane. SMCs lacking Fat1 (Fat1KO) grow faster, consume more oxygen for ATP production, and contain more aspartate. Notably, expression in Fat1KO cells of a modified Fat1 intracellular domain that localizes exclusively to mitochondria largely normalizes oxygen consumption, and the growth advantage of these cells can be suppressed by inhibition of mitochondrial respiration, which suggest that a Fat1-mediated growth control mechanism is intrinsic to mitochondria. Consistent with this idea, Fat1 species associate with multiple respiratory complexes, and Fat1 deletion both increases the activity of complexes I and II and promotes the formation of complex-I-containing supercomplexes. In vivo, Fat1 is expressed in injured human and mouse arteries, and inactivation of SMC Fat1 in mice potentiates the response to vascular damage, with markedly increased medial hyperplasia and neointimal growth, and evidence of higher SMC mitochondrial respiration. These studies suggest that Fat1 controls mitochondrial activity to restrain cell growth during the reparative, proliferative state induced by vascular injury. Given recent reports linking Fat1 to cancer, abnormal kidney and muscle development, and neuropsychiatric disease, this Fat1 function may have importance in other settings of altered cell growth and metabolism.
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27
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Harel T, Yoon WH, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RA, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet 2016; 99:831-845. [PMID: 27640307 DOI: 10.1016/j.ajhg.2016.08.007] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/04/2016] [Indexed: 12/22/2022] Open
Abstract
ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane protein implicated in mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. We identified a recurrent de novo ATAD3A c.1582C>T (p.Arg528Trp) variant by whole-exome sequencing (WES) in five unrelated individuals with a core phenotype of global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. We also describe two families with biallelic variants in ATAD3A, including a homozygous variant in two siblings, and biallelic ATAD3A deletions mediated by nonallelic homologous recombination (NAHR) between ATAD3A and gene family members ATAD3B and ATAD3C. Tissue-specific overexpression of borR534W, the Drosophila mutation homologous to the human c.1582C>T (p.Arg528Trp) variant, resulted in a dramatic decrease in mitochondrial content, aberrant mitochondrial morphology, and increased autophagy. Homozygous null bor larvae showed a significant decrease of mitochondria, while overexpression of borWT resulted in larger, elongated mitochondria. Finally, fibroblasts of an affected individual exhibited increased mitophagy. We conclude that the p.Arg528Trp variant functions through a dominant-negative mechanism that results in small mitochondria that trigger mitophagy, resulting in a reduction in mitochondrial content. ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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Energy Metabolism Plays a Critical Role in Stem Cell Maintenance and Differentiation. Int J Mol Sci 2016; 17:253. [PMID: 26901195 PMCID: PMC4783982 DOI: 10.3390/ijms17020253] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/29/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022] Open
Abstract
Various stem cells gradually turned to be critical players in tissue engineering and regenerative medicine therapies. Current evidence has demonstrated that in addition to growth factors and the extracellular matrix, multiple metabolic pathways definitively provide important signals for stem cell self-renewal and differentiation. In this review, we mainly focus on a detailed overview of stem cell metabolism in vitro. In stem cell metabolic biology, the dynamic balance of each type of stem cell can vary according to the properties of each cell type, and they share some common points. Clearly defining the metabolic flux alterations in stem cells may help to shed light on stemness features and differentiation pathways that control the fate of stem cells.
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Human Mitochondrial DNA-Protein Complexes Attach to a Cholesterol-Rich Membrane Structure. Sci Rep 2015; 5:15292. [PMID: 26478270 PMCID: PMC4609938 DOI: 10.1038/srep15292] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/22/2015] [Indexed: 01/05/2023] Open
Abstract
The helicase Twinkle is indispensable for mtDNA replication in nucleoids. Previously, we showed that Twinkle is tightly membrane-associated even in the absence of mtDNA, which suggests that Twinkle is part of a membrane-attached replication platform. Here we show that this platform is a cholesterol-rich membrane structure. We fractionated mitochondrial membrane preparations on flotation gradients and show that membrane-associated nucleoids accumulate at the top of the gradient. This fraction was shown to be highly enriched in cholesterol, a lipid that is otherwise low abundant in mitochondria. In contrast, more common mitochondrial lipids, and abundant inner-membrane associated proteins concentrated in the bottom-half of these gradients. Gene silencing of ATAD3, a protein with proposed functions related to nucleoid and mitochondrial cholesterol homeostasis, modified the distribution of cholesterol and nucleoids in the gradient in an identical fashion. Both cholesterol and ATAD3 were previously shown to be enriched in ER-mitochondrial junctions, and we detect nucleoid components in biochemical isolates of these structures. Our data suggest an uncommon membrane composition that accommodates platforms for replicating mtDNA, and reconcile apparently disparate functions of ATAD3. We suggest that mtDNA replication platforms are organized in connection with ER-mitochondrial junctions, facilitated by a specialized membrane architecture involving mitochondrial cholesterol.
