1
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Wang C, Cui C, Xu P, Zhu L, Xue H, Chen B, Jiang P. Targeting PDK2 rescues stress-induced impaired brain energy metabolism. Mol Psychiatry 2023; 28:4138-4150. [PMID: 37188779 DOI: 10.1038/s41380-023-02098-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
Depression is a mental illness frequently accompanied by disordered energy metabolism. A dysregulated hypothalamus pituitary adrenal axis response with aberrant glucocorticoids (GCs) release is often observed in patients with depression. However, the associated etiology between GCs and brain energy metabolism remains poorly understood. Here, using metabolomic analysis, we showed that the tricarboxylic acid (TCA) cycle was inhibited in chronic social defeat stress (CSDS)-exposed mice and patients with first-episode depression. Decreased mitochondrial oxidative phosphorylation was concomitant with the impairment of the TCA cycle. In parallel, the activity of pyruvate dehydrogenase (PDH), the gatekeeper of mitochondrial TCA flux, was suppressed, which is associated with the CSDS-induced neuronal pyruvate dehydrogenase kinase 2 (PDK2) expression and consequently enhanced PDH phosphorylation. Considering the well-acknowledged role of GCs in energy metabolism, we further demonstrated that glucocorticoid receptors (GR) stimulated PDK2 expression by directly binding to its promoter region. Meanwhile, silencing PDK2 abrogated glucocorticoid-induced PDH inhibition, restored the neuronal oxidative phosphorylation, and improved the flux of isotope-labeled carbon (U-13C] glucose) into the TCA cycle. Additionally, in vivo, pharmacological inhibition and neuron-specific silencing of GR or PDK2 restored CSDS-induced PDH phosphorylation and exerted antidepressant activities against chronic stress exposure. Taken together, our findings reveal a novel mechanism of depression manifestation, whereby elevated GCs levels regulate PDK2 transcription via GR, thereby impairing brain energy metabolism and contributing to the onset of this condition.
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Affiliation(s)
- Changshui Wang
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, 272000, China
| | - Changmeng Cui
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, 272000, China
| | - Pengfei Xu
- Translational Pharmaceutical Laboratory, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, China
| | - Li Zhu
- Translational Pharmaceutical Laboratory, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, China
| | - Hongjia Xue
- Faculty of Science and Engineering, University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Beibei Chen
- ADFA School of Science, University of New South Wales, Canberra, ACT, Australia
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, China.
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2
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Ning X, Li Q, Zi J, Mei Z, Liu J, Zhang Y, Bi M, Ren Y, Liu X, Lv C, Yao H, Sun J, Rao F, Li S, Liu S. New Set of Isobaric Labeling Reagents for Quantitative 16Plex Proteomics. Anal Chem 2023; 95:5788-5795. [PMID: 36958307 DOI: 10.1021/acs.analchem.3c00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ion signal suppression. We redesigned the original chemical structure of the deuterium isobaric amine-reactive tag developed in our laboratory. We optimized the synthetic pathway to create a new set of 16-plex isobaric tags (IBT-16plex). The novel reagent enabled almost complete labeling of peptides within 90 min, with all labeling reporter ions exhibiting comparable MS/MS signals. Compared to a typical 16plex reagent, TMTpro-16plex, the peptides and proteins identified by IBT-16plex in trypsinized HeLa cells were significantly increased by 14.8 and 8.6%, respectively. Moreover, differences in peptide abundance within 10-fold among multiple groups were barely suppressed in IBT-16plex, whereas the dynamic range in TMTpro-16plex-labeled groups was smaller. After quantitative examination of MCF7 cell proteins, IBT-16plex was confirmed as feasible and useful for evaluating protein responses of glucose-starved MCF7 cells to a glucose-rich medium.
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Affiliation(s)
- Xiaolian Ning
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qidan Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
| | | | - Jie Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Mao Bi
- School of Life Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yan Ren
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xingang Liu
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
| | - Chao Lv
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
| | - Hequan Yao
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Jianguo Sun
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Feng Rao
- School of Life Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Shuwei Li
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
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3
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McGovern AJ, Arevalo MA, Ciordia S, Garcia-Segura LM, Barreto GE. Respirasome Proteins Are Regulated by Sex-Hormone Interactions in the Brain. Int J Mol Sci 2022; 23:ijms232314754. [PMID: 36499081 PMCID: PMC9741126 DOI: 10.3390/ijms232314754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
The existence of sex differences in disease incidence is attributed, in part, to sex differences in metabolism. Uncovering the precise mechanism driving these differences is an extraordinarily complex process influenced by genetics, endogenous hormones, sex-specific lifetime events, individual differences and external environmental/social factors. In fact, such differences may be subtle, but across a life span, increase susceptibility to a pathology. Whilst research persists in the hope of discovering an elegant biological mechanism to underpin sex differences in disease, here, we show, for the first time, that such a mechanism may be subtle in nature but influenced by multiple sex-specific factors. A proteomic dataset was generated from a gonadectomized mouse model treated with Tibolone, a menopausal hormone therapy. Following functional enrichment analysis, we identified that Alzheimer's disease and the electron transport chain-associated pathways were regulated by sex-hormone interactions. Specifically, we identified that the expression of three respirasome proteins, NDUFA2, NDUFA7 and UQCR10, is significantly altered by compounding factors that contribute to sex differences. These proteins function in bioenergetics and produce reactive oxygen species, which are each dysregulated in many diseases with sex differences in incidence. We show sex-specific reprogrammed responses to Tibolone following gonadectomy, which primarily influence the expression of proteins contributing to metabolic pathways. This further infers that metabolic differences may underpin the observed sex differences in disease, but also that hormone therapy research now has potential in exploring sex-specific interventions to produce an effective method of prevention or treatment.
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Affiliation(s)
- Andrew J. McGovern
- Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, V94 T9PX Limerick, Ireland
| | - Maria Angeles Arevalo
- Instituto Cajal, CSIC, 28002 Madrid, Spain
- CIBERFES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergio Ciordia
- Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Luis Miguel Garcia-Segura
- Instituto Cajal, CSIC, 28002 Madrid, Spain
- CIBERFES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - George E. Barreto
- Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, V94 T9PX Limerick, Ireland
- Correspondence: ; Tel.: +353-(0)-61-202676
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4
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Amri N, Tessier N, Bégin R, Vachon L, Bégin P, Bazin R, Loubaki L, Martel C. Blood Endothelial-Cell Extracellular Vesicles as Potential Biomarkers for the Selection of Plasma in COVID-19 Convalescent Plasma Therapy. Cells 2022; 11:cells11193122. [PMID: 36231083 PMCID: PMC9563445 DOI: 10.3390/cells11193122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Despite the advancement of vaccination and therapies currently available, deaths due to the coronavirus disease 2019 (COVID-19) are still heavily documented. Severely infected individuals experience a generalized inflammatory storm, caused by massive secretion of pro-inflammatory cytokines that can lead to endothelial dysfunction, cardiovascular disease, multi-organ failure, and even death. COVID-19 convalescent plasma (CCP) therapy, selected primarily based on anti-SARS-CoV-2 antibody levels, has not been as convincing as expected in the fight against COVID-19. Given the consequences of a dysfunctional endothelium on the progression of the disease, we propose that the selection of plasma for CCP therapy should be based on more specific parameters that take into consideration the effect on vascular inflammation. Thus, in the present study, we have characterized a subset of CCP that have been used for CCP therapy and measured their anti- or pro-inflammatory effect on human coronary artery endothelial cells (HCAECs). Our data revealed that the longer the time lapse between the onset of symptoms and the plasma donation, the more mitochondrial dysfunction can be evidenced. The concentration of blood endothelial cell extracellular vesicles (BEC-EVs) was increased in the plasma of young individuals with mild symptoms. This type of selected convalescent plasma promoted the activation of the blood vascular endothelium, as reflected by the overexpression of ICAM1 and NFκB1 and the downregulation of VE-Cadherin. We propose this mechanism is a warning signal sent by the injured endothelium to trigger self-defense of peripheral blood vessels against excessive inflammation. Therefore, these results are in line with our previous data. They suggest that a more specific selection of COVID-19 convalescent plasma should be based on the time of donation following the onset of the clinical symptoms of the donor, the severity of the symptoms, and the age of the donor. These characteristics are relatively easy to identify in any hospital and would reflect the concentration of plasma BEC-EVs and be optimal in CCP therapy.
