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Omrani M, Chiarelli RR, Acquaviva M, Bassani C, Dalla Costa G, Montini F, Preziosa P, Pagani L, Grassivaro F, Guerrieri S, Romeo M, Sangalli F, Colombo B, Moiola L, Zaffaroni M, Pietroboni A, Protti A, Puthenparampil M, Bergamaschi R, Comi G, Rocca MA, Martinelli V, Filippi M, Farina C. Machine learning-driven diagnosis of multiple sclerosis from whole blood transcriptomics. Brain Behav Immun 2024; 121:269-277. [PMID: 39097200 DOI: 10.1016/j.bbi.2024.07.039] [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: 04/09/2024] [Revised: 07/23/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024] Open
Abstract
Multiple sclerosis (MS) is a neurological disorder characterized by immune dysregulation. It begins with a first clinical manifestation, a clinically isolated syndrome (CIS), which evolves to definite MS in case of further clinical and/or neuroradiological episodes. Here we evaluated the diagnostic value of transcriptional alterations in MS and CIS blood by machine learning (ML). Deep sequencing of more than 200 blood RNA samples comprising CIS, MS and healthy subjects, generated transcriptomes that were analyzed by the binary classification workflow to distinguish MS from healthy subjects and the Time-To-Event pipeline to predict CIS conversion to MS along time. To identify optimal classifiers, we performed algorithm benchmarking by nested cross-validation with the train set in both pipelines and then tested models generated with the train set on an independent dataset for final validation. The binary classification model identified a blood transcriptional signature classifying definite MS from healthy subjects with 97% accuracy, indicating that MS is associated with a clear predictive transcriptional signature in blood cells. When analyzing CIS data with ML survival models, prediction power of CIS conversion to MS was about 72% when using paraclinical data and 74.3% when using blood transcriptomes, indicating that blood-based classifiers obtained at the first clinical event can efficiently predict risk of developing MS. Coupling blood transcriptomics with ML approaches enables retrieval of predictive signatures of CIS conversion and MS state, thus introducing early non-invasive approaches to MS diagnosis.
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Affiliation(s)
- Maryam Omrani
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rosaria Rita Chiarelli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Acquaviva
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Bassani
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gloria Dalla Costa
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Federico Montini
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Preziosa
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | | | - Francesca Grassivaro
- Dipartimento di Neuroscienze, Azienda Ospedale - Università di Padova, Padova, Italy
| | - Simone Guerrieri
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marzia Romeo
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Sangalli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bruno Colombo
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Moiola
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mauro Zaffaroni
- Centro Sclerosi Multipla, ASST della Valle Olona, Ospedale di Gallarate, Gallarate, Italy
| | - Anna Pietroboni
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Marco Puthenparampil
- Dipartimento di Neuroscienze, Azienda Ospedale - Università di Padova, Padova, Italy
| | | | - Giancarlo Comi
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Maria A Rocca
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Vittorio Martinelli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Filippi
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Cinthia Farina
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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Liu X, Wang Q, Zhou M, Wang Y, Wang X, Zhou X, Song Q. DrugFormer: Graph-Enhanced Language Model to Predict Drug Sensitivity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405861. [PMID: 39206872 DOI: 10.1002/advs.202405861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/19/2024] [Indexed: 09/04/2024]
Abstract
Drug resistance poses a crucial challenge in healthcare, with response rates to chemotherapy and targeted therapy remaining low. Individual patient's resistance is exacerbated by the intricate heterogeneity of tumor cells, presenting significant obstacles to effective treatment. To address this challenge, DrugFormer, a novel graph-augmented large language model designed to predict drug resistance at single-cell level is proposed. DrugFormer integrates both serialized gene tokens and gene-based knowledge graphs for the accurate predictions of drug response. After training on comprehensive single-cell data with drug response information, DrugFormer model presents outperformance, with higher F1, precision, and recall in predicting drug response. Based on the scRNA-seq data from refractory multiple myeloma (MM) and acute myeloid leukemia (AML) patients, DrugFormer demonstrates high efficacy in identifying resistant cells and uncovering underlying molecular mechanisms. Through pseudotime trajectory analysisunique drug-resistant cellular states associated with poor patient outcomes are revealed. Furthermore, DrugFormer identifies potential therapeutic targets, such as COX8A, for overcoming drug resistance across different cancer types. In conclusion, DrugFormer represents a significant advancement in the field of drug resistance prediction, offering a powerful tool for unraveling the heterogeneity of cellular response to drugs and guiding personalized treatment strategies.
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Affiliation(s)
- Xiaona Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Qing Wang
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Minghao Zhou
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Yanfei Wang
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Xuefeng Wang
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
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Othonicar MF, Garcia GS, Oliveira MT. The alternative enzymes-bearing tunicates lack multiple widely distributed genes coding for peripheral OXPHOS subunits. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149046. [PMID: 38642871 DOI: 10.1016/j.bbabio.2024.149046] [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: 09/10/2023] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The respiratory chain alternative enzymes (AEs) NDX and AOX from the tunicate Ciona intestinalis (Ascidiacea) have been xenotopically expressed and characterized in human cells in culture and in the model organisms Drosophila melanogaster and mouse, with the purpose of developing bypass therapies to combat mitochondrial diseases in human patients with defective complexes I and III/IV, respectively. The fact that the genes coding for NDX and AOX have been lost from genomes of evolutionarily successful animal groups, such as vertebrates and insects, led us to investigate if the composition of the respiratory chain of Ciona and other tunicates differs significantly from that of humans and Drosophila, to accommodate the natural presence of AEs. We have failed to identify in tunicate genomes fifteen orthologous genes that code for subunits of the respiratory chain complexes; all of these putatively missing subunits are peripheral to complexes I, III and IV in mammals, and many are important for complex-complex interaction in supercomplexes (SCs), such as NDUFA11, UQCR11 and COX7A. Modeling of all respiratory chain subunit polypeptides of Ciona indicates significant structural divergence that is consistent with the lack of these fifteen clear orthologous subunits. We also provide evidence using Ciona AOX expressed in Drosophila that this AE cannot access the coenzyme Q pool reduced by complex I, but it is readily available to oxidize coenzyme Q molecules reduced by glycerophosphate oxidase, a mitochondrial inner membrane-bound dehydrogenase that is not involved in SCs. Altogether, our results suggest that Ciona AEs might have evolved in a mitochondrial inner membrane environment much different from that of mammals and insects, possibly without SCs; this correlates with the preferential functional interaction between these AEs and non-SC dehydrogenases in heterologous mammalian and insect systems. We discuss the implications of these findings for the applicability of Ciona AEs in human bypass therapies and for our understanding of the evolution of animal respiratory chain.
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Affiliation(s)
- Murilo F Othonicar
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Geovana S Garcia
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Marcos T Oliveira
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil.