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Mitochondrial ATAD3A combines with GRP78 to regulate the WASF3 metastasis-promoting protein. Oncogene 2015; 35:333-43. [PMID: 25823022 PMCID: PMC4828935 DOI: 10.1038/onc.2015.86] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/26/2015] [Accepted: 02/16/2015] [Indexed: 02/08/2023]
Abstract
AAA domain containing 3A (ATAD3A) is an integral mitochondrial membrane protein with unknown function, although we now show that high-level expression is associated with poor survival in breast cancer patients. Using a mass spectrometry approach we have demonstrated that ATAD3A interacts with the WASF3 metastasis-promoting protein. Knockdown of ATAD3A leads to decreased WASF3 protein levels in breast and colon cancer cells. Silencing ATAD3A also results in loss of both cell anchorage-independent growth and invasion and suppression of tumor growth and metastasis in vivo using immuno-compromised mice. HSP70 is responsible for stabilizing WASF3 in the cytoplasm, but inactivation of HSP70 does not lead to the loss of WASF3 stability at the mitochondrial membrane, where presumably it is protected through its interaction with ATAD3A. In response to endoplasmic reticulum (ER) stress, increases in the GRP78 protein level leads to increased WASF3 protein levels. We also show that ATAD3A was present in a WASF3-GRP78 complex, and suppression of GRP78 led to destabilization of WASF3 at the mitochondrial membrane, which was ATAD3A dependent. Furthermore, ATAD3A-mediated suppression of CDH1/E-cadherin occurs through its regulation of GRP78-mediated WASF3 stability. Proteolysis experiments using isolated mitochondria demonstrates the presence of the N-terminal end of WASF3 within the mitochondria, which is the interaction site with the N-terminal end of ATAD3A. It appears, therefore, that stabilization of WASF3 function occurs through its interaction with ATAD3A and GRP78, which may provide a bridge between the ER and mitochondria, allowing communication between the two organelles. These findings also suggest that pharmacologic inhibition of ATAD3A could be an effective therapeutic strategy to treat human cancer.
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Li S, Lamarche F, Charton R, Delphin C, Gires O, Hubstenberger A, Schlattner U, Rousseau D. Expression analysis of ATAD3 isoforms in rodent and human cell lines and tissues. Gene 2014; 535:60-9. [DOI: 10.1016/j.gene.2013.10.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/28/2013] [Accepted: 10/31/2013] [Indexed: 11/26/2022]
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Goller T, Seibold UK, Kremmer E, Voos W, Kolanus W. Atad3 function is essential for early post-implantation development in the mouse. PLoS One 2013; 8:e54799. [PMID: 23372768 PMCID: PMC3556029 DOI: 10.1371/journal.pone.0054799] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 12/17/2012] [Indexed: 12/22/2022] Open
Abstract
The mitochondrial AAA+-ATPase ATAD3 is implicated in the regulation of mitochondrial and ER dynamics and was shown to be necessary for larval development in Caenorhabditis elegans. In order to elucidate the relevance of ATAD3 for mammalian development, the phenotype of an Atad3 deficient mouse line was analyzed. Atad3 deficient embryos die around embryonic day E7.5 due to growth retardation and a defective development of the trophoblast lineage immediately after implantation into the uterus. This indicates an essential function of Atad3 for the progression of the first steps of post-implantation development at a time point when mitochondrial biogenesis and ATP production by oxidative phosphorylation are required. Therefore, murine Atad3 plays an important role in the biogenesis of mitochondria in trophoblast stem cells and in differentiating trophoblasts. At the biochemical level, we report here that ATAD3 is present in five native mitochondrial protein complexes of different sizes, indicating complex roles of the protein in mitochondrial architecture and function.
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Affiliation(s)
- Tobias Goller
- LIMES Institute, Program Unit Molecular Cell and Immune Biology, University of Bonn, Bonn, Germany
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