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Affiliation(s)
- Nada Amri
- Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, QC H3T 1J4, Canada
- Montreal Heart Institute, 5000, Belanger Street, Montreal, QC H1T 1C8, Canada
| | - Nolwenn Tessier
- Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, QC H3T 1J4, Canada
- Montreal Heart Institute, 5000, Belanger Street, Montreal, QC H1T 1C8, Canada
| | - Rémi Bégin
- Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, QC H3T 1J4, Canada
- Montreal Heart Institute, 5000, Belanger Street, Montreal, QC H1T 1C8, Canada
| | - Laurent Vachon
- Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, QC H3T 1J4, Canada
- Montreal Heart Institute, 5000, Belanger Street, Montreal, QC H1T 1C8, Canada
| | - Philippe Bégin
- Department of Pediatrics, CHU Sainte-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, QC H3T 1C5, Canada
- Department of Medicine, Centre Hospitalier de l’Université de Montréal, 900, Rue Saint-Denis, Montreal, QC H2X 0A9, Canada
| | - Renée Bazin
- Medical Affairs and Innovation, Héma-Québec, 1070, Avenue des Sciences-de-la-Vie, Québec, QC G1V 5C3, Canada
| | - Lionel Loubaki
- Medical Affairs and Innovation, Héma-Québec, 1070, Avenue des Sciences-de-la-Vie, Québec, QC G1V 5C3, Canada
| | - Catherine Martel
- Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, QC H3T 1J4, Canada
- Montreal Heart Institute, 5000, Belanger Street, Montreal, QC H1T 1C8, Canada
- Correspondence: ; Tel.: +1-(514)-376-3330 (ext. 2977)
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5
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Vikramdeo KS, Sudan SK, Singh AP, Singh S, Dasgupta S. Mitochondrial respiratory complexes: Significance in human mitochondrial disorders and cancers. J Cell Physiol 2022; 237:4049-4078. [PMID: 36074903 DOI: 10.1002/jcp.30869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/18/2022] [Accepted: 08/23/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria are pivotal organelles that govern cellular energy production through the oxidative phosphorylation system utilizing five respiratory complexes. In addition, mitochondria also contribute to various critical signaling pathways including apoptosis, damage-associated molecular patterns, calcium homeostasis, lipid, and amino acid biosynthesis. Among these diverse functions, the energy generation program oversee by mitochondria represents an immaculate orchestration and functional coordination between the mitochondria and nuclear encoded molecules. Perturbation in this program through respiratory complexes' alteration results in the manifestation of various mitochondrial disorders and malignancy, which is alarmingly becoming evident in the recent literature. Considering the clinical relevance and importance of this emerging medical problem, this review sheds light on the timing and nature of molecular alterations in various respiratory complexes and their functional consequences observed in various mitochondrial disorders and human cancers. Finally, we discussed how this wealth of information could be exploited and tailored to develop respiratory complex targeted personalized therapeutics and biomarkers for better management of various incurable human mitochondrial disorders and cancers.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Sarabjeet Kour Sudan
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Ajay P Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Seema Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Santanu Dasgupta
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
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6
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Huang Y, Du Y, Zheng Y, Wen C, Zou H, Huang J, Zhou H, Zhao H, Wu L. Ct-OATP1B3 promotes high-grade serous ovarian cancer metastasis by regulation of fatty acid beta-oxidation and oxidative phosphorylation. Cell Death Dis 2022; 13:556. [PMID: 35717493 PMCID: PMC9206684 DOI: 10.1038/s41419-022-05014-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 01/21/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy mainly due to its extensive metastasis. Cancer-type organic anion transporting polypeptide 1B3 (Ct-OATP1B3), a newly discovered splice variant of solute carrier organic anion transporter family member 1B3 (SLCO1B3), has been reported to be overexpressed in several types of cancer. However, the biological function of Ct-OATP1B3 remains largely unknown. Here, we reveal that Ct-OATP1B3 is overexpressed in HGSOC and promotes the metastasis of HGSOC in vivo and in vitro. Mechanically, Ct-OATP1B3 directly interacts with insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), an RNA-binding protein, which results in enhancement of the mRNA stability and expression of carnitine palmitoyltransferase 1A (CPT1A) and NADH:Ubiquinone Oxidoreductase Subunit A2 (NDUFA2), leading to increased mitochondrial fatty acid beta-oxidation (FAO) and oxidative phosphorylation (OXPHOS) activities. The increased FAO and OXPHOS activities further facilitate adenosine triphosphate (ATP) production and cellular lamellipodia formation, which is the initial step in the processes of tumor cell migration and invasion. Taken together, our study provides an insight into the function and underlying mechanism of Ct-OATP1B3 in HGSOC metastasis, and highlights Ct-OATP1B3 as a novel prognostic marker as well as therapeutic target in HGSOC.
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Affiliation(s)
- Yutang Huang
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Yan Du
- grid.8547.e0000 0001 0125 2443Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China ,grid.8547.e0000 0001 0125 2443Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, 200032 China
| | - Yujie Zheng
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Chunjie Wen
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Hecun Zou
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Jiafeng Huang
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Honghao Zhou
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China ,grid.216417.70000 0001 0379 7164Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha, 410078 China
| | - Hongbo Zhao
- grid.8547.e0000 0001 0125 2443Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China ,grid.8547.e0000 0001 0125 2443Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, 200032 China ,grid.412312.70000 0004 1755 1415Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011 China
| | - Lanxiang Wu
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016 China
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7
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Curtabbi A, Enríquez JA. The ins and outs of the flavin mononucleotide cofactor of respiratory complex I. IUBMB Life 2022; 74:629-644. [PMID: 35166025 DOI: 10.1002/iub.2600] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
The flavin mononucleotide (FMN) cofactor of respiratory complex I occupies a key position in the electron transport chain. Here, the electrons coming from NADH start the sequence of oxidoreduction reactions, which drives the generation of the proton-motive force necessary for ATP synthesis. The overall architecture and the general catalytic proprieties of the FMN site are mostly well established. However, several aspects regarding the complex I flavin cofactor are still unknown. For example, the flavin binding to the N-module, the NADH-oxidizing portion of complex I, lacks a molecular description. The dissociation of FMN from the enzyme is beginning to emerge as an important regulatory mechanism of complex I activity and ROS production. Finally, how mitochondria import and metabolize FMN is still uncertain. This review summarizes the current knowledge on complex I flavin cofactor and discusses the open questions for future research.