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Shu Z, Ji Y, Liu F, Jing Y, Jiao C, Li Y, Zhao Y, Wang G, Zhang J. Proteomics Analysis of the Protective Effect of Polydeoxyribonucleotide Extracted from Sea Cucumber ( Apostichopus japonicus) Sperm in a Hydrogen Peroxide-Induced RAW264.7 Cell Injury Model. Mar Drugs 2024; 22:325. [PMID: 39057434 PMCID: PMC11277713 DOI: 10.3390/md22070325] [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: 06/13/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Sea cucumber viscera contain various naturally occurring active substances, but they are often underutilized during sea cucumber processing. Polydeoxyribonucleotide (PDRN) is an adenosine A2A receptor agonist that activates the A2A receptor to produce various biological effects. Currently, most studies on the activity of PDRN have focused on its anti-inflammatory, anti-apoptotic, and tissue repair properties, yet relatively few studies have investigated its antioxidant activity. In this study, we reported for the first time that PDRN was extracted from the sperm of Apostichopus japonicus (AJS-PDRN), and we evaluated its antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS), and hydroxyl radical scavenging assays. An in vitro injury model was established using H2O2-induced oxidative damage in RAW264.7 cells, and we investigated the protective effect of AJS-PDRN on these cells. Additionally, we explored the potential mechanism by which AJS-PDRN protects RAW264.7 cells from damage using iTRAQ proteomics analysis. The results showed that AJS-PDRN possessed excellent antioxidant activity and could significantly scavenge DPPH, ABTS, and hydroxyl radicals. In vitro antioxidant assays demonstrated that AJS-PDRN was cytoprotective and significantly enhanced the antioxidant capacity of RAW264.7 cells. The results of GO enrichment and KEGG pathway analysis indicate that the protective effects of AJS-PDRN pretreatment on RAW264.7 cells are primarily achieved through the regulation of immune and inflammatory responses, modulation of the extracellular matrix and signal transduction pathways, promotion of membrane repair, and enhancement of cellular antioxidant capacity. The results of a protein-protein interaction (PPI) network analysis indicate that AJS-PDRN reduces cellular oxidative damage by upregulating the expression of intracellular selenoprotein family members. In summary, our findings reveal that AJS-PDRN mitigates H2O2-induced oxidative damage through multiple pathways, underscoring its significant potential in the prevention and treatment of diseases caused by oxidative stress.
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Affiliation(s)
- Zhiqiang Shu
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yizhi Ji
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Fang Liu
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Yuexin Jing
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Chunna Jiao
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Yue Li
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yunping Zhao
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Gongming Wang
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Jian Zhang
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
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Shimada K, Lu Y, Ikawa M. Disruption of testis-enriched cytochrome c oxidase subunit COX6B2 but not COX8C leads to subfertility. Exp Anim 2024; 73:1-10. [PMID: 37423748 PMCID: PMC10877148 DOI: 10.1538/expanim.23-0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
Mammalian sperm flagellum contains the midpiece characterized by a mitochondrial sheath that packs tightly around the axoneme and outer dense fibers. Mitochondria are known as the "powerhouse" of the cell, and produce ATP through the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS). However, the contribution of the TCA cycle and OXPHOS to sperm motility and male fertility is less clear. Cytochrome c oxidase (COX) is an oligomeric complex localized within the mitochondrial inner membrane, and the terminal enzyme of the mitochondrial electron transport chain in eukaryotes. Both COX6B2 and COX8C are testis-enriched COX subunits whose functions in vivo are poorly studied. Here, we generated Cox6b2 and Cox8c knockout (KO) mice using the CRISPR/Cas9 system. We examined their fertility and sperm mitochondrial function to determine the significance of testis-enriched COX subunits in male fertility. The mating test revealed that disrupting COX6B2 induces male subfertility, while disrupting COX8C does not affect male fertility. Cox6b2 KO spermatozoa showed low sperm motility, but mitochondrial function was normal according to oxygen consumption rates. Therefore, low sperm motility seems to cause subfertility in Cox6b2 KO male mice. These results also indicate that testis-enriched COX, COX6B2 and COX8C, are not essential for OXPHOS in mouse spermatozoa.
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Affiliation(s)
- Keisuke Shimada
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yonggang Lu
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Sneha NP, Dharshini SAP, Taguchi YH, Gromiha MM. Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study. Genes (Basel) 2023; 14:1801. [PMID: 37761940 PMCID: PMC10530489 DOI: 10.3390/genes14091801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.
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Affiliation(s)
- Nela Pragathi Sneha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - S. Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - Y.-h. Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan;
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
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Park SW, Park IB, Kang SJ, Bae J, Chun T. Interaction between host cell proteins and open reading frames of porcine circovirus type 2. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:698-719. [PMID: 37970506 PMCID: PMC10640953 DOI: 10.5187/jast.2023.e67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/28/2023] [Accepted: 07/09/2023] [Indexed: 11/17/2023]
Abstract
Postweaning multisystemic wasting syndrome (PMWS) is caused by a systemic inflammation after porcine circovirus type 2 (PCV2) infection. It was one of the most economically important pathogens affecting pig production worldwide before PCV2 vaccine was first introduced in 2006. After the development of a vaccine against PCV2a type, pig farms gradually restored enormous economic losses from PMWS. However, vaccine against PCV2a type could not be fully effective against several different PCV2 genotypes (PCV2b - PCV2h). In addition, PCV2a vaccine itself could generate antigenic drift of PCV2 capsid. Therefore, PCV2 infection still threats pig industry worldwide. PCV2 infection was initially found in local tissues including reproductive, respiratory, and digestive tracks. However, PCV2 infection often leads to a systemic inflammation which can cause severe immunosuppression by depleting peripheral lymphocytes in secondary lymphoid tissues. Subsequently, a secondary infection with other microorganisms can cause PMWS. Eleven putative open reading frames (ORFs) have been predicted to encode PCV2 genome. Among them, gene products of six ORFs from ORF1 to ORF6 have been identified and characterized to estimate its functional role during PCV2 infection. Acquiring knowledge about the specific interaction between each PCV2 ORF protein and host protein might be a key to develop preventive or therapeutic tools to control PCV2 infection. In this article, we reviewed current understanding of how each ORF of PCV2 manipulates host cell signaling related to immune suppression caused by PCV2.
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Affiliation(s)
- Si-Won Park
- Department of Biotechnology, School of
Life Sciences and Biotechnology, Korea University, Seoul
02841, Korea
| | - In-Byung Park
- Department of Biotechnology, School of
Life Sciences and Biotechnology, Korea University, Seoul
02841, Korea
| | - Seok-Jin Kang
- Department of Biotechnology, School of
Life Sciences and Biotechnology, Korea University, Seoul
02841, Korea
| | - Joonbeom Bae
- Department of Biotechnology, School of
Life Sciences and Biotechnology, Korea University, Seoul
02841, Korea
| | - Taehoon Chun
- Department of Biotechnology, School of
Life Sciences and Biotechnology, Korea University, Seoul
02841, Korea
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Abstract
Leigh syndrome, or subacute necrotizing encephalomyelopathy, was initially recognized as a neuropathological entity in 1951. Bilateral symmetrical lesions, typically extending from the basal ganglia and thalamus through brainstem structures to the posterior columns of the spinal cord, are characterized microscopically by capillary proliferation, gliosis, severe neuronal loss, and relative preservation of astrocytes. Leigh syndrome is a pan-ethnic disorder usually with onset in infancy or early childhood, but late-onset forms occur, including in adult life. Over the last six decades it has emerged that this complex neurodegenerative disorder encompasses more than 100 separate monogenic disorders associated with enormous clinical and biochemical heterogeneity. This chapter discusses clinical, biochemical and neuropathological aspects of the disorder, and postulated pathomechanisms. Known genetic causes, including defects of 16 mitochondrial DNA (mtDNA) genes and approaching 100 nuclear genes, are categorized into disorders of subunits and assembly factors of the five oxidative phosphorylation enzymes, disorders of pyruvate metabolism and vitamin and cofactor transport and metabolism, disorders of mtDNA maintenance, and defects of mitochondrial gene expression, protein quality control, lipid remodeling, dynamics, and toxicity. An approach to diagnosis is presented, together with known treatable causes and an overview of current supportive management options and emerging therapies on the horizon.
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Affiliation(s)
- Shamima Rahman
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Metabolic Medicine Department, Great Ormond Street Hospital for Children, London, United Kingdom.
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Protein Transduction Domain-Mediated Delivery of Recombinant Proteins and In Vitro Transcribed mRNAs for Protein Replacement Therapy of Human Severe Genetic Mitochondrial Disorders: The Case of Sco2 Deficiency. Pharmaceutics 2023; 15:pharmaceutics15010286. [PMID: 36678915 PMCID: PMC9861957 DOI: 10.3390/pharmaceutics15010286] [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: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial disorders represent a heterogeneous group of genetic disorders with variations in severity and clinical outcomes, mostly characterized by respiratory chain dysfunction and abnormal mitochondrial function. More specifically, mutations in the human SCO2 gene, encoding the mitochondrial inner membrane Sco2 cytochrome c oxidase (COX) assembly protein, have been implicated in the mitochondrial disorder fatal infantile cardioencephalomyopathy with COX deficiency. Since an effective treatment is still missing, a protein replacement therapy (PRT) was explored using protein transduction domain (PTD) technology. Therefore, the human recombinant full-length mitochondrial protein Sco2, fused to TAT peptide (a common PTD), was produced (fusion Sco2 protein) and successfully transduced into fibroblasts derived from a SCO2/COX-deficient patient. This PRT contributed to effective COX assembly and partial recovery of COX activity. In mice, radiolabeled fusion Sco2 protein was biodistributed in the peripheral tissues of mice and successfully delivered into their mitochondria. Complementary to that, an mRNA-based therapeutic approach has been more recently considered as an innovative treatment option. In particular, a patented, novel PTD-mediated IVT-mRNA delivery platform was developed and applied in recent research efforts. PTD-IVT-mRNA of full-length SCO2 was successfully transduced into the fibroblasts derived from a SCO2/COX-deficient patient, translated in host ribosomes into a nascent chain of human Sco2, imported into mitochondria, and processed to the mature protein. Consequently, the recovery of reduced COX activity was achieved, thus suggesting the potential of this mRNA-based technology for clinical translation as a PRT for metabolic/genetic disorders. In this review, such research efforts will be comprehensibly presented and discussed to elaborate their potential in clinical application and therapeutic usefulness.
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Wang L, Yang Z, He X, Pu S, Yang C, Wu Q, Zhou Z, Cen X, Zhao H. Mitochondrial protein dysfunction in pathogenesis of neurological diseases. Front Mol Neurosci 2022; 15:974480. [PMID: 36157077 PMCID: PMC9489860 DOI: 10.3389/fnmol.2022.974480] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Mitochondria are essential organelles for neuronal function and cell survival. Besides the well-known bioenergetics, additional mitochondrial roles in calcium signaling, lipid biogenesis, regulation of reactive oxygen species, and apoptosis are pivotal in diverse cellular processes. The mitochondrial proteome encompasses about 1,500 proteins encoded by both the nuclear DNA and the maternally inherited mitochondrial DNA. Mutations in the nuclear or mitochondrial genome, or combinations of both, can result in mitochondrial protein deficiencies and mitochondrial malfunction. Therefore, mitochondrial quality control by proteins involved in various surveillance mechanisms is critical for neuronal integrity and viability. Abnormal proteins involved in mitochondrial bioenergetics, dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance have been linked to the pathogenesis of a number of neurological diseases. The goal of this review is to give an overview of these pathways and to summarize the interconnections between mitochondrial protein dysfunction and neurological diseases.
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Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Ziyun Yang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiumei He
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Cheng Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Zuping Zhou
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Hongxia Zhao
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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11
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Sun JJ, Cai Q, Xu M, Liu YN, Li WR, Li J, Ma L, Cai C, Gong XH, Zeng YT, Ren ZR, Zeng F. Loss of Protein Function Causing Severe Phenotypes of Female-Restricted Wieacker Wolff Syndrome due to a Novel Nonsense Mutation in the ZC4H2 Gene. Genes (Basel) 2022; 13:genes13091558. [PMID: 36140726 PMCID: PMC9498907 DOI: 10.3390/genes13091558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
Pathogenic variants of zinc finger C4H2-type containing (ZC4H2) on the X chromosome cause a group of genetic diseases termed ZC4H2-associated rare disorders (ZARD), including Wieacker-Wolff Syndrome (WRWF) and Female-restricted Wieacker-Wolff Syndrome (WRWFFR). In the current study, a de novo c.352C>T (p.Gln118*) mutation in ZC4H2 (NM_018684.4) was identified in a female neonate born with severe arthrogryposis multiplex congenita (AMC) and Pierre-Robin sequence (cleft palate and micrognathia). Plasmids containing the wild-type (WT), mutant-type (MT) ZC4H2, or GFP report gene (N) were transfected in 293T cell lines, respectively. RT-qPCR and western blot analysis showed that ZC4H2 protein could not be detected in the 293T cells transfected with MT ZC4H2. The RNA seq results revealed that the expression profile of the MT group was similar to that of the N group but differed significantly from the WT group, indicating that the c.352C>T mutation resulted in the loss of function of ZC4H2. Differentially expressed genes (DEGs) enrichment analysis showed that c.352C>T mutation inhibited the expression levels of a series of genes involved in the oxidative phosphorylation pathway. Subsequently, expression levels of ZC4H2 were knocked down in neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs) by lentiviral-expressed small hairpin RNAs (shRNAs) against ZC4H2. The results also demonstrated that decreasing the expression of ZC4H2 significantly reduced the growth of NSCs by affecting the expression of genes related to the oxidative phosphorylation signaling pathway. Taken together, our results strongly suggest that ZC4H2 c.352C>T (p.Gln118*) mutation resulted in the loss of protein function and caused WRWFFR.
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Affiliation(s)
- Jing-Jing Sun
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- Department of Neonatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Qin Cai
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Miao Xu
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Yan-Na Liu
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Wan-Rui Li
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Juan Li
- Department of Neonatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Li Ma
- Department of Neonatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Cheng Cai
- Department of Neonatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Xiao-Hui Gong
- Department of Neonatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Yi-Tao Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Zhao-Rui Ren
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
- Correspondence: ; Tel.: +86-21-62472308
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12
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Ling Q, Rioux M, Hu Y, Lee M, Gray SJ. Adeno-associated viral vector serotype 9-based gene replacement therapy for SURF1-related Leigh syndrome. Mol Ther Methods Clin Dev 2021; 23:158-168. [PMID: 34703839 PMCID: PMC8517205 DOI: 10.1016/j.omtm.2021.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 12/20/2022]
Abstract
SURF1 (surfeit locus protein 1)-related Leigh syndrome is an early-onset neurodegenerative disorder, characterized by reduction in complex IV activity, resulting in disrupted mitochondrial function. Currently, there are no treatment options available. To test our hypothesis that adeno-associated viral vector serotype 9 (AAV9)/human SURF1 (hSURF1) gene replacement therapy can provide a potentially meaningful and long-term therapeutic benefit, we conducted preclinical efficacy studies using SURF1 knockout mice and safety evaluations with wild-type (WT) mice. Our data indicate that with a single intrathecal (i.t.) administration, our treatment partially and significantly rescued complex IV activity in all tissues tested, including liver, brain, and muscle. Accordingly, complex IV content (examined via MT-CO1 protein expression level) also increased with our treatment. In a separate group of mice, AAV9/hSURF1 mitigated the blood lactic acidosis induced by exhaustive exercise at 9 months post-dosing. A toxicity study in WT mice showed no adverse effects in either the in-life portion or after microscopic examination of major tissues up to a year following the same treatment regimen. Taken together, our data suggest a single dose, i.t. administration of AAV9/hSURF1 is safe and effective in improving biochemical abnormalities induced by SURF1 deficiency with potential applicability for SURF1-related Leigh syndrome patients.