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Affiliation(s)
- Andrea Curtabbi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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8
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Marra F, Lunetti P, Curcio R, Lasorsa FM, Capobianco L, Porcelli V, Dolce V, Fiermonte G, Scarcia P. An Overview of Mitochondrial Protein Defects in Neuromuscular Diseases. Biomolecules 2021; 11:1633. [PMID: 34827632 PMCID: PMC8615828 DOI: 10.3390/biom11111633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Neuromuscular diseases (NMDs) are dysfunctions that involve skeletal muscle and cause incorrect communication between the nerves and muscles. The specific causes of NMDs are not well known, but most of them are caused by genetic mutations. NMDs are generally progressive and entail muscle weakness and fatigue. Muscular impairments can differ in onset, severity, prognosis, and phenotype. A multitude of possible injury sites can make diagnosis of NMDs difficult. Mitochondria are crucial for cellular homeostasis and are involved in various metabolic pathways; for this reason, their dysfunction can lead to the development of different pathologies, including NMDs. Most NMDs due to mitochondrial dysfunction have been associated with mutations of genes involved in mitochondrial biogenesis and metabolism. This review is focused on some mitochondrial routes such as the TCA cycle, OXPHOS, and β-oxidation, recently found to be altered in NMDs. Particular attention is given to the alterations found in some genes encoding mitochondrial carriers, proteins of the inner mitochondrial membrane able to exchange metabolites between mitochondria and the cytosol. Briefly, we discuss possible strategies used to diagnose NMDs and therapies able to promote patient outcome.
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Affiliation(s)
- Federica Marra
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Rosita Curcio
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Francesco Massimo Lasorsa
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Vito Porcelli
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
| | - Vincenza Dolce
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Giuseppe Fiermonte
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Pasquale Scarcia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
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9
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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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10
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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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11
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Mazzaccara C, Mirra B, Barretta F, Caiazza M, Lombardo B, Scudiero O, Tinto N, Limongelli G, Frisso G. Molecular Epidemiology of Mitochondrial Cardiomyopathy: A Search Among Mitochondrial and Nuclear Genes. Int J Mol Sci 2021; 22:ijms22115742. [PMID: 34072184 PMCID: PMC8197938 DOI: 10.3390/ijms22115742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial Cardiomyopathy (MCM) is a common manifestation of multi-organ Mitochondrial Diseases (MDs), occasionally present in non-syndromic cases. Diagnosis of MCM is complex because of wide clinical and genetic heterogeneity and requires medical, laboratory, and neuroimaging investigations. Currently, the molecular screening for MCM is fundamental part of MDs management and allows achieving the definitive diagnosis. In this article, we review the current genetic knowledge associated with MDs, focusing on diagnosis of MCM and MDs showing cardiac involvement. We searched for publications on mitochondrial and nuclear genes involved in MCM, mainly focusing on genetic screening based on targeted gene panels for the molecular diagnosis of the MCM, by using Next Generation Sequencing. Here we report twelve case reports, four case-control studies, eleven retrospective studies, and two prospective studies, for a total of twenty-nine papers concerning the evaluation of cardiac manifestations in mitochondrial diseases. From the analysis of published causal mutations, we identified 130 genes to be associated with mitochondrial heart diseases. A large proportion of these genes (34.3%) encode for key proteins involved in the oxidative phosphorylation system (OXPHOS), either as directly OXPHOS subunits (22.8%), and as OXPHOS assembly factors (11.5%). Mutations in several mitochondrial tRNA genes have been also reported in multi-organ or isolated MCM (15.3%). This review highlights the main disease-genes, identified by extensive genetic analysis, which could be included as target genes in next generation panels for the molecular diagnosis of patients with clinical suspect of mitochondrial cardiomyopathies.
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Affiliation(s)
- Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
- Correspondence: ; Tel.: +39-0817-462-422
| | - Bruno Mirra
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Martina Caiazza
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Nadia Tinto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Giuseppe Limongelli
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
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12
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Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS. Nat Genet 2021; 53:445-454. [PMID: 33686288 PMCID: PMC8038973 DOI: 10.1038/s41588-021-00787-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 01/14/2021] [Indexed: 01/31/2023]
Abstract
Psychiatric disorders are highly genetically correlated, but little research has been conducted on the genetic differences between disorders. We developed a new method (case-case genome-wide association study; CC-GWAS) to test for differences in allele frequency between cases of two disorders using summary statistics from the respective case-control GWAS, transcending current methods that require individual-level data. Simulations and analytical computations confirm that CC-GWAS is well powered with effective control of type I error. We applied CC-GWAS to publicly available summary statistics for schizophrenia, bipolar disorder, major depressive disorder and five other psychiatric disorders. CC-GWAS identified 196 independent case-case loci, including 72 CC-GWAS-specific loci that were not significant at the genome-wide level in the input case-control summary statistics; two of the CC-GWAS-specific loci implicate the genes KLF6 and KLF16 (from the Krüppel-like family of transcription factors), which have been linked to neurite outgrowth and axon regeneration. CC-GWAS loci replicated convincingly in applications to datasets with independent replication data.
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13
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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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14
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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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15
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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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16
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Dang QCL, Phan DH, Johnson AN, Pasapuleti M, Alkhaldi HA, Zhang F, Vik SB. Analysis of Human Mutations in the Supernumerary Subunits of Complex I. Life (Basel) 2020; 10:life10110296. [PMID: 33233646 PMCID: PMC7699753 DOI: 10.3390/life10110296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
Complex I is the largest member of the electron transport chain in human mitochondria. It comprises 45 subunits and requires at least 15 assembly factors. The subunits can be divided into 14 "core" subunits that carry out oxidation-reduction reactions and proton translocation, as well as 31 additional supernumerary (or accessory) subunits whose functions are less well known. Diminished levels of complex I activity are seen in many mitochondrial disease states. This review seeks to tabulate mutations in the supernumerary subunits of humans that appear to cause disease. Mutations in 20 of the supernumerary subunits have been identified. The mutations were analyzed in light of the tertiary and quaternary structure of human complex I (PDB id = 5xtd). Mutations were found that might disrupt the folding of that subunit or that would weaken binding to another subunit. In some cases, it appeared that no protein was made or, at least, could not be detected. A very common outcome is the lack of assembly of complex I when supernumerary subunits are mutated or missing. We suggest that poor assembly is the result of disrupting the large network of subunit interactions that the supernumerary subunits typically engage in.