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Affiliation(s)
- Qinglan Ling
- Department of Pediatrics, UTSW Medical Center, Dallas, TX 75390, USA
| | - Matthew Rioux
- Department of Pediatrics, UTSW Medical Center, Dallas, TX 75390, USA
| | - Yuhui Hu
- Department of Pediatrics, UTSW Medical Center, Dallas, TX 75390, USA
| | - MinJae Lee
- Department of Population and Data Science, UTSW Medical Center, Dallas, TX 75390, USA
| | - Steven J. Gray
- Department of Pediatrics, UTSW Medical Center, Dallas, TX 75390, USA
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13
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Bakare AB, Lesnefsky EJ, Iyer S. Leigh Syndrome: A Tale of Two Genomes. Front Physiol 2021; 12:693734. [PMID: 34456746 PMCID: PMC8385445 DOI: 10.3389/fphys.2021.693734] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022] Open
Abstract
Leigh syndrome is a rare, complex, and incurable early onset (typically infant or early childhood) mitochondrial disorder with both phenotypic and genetic heterogeneity. The heterogeneous nature of this disorder, based in part on the complexity of mitochondrial genetics, and the significant interactions between the nuclear and mitochondrial genomes has made it particularly challenging to research and develop therapies. This review article discusses some of the advances that have been made in the field to date. While the prognosis is poor with no current substantial treatment options, multiple studies are underway to understand the etiology, pathogenesis, and pathophysiology of Leigh syndrome. With advances in available research tools leading to a better understanding of the mitochondria in health and disease, there is hope for novel treatment options in the future.
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Affiliation(s)
- Ajibola B. Bakare
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Edward J. Lesnefsky
- Division of Cardiology, Pauley Heart Center, Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Physiology/Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR, United States
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14
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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15
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Rotko D, Kudin AP, Zsurka G, Kulawiak B, Szewczyk A, Kunz WS. Molecular and Functional Effects of Loss of Cytochrome c Oxidase Subunit 8A. BIOCHEMISTRY (MOSCOW) 2021; 86:33-43. [PMID: 33705280 DOI: 10.1134/s0006297921010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this work we studied molecular and functional effects of the loss of the smallest nuclear encoded subunit of cytochrome c oxidase COX8A in fibroblasts from a patient with a homozygous splice site mutation and in CRISPR/Cas9 genome-edited HEK293T cells. In both cellular model systems, between 20 to 30% of the residual enzymatic activity of cytochrome c oxidase (COX) was detectable. In immunoblots of BN-PAGE separated mitochondria from both cellular models almost no monomers and dimers of the fully assembled COX could be visualized. Interestingly, supercomplexes of COX formed with complex III and also with complexes I and III retained considerable immunoreactivity, while nearly no immunoreactivity attributable to subassemblies was found. That indicates that COX lacking subunit 8A is stabilized in supercomplexes, while monomers and dimers are rapidly degraded. With transcriptome analysis by 3'-RNA sequencing we failed to detect in our cellular models of COX8A deficiency transcriptional changes of genes involved in the mitochondrial unfolded protein response (mtUPR) and the integrated stress response (ISR). Thus, our data strongly suggest that the smallest subunit of cytochrome c oxidase COX8A is required for maintenance of the structural stability of COX monomers and dimers.
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Affiliation(s)
- Daria Rotko
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland
| | - Alexei P Kudin
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany.
| | - Gábor Zsurka
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Department of Epileptology, University Bonn Medical Center, Venusberg-Campus 1, Bonn, 53127, Germany
| | - Bogusz Kulawiak
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland.
| | - Adam Szewczyk
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland.
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Department of Epileptology, University Bonn Medical Center, Venusberg-Campus 1, Bonn, 53127, Germany
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16
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Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J 2021; 477:4085-4132. [PMID: 33151299 PMCID: PMC7657662 DOI: 10.1042/bcj20190767] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
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17
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Jain PN, Robertson M, Lasa JJ, Shekerdemian L, Guffey D, Zhang Y, Lingappan K, Checchia P, Coarfa C. Altered metabolic and inflammatory transcriptomics after cardiac surgery in neonates with congenital heart disease. Sci Rep 2021; 11:4965. [PMID: 33654130 PMCID: PMC7925649 DOI: 10.1038/s41598-021-83882-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
The study examines the whole blood transcriptome profile before and after cardiopulmonary bypass (CPB) in neonates with hypoplastic left heart syndrome (HLHS), a severe form of congenital heart disease, that can develop low cardiac output syndrome (LCOS). Whole blood mRNA transcriptome profiles of 13 neonates with HLHS before and after their first palliative surgery were analyzed to determine differentially expressed genes and pathways. The median age and weight at surgery were 4 days and 3.2 kg, respectively. Of the 13 patients, 8 developed LCOS. There was no significant difference between CPB, aortic cross clamp, deep hypothermic cardiac arrest times between patients that develop LCOS and those that do not. Upon comparing differential gene expression profiles between patients that develop LCOS and those that do not in pre-operative samples, 1 gene was up-regulated and 13 were down regulated. In the post-operative samples, 4 genes were up-regulated, and 4 genes were down regulated when patients that develop LCOS were compared to those that do not. When comparing post-operative samples to pre-operative samples in the patients that do not develop LCOS, 1484 genes were up-regulated, and 1388 genes were down regulated; while patients that developed LCOS had 2423 up-regulated genes, and 2414 down regulated genes for the same pre to post-operative comparison. Pathway analysis revealed differential regulation of inflammatory pathways (IL signaling, PDGF, NOTCH1, NGF, GPCR) and metabolic pathways (heme metabolism, oxidative phosphorylation, protein metabolism including amino acid and derivatives, fatty acid metabolism, TCA cycle and respiratory electron transport chain). By identifying altered transcriptome profiles related to inflammation and metabolism in neonates with HLHS who develop LCOS after CPB, this study opens for exploration novel pathways and potential therapeutic targets to improve outcomes in this high-risk population.
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Affiliation(s)
- Parag N Jain
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.
| | | | - Javier J Lasa
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Lara Shekerdemian
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | | | - Yuhao Zhang
- Baylor College of Medicine, Houston, TX, USA
| | - Krithika Lingappan
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Paul Checchia
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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18
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Aly KA, Moutaoufik MT, Phanse S, Zhang Q, Babu M. From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 2021; 24:102030. [PMID: 33521598 PMCID: PMC7820543 DOI: 10.1016/j.isci.2020.102030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial (mt) dysfunction is linked to rare diseases (RDs) such as respiratory chain complex (RCC) deficiency, MELAS, and ARSACS. Yet, how altered mt protein networks contribute to these ailments remains understudied. In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs. Accordingly, we discuss innovative untargeted label-free proteomics in identifying RD-specific mt or other macromolecular assemblies and mapping of protein networks in complex tissue, organoid, and stem cell-differentiated neurons. Furthermore, tag- and label-based proteomics, genealogical proteomics, and combinatorial affinity purification-mass spectrometry, along with advancements in detecting and integrating transient PPIs with single-cell proteomics and transcriptomics, collectively offer seminal follow-ups to enrich for RD-relevant networks, with implications in RD precision medicine.
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Affiliation(s)
- Khaled A. Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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19
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Opačić M, Ristić AJ, Sokić D, Baščarević V, Raičević S, Savić S, Zorović M, Živin M, Šelih VS, Spasojević I, Savić D. Regional distribution of cytochrome c oxidase activity and copper in sclerotic hippocampi of epilepsy patients. Brain Behav 2021. [PMCID: PMC7882178 DOI: 10.1002/brb3.1986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction Disruption of copper homeostasis and dysfunction of mitochondria have been documented in sclerotic hippocampi (HS) of patients with mesial temporal lobe epilepsy (mTLE). However, a potential link between these pathological changes has not been tackled so far. Herein, we analyzed regional distribution of neuron somata density, copper concentration, and the activity of cytochrome c oxidase (CCO), a component of mitochondrial electron transport chain and copper‐containing metalloprotein, in HS. Methods Histochemical staining and laser ablation inductively coupled plasma mass spectrometry were carried out to construct comparable maps of these parameters in coronal sections of hippocampi of 3 mTLE‐HS patients and 3 control subjects. Results Copper levels were decreased in all regions of HS with pyramidal neuron somata. CCO activity was significantly reduced in stratum pyramidale (PY) 1 and cornu Ammonis field 4, the two regions with significant reduction in neuron somata density. CCO activity was also lower in layers that contain apical dendrites of pyramidal neurons and mossy fibers. It appears that copper deficiency in PY2 and PY3 comes before CCO activity reduction and neuronal loss. A strong positive correlation was found between neuron density, Cu concentration, and CCO activity. Conclusions Presented results imply that pathological alterations in Cu and energy metabolism could be involved in the development of HS. A limitation of this study was the relatively small number of patients. However, presented results underline copper deficiency as a component of pathological mechanisms of epilepsy and warrant further investigation of cuproproteins and members of copper transport machinery.
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Affiliation(s)
- Miloš Opačić
- Department of Life Sciences Institute for Multidisciplinary Research University of Belgrade Belgrade Serbia
| | - Aleksandar J. Ristić
- Centre for Epilepsy and Sleep Disorders Neurology Clinic Clinical Centre of Serbia Belgrade Serbia
| | - Dragoslav Sokić
- Centre for Epilepsy and Sleep Disorders Neurology Clinic Clinical Centre of Serbia Belgrade Serbia
| | | | - Savo Raičević
- Institute for Neurosurgery Clinical Centre of Serbia Belgrade Serbia
| | - Slobodan Savić
- Institute of Forensic Medicine ‘Milovan Milovanović’ Medical School University of Belgrade Belgrade Serbia
| | - Maja Zorović
- Brain Research Laboratory Institute of Pathophysiology Medical Faculty University of Ljubljana Ljubljana Slovenia
| | - Marko Živin
- Brain Research Laboratory Institute of Pathophysiology Medical Faculty University of Ljubljana Ljubljana Slovenia
| | - Vid Simon Šelih
- Department of Analytical Chemistry National Institute of Chemistry Ljubljana Slovenia
| | - Ivan Spasojević
- Department of Life Sciences Institute for Multidisciplinary Research University of Belgrade Belgrade Serbia
| | - Danijela Savić
- Department of Neurobiology Institute for Biological Research ‘Siniša Stanković’ – National Institute of Republic of Serbia University of Belgrade Belgrade Serbia
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20
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Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions. Int J Mol Sci 2021; 22:ijms22020586. [PMID: 33435522 PMCID: PMC7827222 DOI: 10.3390/ijms22020586] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are ubiquitous intracellular organelles found in almost all eukaryotes and involved in various aspects of cellular life, with a primary role in energy production. The interest in this organelle has grown stronger with the discovery of their link to various pathologies, including cancer, aging and neurodegenerative diseases. Indeed, dysfunctional mitochondria cannot provide the required energy to tissues with a high-energy demand, such as heart, brain and muscles, leading to a large spectrum of clinical phenotypes. Mitochondrial defects are at the origin of a group of clinically heterogeneous pathologies, called mitochondrial diseases, with an incidence of 1 in 5000 live births. Primary mitochondrial diseases are associated with genetic mutations both in nuclear and mitochondrial DNA (mtDNA), affecting genes involved in every aspect of the organelle function. As a consequence, it is difficult to find a common cause for mitochondrial diseases and, subsequently, to offer a precise clinical definition of the pathology. Moreover, the complexity of this condition makes it challenging to identify possible therapies or drug targets.
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21
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Fernandez-Vizarra E, Zeviani M. Mitochondrial disorders of the OXPHOS system. FEBS Lett 2020; 595:1062-1106. [PMID: 33159691 DOI: 10.1002/1873-3468.13995] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/21/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are among the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase [also called complex V (cV)]. The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by cV to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here, we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.
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Affiliation(s)
- Erika Fernandez-Vizarra
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Massimo Zeviani
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Neurosciences, University of Padova, Italy
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22
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Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae. Life (Basel) 2020; 10:life10110304. [PMID: 33238568 PMCID: PMC7700678 DOI: 10.3390/life10110304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast.
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Cytochrome c oxidase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148335. [PMID: 33171185 DOI: 10.1016/j.bbabio.2020.148335] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Cytochrome c oxidase (COX) deficiency is characterized by a high degree of genetic and phenotypic heterogeneity, partly reflecting the extreme structural complexity, multiple post-translational modification, variable, tissue-specific composition, and the high number of and intricate connections among the assembly factors of this enzyme. In fact, decreased COX specific activity can manifest with different degrees of severity, affect the whole organism or specific tissues, and develop a wide spectrum of disease natural history, including disease onsets ranging from birth to late adulthood. More than 30 genes have been linked to COX deficiency, but the list is still incomplete and in fact constantly updated. We here discuss the current knowledge about COX in health and disease, focusing on genetic aetiology and link to clinical manifestations. In addition, information concerning either fundamental biological features of the enzymes or biochemical signatures of its defects have been provided by experimental in vivo models, including yeast, fly, mouse and fish, which expanded our knowledge on the functional features and the phenotypical consequences of different forms of COX deficiency.
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24
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Čunátová K, Reguera DP, Houštěk J, Mráček T, Pecina P. Role of cytochrome c oxidase nuclear-encoded subunits in health and disease. Physiol Res 2020; 69:947-965. [PMID: 33129245 DOI: 10.33549/physiolres.934446] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of mitochondrial electron transport chain, couples electron transport to oxygen with generation of proton gradient indispensable for the production of vast majority of ATP molecules in mammalian cells. The review summarizes current knowledge of COX structure and function of nuclear-encoded COX subunits, which may modulate enzyme activity according to various conditions. Moreover, some nuclear-encoded subunits posess tissue-specific and development-specific isoforms, possibly enabling fine-tuning of COX function in individual tissues. The importance of nuclear-encoded subunits is emphasized by recently discovered pathogenic mutations in patients with severe mitopathies. In addition, proteins substoichiometrically associated with COX were found to contribute to COX activity regulation and stabilization of the respiratory supercomplexes. Based on the summarized data, a model of three levels of quaternary COX structure is postulated. Individual structural levels correspond to subunits of the i) catalytic center, ii) nuclear-encoded stoichiometric subunits and iii) associated proteins, which may constitute several forms of COX with varying composition and differentially regulated function.
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Affiliation(s)
- K Čunátová
- Department of Bioenergetics, Institute of Physiology CAS, Prague, Czech Republic. ,
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25
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Functions of Cytochrome c oxidase Assembly Factors. Int J Mol Sci 2020; 21:ijms21197254. [PMID: 33008142 PMCID: PMC7582755 DOI: 10.3390/ijms21197254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome c oxidase is the terminal complex of eukaryotic oxidative phosphorylation in mitochondria. This process couples the reduction of electron carriers during metabolism to the reduction of molecular oxygen to water and translocation of protons from the internal mitochondrial matrix to the inter-membrane space. The electrochemical gradient formed is used to generate chemical energy in the form of adenosine triphosphate to power vital cellular processes. Cytochrome c oxidase and most oxidative phosphorylation complexes are the product of the nuclear and mitochondrial genomes. This poses a series of topological and temporal steps that must be completed to ensure efficient assembly of the functional enzyme. Many assembly factors have evolved to perform these steps for insertion of protein into the inner mitochondrial membrane, maturation of the polypeptide, incorporation of co-factors and prosthetic groups and to regulate this process. Much of the information about each of these assembly factors has been gleaned from use of the single cell eukaryote Saccharomyces cerevisiae and also mutations responsible for human disease. This review will focus on the assembly factors of cytochrome c oxidase to highlight some of the outstanding questions in the assembly of this vital enzyme complex.