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17
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Gropman A, Uittenbogaard M, Brantner CA, Wang Y, Wong LJ, Chiaramello A. Molecular genetic and mitochondrial metabolic analyses confirm the suspected mitochondrial etiology in a pediatric patient with an atypical form of alternating hemiplegia of childhood. Mol Genet Metab Rep 2020; 24:100609. [PMID: 32489883 PMCID: PMC7262444 DOI: 10.1016/j.ymgmr.2020.100609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 02/05/2023] Open
Abstract
Alternative hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder with an extensive phenotypic variability, resulting in a challenging clinical diagnosis. About 75% of AHC cases are caused by pathogenic variants mapping in the ATP1A3, ATP1A2 or GLUT1 gene, leaving many AHC patients clinically and genetically undiagnosed. In this study, we report the case of a 9-year old proband clinically diagnosed with an atypical form of AHC presenting a suspected mitochondrial etiology and an obscure genetic diagnosis. Long-range PCR followed by next generation sequencing of the proband's mitochondrial genome identified a novel mitochondrial variant, m.12302C > A, mapping in the MT-TL2 gene with a low heteroplasmic level in blood and fibroblasts. Whole exome sequencing revealed three known and novel pathogenic variants with different parental inheritance, all involved in the mitochondrial energy metabolism and thus far not associated with AHC. Live-cell mitochondrial metabolic study showed dysregulated mitochondrial oxidative phosphorylation pathway and metabolic plasticity preventing an efficient switch to glycolysis to sustain ATP homeostasis, congruent with the suspected mitochondrial etiology. In conclusion, our comprehensive genetic and metabolic analyses suggest an oligogenic inheritance among the nuclear and mitochondrial variants for the mitochondrial etiology of proband's atypical form of AHC, thereby providing critical insight in terms of genetic clues and bioenergetic deficit. This approach also improves the diagnostic process of atypical form of AHC with an unclear genotype-phenotype correlation to personalize therapeutic interventions.
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Affiliation(s)
- Andrea Gropman
- Children's National Medical Center, Division of Neurogenetics and Developmental Pediatrics, Washington, DC 20010, USA
| | - Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Christine A Brantner
- GW Nanofabrication and Imaging Center, Office of the Vice-President for Research, George Washington University, Washington, DC 20052, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Chiaramello
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
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18
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Quantitative proteomics to study aging in rabbit liver. Mech Ageing Dev 2020; 187:111227. [PMID: 32126221 DOI: 10.1016/j.mad.2020.111227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 01/24/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022]
Abstract
Aging globally effects cellular and organismal metabolism across a range of mammalian species, including humans and rabbits. Rabbits (Oryctolagus cuniculus are an attractive model system of aging due to their genetic similarity with humans and their short lifespans. This model can be used to understand metabolic changes in aging especially in major organs such as liver where we detected pronounced variations in fat metabolism, mitochondrial dysfunction, and protein degradation. Such changes in the liver are consistent across several mammalian species however in rabbits the downstream effects of these changes have not yet been explored. We have applied proteomics to study changes in the liver proteins from young, middle, and old age rabbits using a multiplexing cPILOT strategy. This resulted in the identification of 2,586 liver proteins, among which 45 proteins had significant p < 0.05) changes with aging. Seven proteins were differentially-expressed at all ages and include fatty acid binding protein, aldehyde dehydrogenase, enoyl-CoA hydratase, 3-hydroxyacyl CoA dehydrogenase, apolipoprotein C3, peroxisomal sarcosine oxidase, adhesion G-protein coupled receptor, and glutamate ionotropic receptor kinate. Insights to how alterations in metabolism affect protein expression in liver have been gained and demonstrate the utility of rabbit as a model of aging.
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19
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Alagia M, Cappuccio G, Torella A, D'Amico A, Mazio F, Romano A, Fecarotta S, Casari G, Nigro V, Brunetti-Pierri N. Cavitating and tigroid-like leukoencephalopathy in a case of NDUFA2-related disorder. JIMD Rep 2020; 52:11-16. [PMID: 32154054 PMCID: PMC7052689 DOI: 10.1002/jmd2.12094] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/30/2022] Open
Abstract
Biallelic variants in nuclear gene NDUFA2 have been reported so far in only three children with variable presentations including Leigh syndrome or leukoencephalopathy. Herein, we report a further female child affected by NDUFA2‐related disorder presenting with cavitating and tigroid‐like pattern of leukodystrophy and without systemic biochemical abnormalities of mitochondrial disorders.
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Affiliation(s)
- Marianna Alagia
- Department of Translational Medicine Federico II University Naples Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine Federico II University Naples Italy.,Telethon Institute of Genetics and Medicine Naples Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine Naples Italy.,Medical Genetics, Department of Biochemistry, Biophysics and General Pathology University of Campania 'Luigi Vanvitelli' Naples Italy
| | - Alessandra D'Amico
- Department of Advanced Biomedical Sciences Federico II University Naples Italy
| | - Federica Mazio
- Department of Neurosciences, Division of Neuroradiology Ospedale Santobono-Pausilipon Naples Italy
| | - Alfonso Romano
- Department of Translational Medicine Federico II University Naples Italy
| | - Simona Fecarotta
- Department of Translational Medicine Federico II University Naples Italy
| | - Giorgio Casari
- Telethon Institute of Genetics and Medicine Naples Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine Naples Italy.,Medical Genetics, Department of Biochemistry, Biophysics and General Pathology University of Campania 'Luigi Vanvitelli' Naples Italy
| | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine Federico II University Naples Italy.,Telethon Institute of Genetics and Medicine Naples Italy
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20
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Multisystem mitochondrial diseases due to mutations in mtDNA-encoded subunits of complex I. BMC Pediatr 2020; 20:41. [PMID: 31996177 PMCID: PMC6988306 DOI: 10.1186/s12887-020-1912-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022] Open
Abstract
Background Maternally inherited complex I deficiencies due to mutations in MT-ND genes represent a heterogeneous group of multisystem mitochondrial disorders (MD) with a unfavourable prognosis. The aim of the study was to characterize the impact of the mutations in MT-ND genes, including the novel m.13091 T > C variant, on the course of the disease, and to analyse the activities of respiratory chain complexes, the amount of protein subunits, and the mitochondrial energy-generating system (MEGS) in available muscle biopsies and cultivated fibroblasts. Methods The respiratory chain complex activities were measured by spectrophotometry, MEGS were analysed using radiolabelled substrates, and protein amount by SDS-PAGE or BN-PAGE in muscle or fibroblasts. Results In our cohort of 106 unrelated families carrying different mtDNA mutations, we found heteroplasmic mutations in the genes MT-ND1, MT-ND3, and MT-ND5, including the novel variant m.13091 T > C, in 13 patients with MD from 12 families. First symptoms developed between early childhood and adolescence and progressed to multisystem disease with a phenotype of Leigh or MELAS syndromes. MRI revealed bilateral symmetrical involvement of deep grey matter typical of Leigh syndrome in 6 children, cortical/white matter stroke-like lesions suggesting MELAS syndrome in 3 patients, and a combination of cortico-subcortical lesions and grey matter involvement in 4 patients. MEGS indicated mitochondrial disturbances in all available muscle samples, as well as a significantly decreased oxidation of [1-14C] pyruvate in fibroblasts. Spectrophotometric analyses revealed a low activity of complex I and/or complex I + III in all muscle samples except one, but the activities in fibroblasts were mostly normal. No correlation was found between complex I activities and mtDNA mutation load, but higher levels of heteroplasmy were generally found in more severely affected patients. Conclusions Maternally inherited complex I deficiencies were found in 11% of families with mitochondrial diseases in our region. Six patients manifested with Leigh, three with MELAS. The remaining four patients presented with an overlap between these two syndromes. MEGS, especially the oxidation of [1-14C] pyruvate in fibroblasts might serve as a sensitive indicator of functional impairment due to MT-ND mutations. Early onset of the disease and higher level of mtDNA heteroplasmy were associated with a worse prognosis.