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26
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Saneto RP. Mitochondrial diseases: expanding the diagnosis in the era of genetic testing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2020; 4:384-428. [PMID: 33426505 PMCID: PMC7791531 DOI: 10.20517/jtgg.2020.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are clinically and genetically heterogeneous. These diseases were initially described a little over three decades ago. Limited diagnostic tools created disease descriptions based on clinical, biochemical analytes, neuroimaging, and muscle biopsy findings. This diagnostic mechanism continued to evolve detection of inherited oxidative phosphorylation disorders and expanded discovery of mitochondrial physiology over the next two decades. Limited genetic testing hampered the definitive diagnostic identification and breadth of diseases. Over the last decade, the development and incorporation of massive parallel sequencing has identified approximately 300 genes involved in mitochondrial disease. Gene testing has enlarged our understanding of how genetic defects lead to cellular dysfunction and disease. These findings have expanded the understanding of how mechanisms of mitochondrial physiology can induce dysfunction and disease, but the complete collection of disease-causing gene variants remains incomplete. This article reviews the developments in disease gene discovery and the incorporation of gene findings with mitochondrial physiology. This understanding is critical to the development of targeted therapies.
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Affiliation(s)
- Russell P. Saneto
- Center for Integrative Brain Research, Neuroscience Institute, Seattle, WA 98101, USA
- Department of Neurology/Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, WA 98105, USA
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27
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Barros MH, McStay GP. Modular biogenesis of mitochondrial respiratory complexes. Mitochondrion 2019; 50:94-114. [PMID: 31669617 DOI: 10.1016/j.mito.2019.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.
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Affiliation(s)
- Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil.
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, United Kingdom.
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28
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Signes A, Cerutti R, Dickson AS, Benincá C, Hinchy EC, Ghezzi D, Carrozzo R, Bertini E, Murphy MP, Nathan JA, Viscomi C, Fernandez-Vizarra E, Zeviani M. APOPT1/COA8 assists COX assembly and is oppositely regulated by UPS and ROS. EMBO Mol Med 2019; 11:e9582. [PMID: 30552096 PMCID: PMC6328941 DOI: 10.15252/emmm.201809582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Loss-of-function mutations in APOPT1, a gene exclusively found in higher eukaryotes, cause a characteristic type of cavitating leukoencephalopathy associated with mitochondrial cytochrome c oxidase (COX) deficiency. Although the genetic association of APOPT1 pathogenic variants with isolated COX defects is now clear, the biochemical link between APOPT1 function and COX has remained elusive. We investigated the molecular role of APOPT1 using different approaches. First, we generated an Apopt1 knockout mouse model which shows impaired motor skills, e.g., decreased motor coordination and endurance, associated with reduced COX activity and levels in multiple tissues. In addition, by achieving stable expression of wild-type APOPT1 in control and patient-derived cultured cells we ruled out a role of this protein in apoptosis and established instead that this protein is necessary for proper COX assembly and function. On the other hand, APOPT1 steady-state levels were shown to be controlled by the ubiquitination-proteasome system (UPS). Conversely, in conditions of increased oxidative stress, APOPT1 is stabilized, increasing its mature intramitochondrial form and thereby protecting COX from oxidatively induced degradation.
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Affiliation(s)
- Alba Signes
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Raffaele Cerutti
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna S Dickson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cristiane Benincá
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Michael P Murphy
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Carlo Viscomi
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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29
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Otero MG, Tiongson E, Diaz F, Haude K, Panzer K, Collier A, Kim J, Adams D, Tifft CJ, Cui H, Millian Zamora F, Au MG, Graham JM, Buckley DJ, Lewis R, Toro C, Bai R, Turner L, Mathews KD, Gahl W, Pierson TM. Novel pathogenic COX20 variants causing dysarthria, ataxia, and sensory neuropathy. Ann Clin Transl Neurol 2018; 6:154-160. [PMID: 30656193 PMCID: PMC6331954 DOI: 10.1002/acn3.661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 09/04/2018] [Accepted: 09/10/2018] [Indexed: 01/28/2023] Open
Abstract
COX20/FAM36A encodes a mitochondrial complex IV assembly factor important for COX2 activation. Only one homozygous COX20 missense mutation has been previously described in two separate consanguineous families. We report four subjects with features that include childhood hypotonia, areflexia, ataxia, dysarthria, dystonia, and sensory neuropathy. Exome sequencing in all four subjects identified the same novel COX20 variants. One variant affected the splice donor site of intron‐one (c.41A>G), while the other variant (c.157+3G>C) affected the splice donor site of intron‐two. cDNA and protein analysis indicated that no full‐length cDNA or protein was generated. These subjects expand the phenotype associated with COX20 deficiency.
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Affiliation(s)
- Maria G Otero
- Board of Governors Regenerative Medicine Institute Cedars-Sinai Medical Center Los Angeles California
| | - Emmanuelle Tiongson
- Division of Neurology Children's Hospital of Los Angeles Los Angeles California
| | - Frank Diaz
- Department of Neurology Cedars-Sinai Medical Center Los Angeles California
| | | | - Karin Panzer
- Department of Pediatrics University of Iowa Stead Family Children's Hospital Iowa City Iowa
| | - Ashley Collier
- Provincial Medical Genetics Program Eastern Health St. John's Newfoundland and Labrador Canada
| | - Jaemin Kim
- Board of Governors Regenerative Medicine Institute Cedars-Sinai Medical Center Los Angeles California
| | - David Adams
- NIH Undiagnosed Diseases Program NIH Office of Rare Diseases Research and NHGRI Bethesda Maryland.,Office of the Clinical Director NHGRI, NIH Bethesda Maryland
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program NIH Office of Rare Diseases Research and NHGRI Bethesda Maryland.,Office of the Clinical Director NHGRI, NIH Bethesda Maryland
| | | | | | - Margaret G Au
- Department of Pediatrics Cedars-Sinai Medical Center Los Angeles California
| | - John M Graham
- Department of Pediatrics Cedars-Sinai Medical Center Los Angeles California
| | - David J Buckley
- Department of Pediatrics Janeway Health Centre St. John's Newfoundland and Labrador Canada
| | - Richard Lewis
- Department of Neurology Cedars-Sinai Medical Center Los Angeles California
| | - Camilo Toro
- NIH Undiagnosed Diseases Program NIH Office of Rare Diseases Research and NHGRI Bethesda Maryland.,Office of the Clinical Director NHGRI, NIH Bethesda Maryland
| | | | - Lesley Turner
- Faculty of Medicine Memorial University of Newfoundland St. John's Newfoundland Canada
| | - Katherine D Mathews
- Provincial Medical Genetics Program Eastern Health St. John's Newfoundland and Labrador Canada.,Department of Neurology University of Iowa Stead Family Children's Hospital Iowa City Iowa
| | - William Gahl
- NIH Undiagnosed Diseases Program NIH Office of Rare Diseases Research and NHGRI Bethesda Maryland.,Office of the Clinical Director NHGRI, NIH Bethesda Maryland
| | - Tyler Mark Pierson
- Board of Governors Regenerative Medicine Institute Cedars-Sinai Medical Center Los Angeles California.,Department of Neurology Cedars-Sinai Medical Center Los Angeles California.,Department of Pediatrics Cedars-Sinai Medical Center Los Angeles California
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30
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Roos S, Sofou K, Hedberg-Oldfors C, Kollberg G, Lindgren U, Thomsen C, Tulinius M, Oldfors A. Mitochondrial complex IV deficiency caused by a novel frameshift variant in MT-CO2 associated with myopathy and perturbed acylcarnitine profile. Eur J Hum Genet 2018; 27:331-335. [PMID: 30315213 DOI: 10.1038/s41431-018-0286-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/04/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial myopathies are a heterogeneous group of disorders associated with a wide range of clinical phenotypes. We present a 16-year-old girl with a history of exercise intolerance since childhood. Acylcarnitine species suggestive of multiple acyl-CoA dehydrogenase deficiency were found in serum, however genetic analysis did not reveal variants in genes associated with this disorder. Biochemical analyses of skeletal muscle mitochondria revealed an isolated and extremely low activity of cytochrome c oxidase (COX). This finding was confirmed by enzyme histochemistry, which demonstrated an almost complete absence of fibers with normal COX activity. Whole-exome sequencing revealed a single base-pair deletion (m.8088delT) in MT-CO2, which encodes subunit 2 of COX, resulting in a premature stop codon. Restriction fragment length polymorphism-analysis confirmed mtDNA heteroplasmy with high mutant load in skeletal muscle, the only clinically affected tissue, but low levels in other investigated tissues. Single muscle fiber analysis showed segregation of the mutant genotype with respiratory chain dysfunction. Immuno-histochemical studies indicated that the truncating variant in COX2 has an inhibitory effect on the assembly of the COX holoenzyme.
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Affiliation(s)
- Sara Roos
- Department of Pathology and Genetics and Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
| | - Kalliopi Sofou
- Department of Pediatrics, The Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Carola Hedberg-Oldfors
- Department of Pathology and Genetics and Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gittan Kollberg
- Department of Clinical Chemistry, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Lindgren
- Department of Pathology and Genetics and Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Christer Thomsen
- Department of Pathology and Genetics and Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mar Tulinius
- Department of Pediatrics, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anders Oldfors
- Department of Pathology and Genetics and Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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31
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Regulation of mitochondrial respiration and ATP synthesis via cytochrome c oxidase. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2018. [DOI: 10.1007/s12210-018-0710-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Finsterer J, Zarrouk-Mahjoub S. Contribution of the MRPS22 variant and a Down mosaic to the phenotype. Metab Brain Dis 2018; 33:11-12. [PMID: 28963669 DOI: 10.1007/s11011-017-0115-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Josef Finsterer
- Krankenanstalt Rudolfstiftung, Postfach 20, 1180, Vienna, Austria.
| | - Sinda Zarrouk-Mahjoub
- University of Tunis El Manar and Genomics Platform, Pasteur Institute of Tunis, Tunis, Tunisia
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33
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de Haas R, Das D, Garanto A, Renkema HG, Greupink R, van den Broek P, Pertijs J, Collin RWJ, Willems P, Beyrath J, Heerschap A, Russel FG, Smeitink JA. Therapeutic effects of the mitochondrial ROS-redox modulator KH176 in a mammalian model of Leigh Disease. Sci Rep 2017; 7:11733. [PMID: 28916769 PMCID: PMC5601915 DOI: 10.1038/s41598-017-09417-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/24/2017] [Indexed: 01/26/2023] Open
Abstract
Leigh Disease is a progressive neurometabolic disorder for which a clinical effective treatment is currently still lacking. Here, we report on the therapeutic efficacy of KH176, a new chemical entity derivative of Trolox, in Ndufs4 -/- mice, a mammalian model for Leigh Disease. Using in vivo brain diffusion tensor imaging, we show a loss of brain microstructural coherence in Ndufs4 -/- mice in the cerebral cortex, external capsule and cerebral peduncle. These findings are in line with the white matter diffusivity changes described in mitochondrial disease patients. Long-term KH176 treatment retained brain microstructural coherence in the external capsule in Ndufs4 -/- mice and normalized the increased lipid peroxidation in this area and the cerebral cortex. Furthermore, KH176 treatment was able to significantly improve rotarod and gait performance and reduced the degeneration of retinal ganglion cells in Ndufs4 -/- mice. These in vivo findings show that further development of KH176 as a potential treatment for mitochondrial disorders is worthwhile to pursue. Clinical trial studies to explore the potency, safety and efficacy of KH176 are ongoing.
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Affiliation(s)
- Ria de Haas
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pharmacology and Toxicology, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Devashish Das
- Department of Radiology and Nuclear Medicine, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Herma G Renkema
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rick Greupink
- Department of Pharmacology and Toxicology, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Petra van den Broek
- Department of Pharmacology and Toxicology, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeanne Pertijs
- Department of Pharmacology and Toxicology, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Willems
- Department of Biochemistry, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Arend Heerschap
- Department of Radiology and Nuclear Medicine, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans G Russel
- Department of Pharmacology and Toxicology, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan A Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.
- Khondrion BV, Nijmegen, The Netherlands.
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34
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Abu-Libdeh B, Douiev L, Amro S, Shahrour M, Ta-Shma A, Miller C, Elpeleg O, Saada A. Mutation in the COX4I1 gene is associated with short stature, poor weight gain and increased chromosomal breaks, simulating Fanconi anemia. Eur J Hum Genet 2017; 25:1142-1146. [PMID: 28766551 DOI: 10.1038/ejhg.2017.112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 11/09/2022] Open
Abstract
We describe a novel autosomal recessive form of mitochondrial disease in a child with short stature, poor weight gain, and mild dysmorphic features with highly suspected Fanconi anemia due to a mutation in COX4I1 gene. Whole Exome Sequencing was performed then followed by Sanger confirmation, identified a K101N mutation in COX4I1, segregating with the disease. This nuclear gene encodes the common isoform of cytochrome c oxidase (COX) subunit 4 (COX 4-1), an integral regulatory part of COX (respiratory chain complex IV) the terminal electron acceptor of the mitochondrial respiratory chain. The patient's fibroblasts disclosed decreased COX activity, impaired ATP production, elevated ROS production, decreased expression of COX4I1 mRNA and undetectable (COX4) protein. COX activity and ATP production were restored by lentiviral transfection with the wild-type gene. Our results demonstrate the first human mutation in the COX4I1 gene linked to diseases and confirm its role in the pathogenesis. Thus COX4I1 mutations should be considered in any patient with features suggestive of this diagnosis.
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Affiliation(s)
- Bassam Abu-Libdeh
- Department of Pediatrics, Makassed Hospital and Al-Quds University, Jerusalem, Palestinian Authority
| | - Liza Douiev
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel.,Department of Genetic and Metabolic Diseases, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Sarah Amro
- Department of Pediatrics, Makassed Hospital and Al-Quds University, Jerusalem, Palestinian Authority
| | - Maher Shahrour
- Department of Pediatrics, Makassed Hospital and Al-Quds University, Jerusalem, Palestinian Authority
| | - Asaf Ta-Shma
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Chaya Miller
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel.,Department of Genetic and Metabolic Diseases, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel.,Department of Genetic and Metabolic Diseases, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
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35
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Kytövuori L, Kärppä M, Tuominen H, Uusimaa J, Saari M, Hinttala R, Majamaa K. Case report: a novel frameshift mutation in the mitochondrial cytochrome c oxidase II gene causing mitochondrial disorder. BMC Neurol 2017; 17:96. [PMID: 28521807 PMCID: PMC5437394 DOI: 10.1186/s12883-017-0883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Mitochondrial cytochrome c oxidase 2, MT-CO2, encodes one of the three subunits, which form the catalytic core of cytochrome c oxidase (COX), complex IV. Mutations in MT-CO2 are rare and the associated phenotypes are variable including nonsyndromic and syndromic forms of mitochondrial diseases. Case presentation We describe a 30-year-old man with cognitive decline, epilepsy, psychosis, exercise intolerance, sensorineural hearing impairment, retinitis pigmentosa, cataract and lactic acidosis. COX-deficient fibers and ragged red fibers were abundant in the muscle. Sequencing of mitochondrial DNA (mtDNA) revealed a novel frameshift mutation m.8156delG that was predicted to cause altered C-terminal amino acid sequence and to lead to truncation of the COX subunit 2. The deletion was heteroplasmic being present in 26% of the mtDNA in blood, 33% in buccal mucosa and 95% in muscle. Deletion heteroplasmy correlated with COX-deficiency in muscle histochemistry. The mother and the siblings of the proband did not harbor the deletion. Conclusions The clinical features and muscle histology of the proband suggested a mitochondrial disorder. The m.8156delG deletion is a new addition to the short list of pathogenic mutations in the mtDNA-encoded subunits of COX. This case illustrates the importance of mtDNA sequence analysis in patients with an evident mitochondrial disorder.