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21
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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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22
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Attenuation of Equine Lentivirus Alters Mitochondrial Protein Expression Profile from Inflammation to Apoptosis. J Virol 2019; 93:JVI.00653-19. [PMID: 31391270 DOI: 10.1128/jvi.00653-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/23/2019] [Indexed: 12/18/2022] Open
Abstract
Equine infectious anemia virus (EIAV) is an equine lentivirus similar to HIV-1, targets host immune cells, and causes a life-long infection in horses. The Chinese live EIAV vaccine is attenuated from long-term passaging of a highly virulent strain in vitro The parent pathogenic strain (EIAVDLV34) induces a host inflammatory storm to cause severe pathological injury of animals. However, the vaccine strain (EIAVDLV121) induces a high level of apoptosis to eliminate infected cells. To investigate how these processes are regulated, we performed a comparative proteomics analysis and functional study in equine monocyte-derived macrophages (eMDMs) and found that the divergent mitochondrial protein expression profiles caused by EIAV strains with different virulence led to disparate mitochondrial function, morphology, and metabolism. This in turn promoted the distinct transformation of macrophage inflammatory polarization and intrinsic apoptosis. In EIAVDLV34-infected cells, a high level of glycolysis and increased mitochondrial fragmentation were induced, resulting in the M1-polarized proinflammatory-type transformation of macrophages and the subsequent production of a strong inflammatory response. Following infection with EIAVDLV121, the infected cells were transformed into M2-polarized anti-inflammatory macrophages by inhibition of glycolysis. In this case, a decrease in the mitochondrial membrane potential and impairment of the electron transport chain led to increased levels of apoptosis and reactive oxygen species. These results correlated with viral pathogenicity loss and may help provide an understanding of the key mechanism of lentiviral attenuation.IMPORTANCE Following viral infection, the working pattern and function of the cell can be transformed through the impact on mitochondria. It still unknown how the mitochondrial response changes in cells infected with viruses in the process of virulence attenuation. EIAVDLV121 is the only effective lentiviral vaccine for large-scale use in the world. EIAVDLV34 is the parent pathogenic strain. Unlike EIAVDLV34-induced inflammation storms, EIAVDLV121 can induce high levels of apoptosis. For the first time, we found that, after the mitochondrial protein expression profile is altered, EIAVDLV34-infected cells are transformed into M1-polarized-type macrophages and cause inflammatory injury and that the intrinsic apoptosis pathway is activated in EIAVDLV121-infected cells. These studies shed light on how the mitochondrial protein expression profile changes between cells infected by pathogenic lentivirus strains and cells infected by attenuated lentivirus strains to drive different cellular responses, especially from inflammation to apoptosis.
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23
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Barshad G, Zlotnikov-Poznianski N, Gal L, Schuldiner M, Mishmar D. Disease-causing mutations in subunits of OXPHOS complex I affect certain physical interactions. Sci Rep 2019; 9:9987. [PMID: 31292494 PMCID: PMC6620328 DOI: 10.1038/s41598-019-46446-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial complex I (CI) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human CI structure, and from two non-human mammals, enabled predicting the impact of mutations on interactions involving each of the 44 CI subunits. However, experimentally assessing the impact of the predicted interactions requires an easy and high-throughput method. Here, we created such a platform by cloning all 37 nuclear DNA (nDNA) and 7 mitochondrial DNA (mtDNA)-encoded human CI subunits into yeast expression vectors to serve as both 'prey' and 'bait' in the split murine dihydrofolate reductase (mDHFR) protein complementation assay (PCA). We first demonstrated the capacity of this approach and then used it to examine reported pathological OXPHOS CI mutations that occur at subunit interaction interfaces. Our results indicate that a pathological frame-shift mutation in the MT-ND2 gene, causing the replacement of 126 C-terminal residues by a stretch of only 30 amino acids, resulted in loss of specificity in ND2-based interactions involving these residues. Hence, the split mDHFR PCA is a powerful assay for assessing the impact of disease-causing mutations on pairwise protein-protein interactions in the context of a large protein complex, thus offering a possible mechanistic explanation for the underlying pathogenicity.
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Affiliation(s)
- Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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24
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LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism. Proc Natl Acad Sci U S A 2019; 116:4940-4945. [PMID: 30796188 PMCID: PMC6421467 DOI: 10.1073/pnas.1809105116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Short peptides are encoded in genomes of all organisms and have important functions. Due to the small size of such open reading frames, they are frequently overlooked by automatic genome annotation. We investigated the gene that was misannotated as long noncoding RNA LINC00116 and demonstrated that this gene codes for a 56-amino-acid-long peptide, Mtln, which is localized in mitochondria. Inactivation of the Mtln coding gene leads to reduction of oxygen consumption attributed to respiratory complex I activity and perturbs lipid composition of the cell. This influence is mediated by Mtln interaction with NADH-dependent cytochrome b5 reductase. Disruption of the mitochondrial localization of the latter phenocopies Mtln inactivation. Genes coding for small peptides have been frequently misannotated as long noncoding RNA (lncRNA) genes. Here we have demonstrated that one such transcript is translated into a 56-amino-acid-long peptide conserved in chordates, corroborating the work published while this manuscript was under review. The Mtln peptide could be detected in mitochondria of mouse cell lines and tissues. In line with its mitochondrial localization, lack of the Mtln decreases the activity of mitochondrial respiratory chain complex I. Unlike the integral components and assembly factors of NADH:ubiquinone oxidoreductase, Mtln does not alter its enzymatic activity directly. Interaction of Mtln with NADH-dependent cytochrome b5 reductase stimulates complex I functioning most likely by providing a favorable lipid composition of the membrane. Study of Mtln illuminates the importance of small peptides, whose genes might frequently be misannotated as lncRNAs, for the control of vitally important cellular processes.
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25
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Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth. Sci Rep 2019; 9:1920. [PMID: 30760828 PMCID: PMC6374450 DOI: 10.1038/s41598-019-38566-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/28/2018] [Indexed: 12/17/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of renal failure. We have recently shown that inhibiting miR-17~92 is a potential novel therapeutic approach for ADPKD. However, miR-17~92 is a polycistronic cluster that encodes microRNAs (miRNAs) belonging to the miR-17, miR-18, miR-19 and miR-25 families, and the relative pathogenic contribution of these miRNA families to ADPKD progression is unknown. Here we performed an in vivo anti-miR screen to identify the miRNA drug targets within the miR-17~92 miRNA cluster. We designed anti-miRs to individually inhibit miR-17, miR-18, miR-19 or miR-25 families in an orthologous ADPKD model. Treatment with anti-miRs against the miR-17 family reduced cyst proliferation, kidney-weight-to-body-weight ratio and cyst index. In contrast, treatment with anti-miRs against the miR-18, 19, or 25 families did not affect cyst growth. Anti-miR-17 treatment recapitulated the gene expression pattern observed after miR-17~92 genetic deletion and was associated with upregulation of mitochondrial metabolism, suppression of the mTOR pathway, and inhibition of cyst-associated inflammation. Our results argue against functional cooperation between the various miR-17~92 cluster families in promoting cyst growth, and instead point to miR-17 family as the primary therapeutic target for ADPKD.
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Adav SS, Park JE, Sze SK. Quantitative profiling brain proteomes revealed mitochondrial dysfunction in Alzheimer's disease. Mol Brain 2019; 12:8. [PMID: 30691479 PMCID: PMC6350377 DOI: 10.1186/s13041-019-0430-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/22/2019] [Indexed: 11/10/2022] Open
Abstract
Mitochondrial dysfunction is a key feature in both aging and neurodegenerative diseases including Alzheimer’s disease (AD), but the molecular signature that distinguishes pathological changes in the AD from healthy aging in the brain mitochondria remain poorly understood. In order to unveil AD specific mitochondrial dysfunctions, this study adopted a discovery-driven approach with isobaric tag for relative and absolute quantitation (iTRAQ) and label-free quantitative proteomics, and profiled the mitochondrial proteomes in human brain tissues of healthy and AD individuals. LC-MS/MS-based iTRAQ quantitative proteomics approach revealed differentially altered mitochondriomes that distinguished the AD’s pathophysiology-induced from aging-associated changes. Our results showed that dysregulated mitochondrial complexes including electron transport chain (ETC) and ATP-synthase are the potential driver for pathology of the AD. The iTRAQ results were cross-validated with independent label-free quantitative proteomics experiments to confirm that the subunit of electron transport chain complex I, particularly NDUFA4 and NDUFA9 were altered in AD patients, suggesting destabilization of the junction between membrane and matrix arms of mitochondrial complex I impacted the mitochondrial functions in the AD. iTRAQ quantitative proteomics of brain mitochondriomes revealed disparity in healthy aging and age-dependent AD.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
| | - Jung Eun Park
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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27
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Ratcliffe LE, Vázquez Villaseñor I, Jennings L, Heath PR, Mortiboys H, Schwartzentruber A, Karyka E, Simpson JE, Ince PG, Garwood CJ, Wharton SB. Loss of IGF1R in Human Astrocytes Alters Complex I Activity and Support for Neurons. Neuroscience 2018; 390:46-59. [PMID: 30056117 PMCID: PMC6372003 DOI: 10.1016/j.neuroscience.2018.07.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 11/15/2022]
Abstract
We have established a novel human astrocyte-neuron co-culture system. Astrocytes provided contact-mediated support for neurite outgrowth. IGF1R-impaired astrocytes are less able to protect neurons under stress conditions. Microarray analysis of these astrocytes identified changes in energy metabolism.
The insulin/insulin-like growth factor 1 (IGF1) signaling pathways are implicated in longevity and in progression of Alzheimer’s disease. Previously, we showed that insulin-like growth factor 1 receptor (IGF1R) and downstream signaling transcripts are reduced in astrocytes in human brain with progression of Alzheimer’s neuropathology and developed a model of IGF1 signaling impairment in human astrocytes using an IGF1R-specific monoclonal antibody, MAB391. Here, we have established a novel human astrocyte-neuron co-culture system to determine whether loss of astrocytic IGF1R affects their support for neurons. Astrocyte-neuron co-cultures were developed using human primary astrocytes and differentiated Lund Human Mesencephalic Cells (LUHMES). Neurite outgrowth assays, performed to measure astrocytic support for neurons, showed astrocytes provided contact-mediated support for neurite outgrowth. Loss of IGF1R did not affect neurite outgrowth under control conditions but when challenged with hydrogen peroxide IGF1R-impaired astrocytes were less able to protect LUHMES. To determine how loss of IGF1R affects neuronal support MAB391-treated astrocytes were FACS sorted from GFP-LUHMES and their transcriptomic profile was investigated using microarrays. Changes in transcripts involved in astrocyte energy metabolism were identified, particularly NDUFA2 and NDUFB6, which are related to complex I assembly. Loss of complex I activity in MAB391-treated astrocytes validated these findings. In conclusion, reduced IGF1 signaling in astrocytes impairs their support for neurons under conditions of stress and this is associated with defects in the mitochondrial respiratory chain in astrocytes.
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Affiliation(s)
- Laura E Ratcliffe
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Irina Vázquez Villaseñor
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Luke Jennings
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Aurelie Schwartzentruber
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Evangelia Karyka
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Paul G Ince
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK.
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
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28
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Wang Y, Berkowitz O, Selinski J, Xu Y, Hartmann A, Whelan J. Stress responsive mitochondrial proteins in Arabidopsis thaliana. Free Radic Biol Med 2018; 122:28-39. [PMID: 29555593 DOI: 10.1016/j.freeradbiomed.2018.03.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/05/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
Abstract
In the last decade plant mitochondria have emerged as a target, sensor and initiator of signalling cascades to a variety of stress and adverse growth conditions. A combination of various 'omic profiling approaches combined with forward and reverse genetic studies have defined how mitochondria respond to stress and the signalling pathways and regulators of these responses. Reactive oxygen species (ROS)-dependent and -independent pathways, specific metabolites, complex I dysfunction, and the mitochondrial unfolded protein response (UPR) pathway have been proposed to date. These pathways are regulated by kinases (sucrose non-fermenting response like kinase; cyclin dependent protein kinase E 1) and transcription factors from the abscisic acid-related, WRKY and NAC families. A number of independent studies have revealed that these mitochondrial signalling pathways interact with a variety of phytohormone signalling pathways. While this represents significant progress in the last decade there are more pathways to be uncovered. Post-transcriptional/translational regulation is also a likely determinant of the mitochondrial stress response. Unbiased analyses of the expression of genes encoding mitochondrial proteins in a variety of stress conditions reveal a modular network exerting a high degree of anterograde control. As abiotic and biotic stresses have significant impact on the yield of important crops such as rice, wheat and barley we will give an outlook of how knowledge gained in Arabidopsis may help to increase crop production and how emerging technologies may contribute.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
| | - Jennifer Selinski
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Yue Xu
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Andreas Hartmann
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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29
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Garcia CJ, Khajeh J, Coulanges E, Chen EIJ, Owusu-Ansah E. Regulation of Mitochondrial Complex I Biogenesis in Drosophila Flight Muscles. Cell Rep 2018; 20:264-278. [PMID: 28683319 DOI: 10.1016/j.celrep.2017.06.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 01/16/2023] Open
Abstract
The flight muscles of Drosophila are highly enriched with mitochondria, but the mechanism by which mitochondrial complex I (CI) is assembled in this tissue has not been described. We report the mechanism of CI biogenesis in Drosophila flight muscles and show that it proceeds via the formation of ∼315, ∼550, and ∼815 kDa CI assembly intermediates. Additionally, we define specific roles for several CI subunits in the assembly process. In particular, we show that dNDUFS5 is required for converting an ∼700 kDa transient CI assembly intermediate into the ∼815 kDa assembly intermediate. Importantly, incorporation of dNDUFS5 into CI is necessary to stabilize or promote incorporation of dNDUFA10 into the complex. Our findings highlight the potential of studies of CI biogenesis in Drosophila to uncover the mechanism of CI assembly in vivo and establish Drosophila as a suitable model organism and resource for addressing questions relevant to CI biogenesis in humans.