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Affiliation(s)
- Laura Kytövuori
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland. .,Department of Neurology, Oulu University Hospital, P.O. Box 20, OYS, FI-90029, Oulu, Finland.
| | - Mikko Kärppä
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, OYS, FI-90029, Oulu, Finland
| | - Hannu Tuominen
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu and Department of Pathology, Oulu University Hospital, Oulu, Finland
| | - Johanna Uusimaa
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,PEDEGO Research Unit, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Markku Saari
- Turku Centre for Biotechnology, Cell Imaging Core, University of Turku, FI-20520, Turku, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,PEDEGO Research Unit, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, OYS, FI-90029, Oulu, Finland
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Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1534056. [PMID: 28593021 PMCID: PMC5448071 DOI: 10.1155/2017/1534056] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023]
Abstract
Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen. COX consists of 14 subunits, three and eleven encoded, respectively, by the mitochondrial and nuclear DNA. Tissue- and condition-specific isoforms have only been reported for COX but not for the other oxidative phosphorylation complexes, suggesting a fundamental requirement to fine-tune and regulate the essentially irreversible reaction catalyzed by COX. This article briefly discusses the assembly of COX in mammals and then reviews the functions of the six nuclear-encoded COX subunits that are expressed as isoforms in specialized tissues including those of the liver, heart and skeletal muscle, lung, and testes: COX IV-1, COX IV-2, NDUFA4, NDUFA4L2, COX VIaL, COX VIaH, COX VIb-1, COX VIb-2, COX VIIaH, COX VIIaL, COX VIIaR, COX VIIIH/L, and COX VIII-3. We propose a model in which the isoforms mediate the interconnected regulation of COX by (1) adjusting basal enzyme activity to mitochondrial capacity of a given tissue; (2) allosteric regulation to adjust energy production to need; (3) altering proton pumping efficiency under certain conditions, contributing to thermogenesis; (4) providing a platform for tissue-specific signaling; (5) stabilizing the COX dimer; and (6) modulating supercomplex formation.
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Mutated PET117 causes complex IV deficiency and is associated with neurodevelopmental regression and medulla oblongata lesions. Hum Genet 2017; 136:759-769. [PMID: 28386624 PMCID: PMC5429353 DOI: 10.1007/s00439-017-1794-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/31/2017] [Indexed: 10/30/2022]
Abstract
The genetic basis of the many progressive, multi systemic, mitochondrial diseases that cause a lack of cellular ATP production is heterogeneous, with defects found both in the mitochondrial genome as well as in the nuclear genome. Many different mutations have been found in the genes encoding subunits of the enzyme complexes of the oxidative phosphorylation system. In addition, mutations in genes encoding proteins involved in the assembly of these complexes are known to cause mitochondrial disorders. Here we describe two sisters with a mitochondrial disease characterized by lesions in the medulla oblongata, as demonstrated by brain magnetic resonance imaging, and an isolated complex IV deficiency and reduced levels of individual complex IV subunits. Whole exome sequencing revealed a homozygous nonsense mutation resulting in a premature stop codon in the gene encoding Pet117, a small protein that has previously been predicted to be a complex IV assembly factor. PET117 has not been identified as a mitochondrial disease gene before. Lentiviral complementation of patient fibroblasts with wild-type PET117 restored the complex IV deficiency, proving that the gene defect is responsible for the complex IV deficiency in the patients, and indicating a pivotal role of this protein in the proper functioning of complex IV. Although previous studies had suggested a possible role of this protein in the insertion of copper into complex IV, studies in patient fibroblasts could not confirm this. This case presentation thus implicates mutations in PET117 as a novel cause of mitochondrial disease.
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Baertling F, Al-Murshedi F, Sánchez-Caballero L, Al-Senaidi K, Joshi NP, Venselaar H, van den Brand MAM, Nijtmans LGJ, Rodenburg RJT. Mutation in mitochondrial complex IV subunit COX5A causes pulmonary arterial hypertension, lactic acidemia, and failure to thrive. Hum Mutat 2017; 38:692-703. [DOI: 10.1002/humu.23210] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/14/2017] [Accepted: 02/25/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Fabian Baertling
- Department of Pediatrics; Radboud Centre for Mitochondrial Medicine; Radboud University Medical Centre; Nijmegen The Netherlands
- Department of General Pediatrics, Neonatology and Pediatric Cardiology; University Children's Hospital Duesseldorf; Heinrich Heine University; Düsseldorf Germany
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic; Department of Genetics; Sultan Qaboos University Hospital; Sultan Qaboos University; Muscat Oman
| | - Laura Sánchez-Caballero
- Department of Pediatrics; Radboud Centre for Mitochondrial Medicine; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Khalfan Al-Senaidi
- Pediatric Cardiology Unit; Department of Child Health; Sultan Qaboos University Hospital; Sultan Qaboos University; Muscat Oman
| | - Niranjan P Joshi
- Pediatric Cardiology Unit; Department of Child Health; Sultan Qaboos University Hospital; Sultan Qaboos University; Muscat Oman
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics; Radboud University; Nijmegen The Netherlands
| | - Mariël AM van den Brand
- Department of Pediatrics; Radboud Centre for Mitochondrial Medicine; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Leo GJ Nijtmans
- Department of Pediatrics; Radboud Centre for Mitochondrial Medicine; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Richard JT Rodenburg
- Department of Pediatrics; Radboud Centre for Mitochondrial Medicine; Radboud University Medical Centre; Nijmegen The Netherlands
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39
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Alston CL, Rocha MC, Lax NZ, Turnbull DM, Taylor RW. The genetics and pathology of mitochondrial disease. J Pathol 2016; 241:236-250. [PMID: 27659608 PMCID: PMC5215404 DOI: 10.1002/path.4809] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/30/2022]
Abstract
Mitochondria are double-membrane-bound organelles that are present in all nucleated eukaryotic cells and are responsible for the production of cellular energy in the form of ATP. Mitochondrial function is under dual genetic control - the 16.6-kb mitochondrial genome, with only 37 genes, and the nuclear genome, which encodes the remaining ∼1300 proteins of the mitoproteome. Mitochondrial dysfunction can arise because of defects in either mitochondrial DNA or nuclear mitochondrial genes, and can present in childhood or adulthood in association with vast clinical heterogeneity, with symptoms affecting a single organ or tissue, or multisystem involvement. There is no cure for mitochondrial disease for the vast majority of mitochondrial disease patients, and a genetic diagnosis is therefore crucial for genetic counselling and recurrence risk calculation, and can impact on the clinical management of affected patients. Next-generation sequencing strategies are proving pivotal in the discovery of new disease genes and the diagnosis of clinically affected patients; mutations in >250 genes have now been shown to cause mitochondrial disease, and the biochemical, histochemical, immunocytochemical and neuropathological characterization of these patients has led to improved diagnostic testing strategies and novel diagnostic techniques. This review focuses on the current genetic landscape associated with mitochondrial disease, before focusing on advances in studying associated mitochondrial pathology in two, clinically relevant organs - skeletal muscle and brain. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Mariana C Rocha
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Nichola Z Lax
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
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