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Affiliation(s)
- Christian Joel Garcia
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jahan Khajeh
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Emmanuel Coulanges
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Emily I-Ju Chen
- Proteomics Shared Resource at the Herbert Irving Comprehensive Cancer Center and Department of Pharmacology, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA; The Robert N. Butler Columbia Aging Center, Columbia University Medical Center, New York, NY 10032, USA.
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30
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Terron A, Bal-Price A, Paini A, Monnet-Tschudi F, Bennekou SH, Leist M, Schildknecht S. An adverse outcome pathway for parkinsonian motor deficits associated with mitochondrial complex I inhibition. Arch Toxicol 2018; 92:41-82. [PMID: 29209747 PMCID: PMC5773657 DOI: 10.1007/s00204-017-2133-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/22/2017] [Indexed: 12/21/2022]
Abstract
Epidemiological studies have observed an association between pesticide exposure and the development of Parkinson's disease, but have not established causality. The concept of an adverse outcome pathway (AOP) has been developed as a framework for the organization of available information linking the modulation of a molecular target [molecular initiating event (MIE)], via a sequence of essential biological key events (KEs), with an adverse outcome (AO). Here, we present an AOP covering the toxicological pathways that link the binding of an inhibitor to mitochondrial complex I (i.e., the MIE) with the onset of parkinsonian motor deficits (i.e., the AO). This AOP was developed according to the Organisation for Economic Co-operation and Development guidelines and uploaded to the AOP database. The KEs linking complex I inhibition to parkinsonian motor deficits are mitochondrial dysfunction, impaired proteostasis, neuroinflammation, and the degeneration of dopaminergic neurons of the substantia nigra. These KEs, by convention, were linearly organized. However, there was also evidence of additional feed-forward connections and shortcuts between the KEs, possibly depending on the intensity of the insult and the model system applied. The present AOP demonstrates mechanistic plausibility for epidemiological observations on a relationship between pesticide exposure and an elevated risk for Parkinson's disease development.
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Affiliation(s)
| | | | - Alicia Paini
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, Universitätsstr. 10, PO Box M657, 78457, Konstanz, Germany
| | - Stefan Schildknecht
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, Universitätsstr. 10, PO Box M657, 78457, Konstanz, Germany.
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31
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Perrier S, Gauquelin L, Tétreault M, Tran L, Webb N, Srour M, Mitchell J, Brunel-Guitton C, Majewski J, Long V, Keller S, Gambello M, Simons C, Vanderver A, Bernard G. Recessive mutations in NDUFA2
cause mitochondrial leukoencephalopathy. Clin Genet 2017; 93:396-400. [DOI: 10.1111/cge.13126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/07/2017] [Accepted: 08/13/2017] [Indexed: 11/30/2022]
Affiliation(s)
- S. Perrier
- Department of Neurology and Neurosurgery; McGill University; Montreal Canada
| | - L. Gauquelin
- Department of Neurology and Neurosurgery; McGill University; Montreal Canada
- Department of Pediatrics; McGill University; Montreal Canada
| | - M. Tétreault
- Department of Human Genetics; McGill University; Montreal Canada
- McGill University and Genome Quebec Innovation Centre; Montreal Canada
| | - L.T. Tran
- Department of Neurology and Neurosurgery; McGill University; Montreal Canada
- Department of Pediatrics; McGill University; Montreal Canada
- Department of Medical Genetics, Montreal Children's Hospital; McGill University Health Center; Montreal Canada
- Child Health and Human Development Program; Research Institute of the McGill University Health Centre; Montreal Canada
| | - N. Webb
- Department of Human Genetics; McGill University; Montreal Canada
- Division of Medical Genetics, Department of Pediatrics; CHU Sainte-Justine and Université de Montréal; Montreal Canada
- Montreal Neurological Institute; McGill University; Montreal Canada
| | - M. Srour
- Department of Neurology and Neurosurgery; McGill University; Montreal Canada
- Department of Pediatrics; McGill University; Montreal Canada
- Child Health and Human Development Program; Research Institute of the McGill University Health Centre; Montreal Canada
| | - J.J. Mitchell
- Department of Pediatrics; McGill University; Montreal Canada
- Department of Medical Genetics, Montreal Children's Hospital; McGill University Health Center; Montreal Canada
| | - C. Brunel-Guitton
- Division of Medical Genetics, Department of Pediatrics; CHU Sainte-Justine and Université de Montréal; Montreal Canada
| | - J. Majewski
- Department of Human Genetics; McGill University; Montreal Canada
- McGill University and Genome Quebec Innovation Centre; Montreal Canada
| | - V. Long
- Department of Human Genetics, Division of Medical Genetics; Emory University School of Medicine; Atlanta Georgia
| | - S. Keller
- Department of Pediatrics, Division of Pediatric Neurology; Emory University School of Medicine; Atlanta Georgia
| | - M.J. Gambello
- Department of Human Genetics, Division of Medical Genetics; Emory University School of Medicine; Atlanta Georgia
| | - C. Simons
- Institute for Molecular Bioscience; The University of Queensland; St. Lucia Australia
| | - A. Vanderver
- Department of Neurology, Perelman School of Medicine; University of Pennsylvania; Philadelphia Pennsylvania
- Division of Neurology; Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - G. Bernard
- Department of Neurology and Neurosurgery; McGill University; Montreal Canada
- Department of Pediatrics; McGill University; Montreal Canada
- Department of Medical Genetics, Montreal Children's Hospital; McGill University Health Center; Montreal Canada
- Child Health and Human Development Program; Research Institute of the McGill University Health Centre; Montreal Canada
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32
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Sofou K, de Coo IFM, Ostergaard E, Isohanni P, Naess K, De Meirleir L, Tzoulis C, Uusimaa J, Lönnqvist T, Bindoff LA, Tulinius M, Darin N. Phenotype-genotype correlations in Leigh syndrome: new insights from a multicentre study of 96 patients. J Med Genet 2017; 55:21-27. [PMID: 29101127 DOI: 10.1136/jmedgenet-2017-104891] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/21/2017] [Accepted: 10/04/2017] [Indexed: 01/24/2023]
Abstract
BACKGROUND Leigh syndrome is a phenotypically and genetically heterogeneous mitochondrial disorder. While some genetic defects are associated with well-described phenotypes, phenotype-genotype correlations in Leigh syndrome are not fully explored. OBJECTIVE We aimed to identify phenotype-genotype correlations in Leigh syndrome in a large cohort of systematically evaluated patients. METHODS We studied 96 patients with genetically confirmed Leigh syndrome diagnosed and followed in eight European centres specialising in mitochondrial diseases. RESULTS We found that ataxia, ophthalmoplegia and cardiomyopathy were more prevalent among patients with mitochondrial DNA defects. Patients with mutations in MT-ND and NDUF genes with complex I deficiency shared common phenotypic features, such as early development of central nervous system disease, followed by high occurrence of cardiac and ocular manifestations. The cerebral cortex was affected in patients with NDUF mutations significantly more often than the rest of the cohort. Patients with the m.8993T>G mutation in MT-ATP6 gene had more severe clinical and radiological manifestations and poorer disease outcome compared with patients with the m.8993T>C mutation. CONCLUSION Our study provides new insights into phenotype-genotype correlations in Leigh syndrome and particularly in patients with complex I deficiency and with defects in the mitochondrial ATP synthase.
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Affiliation(s)
- Kalliopi Sofou
- Department of Pediatrics, The Queen Silvia Children's Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Irenaeus F M de Coo
- Department of Neurology, The Erasmus University Medical Center, Rotterdam, Netherlands
| | - Elsebet Ostergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Pirjo Isohanni
- Department of Paediatric Neurology, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Molecular Neurology, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Linda De Meirleir
- Department of Paediatric Neurology, University Hospital Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Charalampos Tzoulis
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Johanna Uusimaa
- Department of Paediatrics, Institute of Clinical Medicine, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Tuula Lönnqvist
- Department of Paediatric Neurology, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Laurence Albert Bindoff
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Már Tulinius
- Department of Pediatrics, The Queen Silvia Children's Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Niklas Darin
- Department of Pediatrics, The Queen Silvia Children's Hospital, University of Gothenburg, Gothenburg, Sweden
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33
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Koopman WJ, Beyrath J, Fung CW, Koene S, Rodenburg RJ, Willems PH, Smeitink JA. Mitochondrial disorders in children: toward development of small-molecule treatment strategies. EMBO Mol Med 2017; 8:311-27. [PMID: 26951622 PMCID: PMC4818752 DOI: 10.15252/emmm.201506131] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This review presents our current understanding of the pathophysiology and potential treatment strategies with respect to mitochondrial disease in children. We focus on pathologies due to mutations in nuclear DNA‐encoded structural and assembly factors of the mitochondrial oxidative phosphorylation (OXPHOS) system, with a particular emphasis on isolated mitochondrial complex I deficiency. Following a brief introduction into mitochondrial disease and OXPHOS function, an overview is provided of the diagnostic process in children with mitochondrial disorders. This includes the impact of whole‐exome sequencing and relevance of cellular complementation studies. Next, we briefly present how OXPHOS mutations can affect cellular parameters, primarily based on studies in patient‐derived fibroblasts, and how this information can be used for the rational design of small‐molecule treatment strategies. Finally, we discuss clinical trial design and provide an overview of small molecules that are currently being developed for treatment of mitochondrial disease.
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Affiliation(s)
- Werner Jh Koopman
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Cheuk-Wing Fung
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong
| | - Saskia Koene
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Hgm Willems
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Am Smeitink
- Centre for Systems Biology and Bioenergetics, Radboud University Medical Center, Nijmegen, The Netherlands Khondrion BV, Nijmegen, The Netherlands Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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34
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Lv L, Wang Y, Feng W, Hernandez JA, Huang W, Zheng Y, Zhou X, Lv S, Chen Y, Yuan ZG. iTRAQ-based differential proteomic analysis in Mongolian gerbil brains chronically infected with Toxoplasma gondii. J Proteomics 2017; 160:74-83. [DOI: 10.1016/j.jprot.2017.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/13/2017] [Accepted: 03/13/2017] [Indexed: 12/12/2022]
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35
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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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Quantifying ROS levels using CM-H 2 DCFDA and HyPer. Methods 2016; 109:3-11. [DOI: 10.1016/j.ymeth.2016.06.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 11/24/2022] Open
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Gerards M, Sallevelt SCEH, Smeets HJM. Leigh syndrome: Resolving the clinical and genetic heterogeneity paves the way for treatment options. Mol Genet Metab 2016; 117:300-12. [PMID: 26725255 DOI: 10.1016/j.ymgme.2015.12.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022]
Abstract
Leigh syndrome is a progressive neurodegenerative disorder, affecting 1 in 40,000 live births. Most patients present with symptoms between the ages of three and twelve months, but adult onset Leigh syndrome has also been described. The disease course is characterized by a rapid deterioration of cognitive and motor functions, in most cases resulting in death due to respiratory failure. Despite the high genetic heterogeneity of Leigh syndrome, patients present with identical, symmetrical lesions in the basal ganglia or brainstem on MRI, while additional clinical manifestations and age of onset varies from case to case. To date, mutations in over 60 genes, both nuclear and mitochondrial DNA encoded, have been shown to cause Leigh syndrome, still explaining only half of all cases. In most patients, these mutations directly or indirectly affect the activity of the mitochondrial respiratory chain or pyruvate dehydrogenase complex. Exome sequencing has accelerated the discovery of new genes and pathways involved in Leigh syndrome, providing novel insights into the pathophysiological mechanisms. This is particularly important as no general curative treatment is available for this devastating disorder, although several recent studies imply that early treatment might be beneficial for some patients depending on the gene or process affected. Timely, gene-based personalized treatment may become an important strategy in rare, genetically heterogeneous disorders like Leigh syndrome, stressing the importance of early genetic diagnosis and identification of new genes/pathways. In this review, we provide a comprehensive overview of the most important clinical manifestations and genes/pathways involved in Leigh syndrome, and discuss the current state of therapeutic interventions in patients.
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Affiliation(s)
- Mike Gerards
- Department of Clinical Genetics, Research School GROW, Maastricht University Medical Centre, Maastricht, The Netherlands; Maastricht Center for Systems Biology (MaCSBio), Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Research School GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Hubert J M Smeets
- Department of Clinical Genetics, Research School GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
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Chintalapudi SR, Morales-Tirado VM, Williams RW, Jablonski MM. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells. FEBS J 2016; 283:678-93. [PMID: 26663874 DOI: 10.1111/febs.13620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vanessa M Morales-Tirado
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
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Forkink M, Basit F, Teixeira J, Swarts HG, Koopman WJH, Willems PHGM. Complex I and complex III inhibition specifically increase cytosolic hydrogen peroxide levels without inducing oxidative stress in HEK293 cells. Redox Biol 2015; 6:607-616. [PMID: 26516986 PMCID: PMC4635408 DOI: 10.1016/j.redox.2015.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 12/17/2022] Open
Abstract
Inhibitor studies with isolated mitochondria demonstrated that complex I (CI) and III (CIII) of the electron transport chain (ETC) can act as relevant sources of mitochondrial reactive oxygen species (ROS). Here we studied ROS generation and oxidative stress induction during chronic (24h) inhibition of CI and CIII using rotenone (ROT) and antimycin A (AA), respectively, in intact HEK293 cells. Both inhibitors stimulated oxidation of the ROS sensor hydroethidine (HEt) and increased mitochondrial NAD(P)H levels without major effects on cell viability. Integrated analysis of cells stably expressing cytosolic- or mitochondria-targeted variants of the reporter molecules HyPer (H2O2-sensitive and pH-sensitive) and SypHer (H2O2-insensitive and pH-sensitive), revealed that CI- and CIII inhibition increased cytosolic but not mitochondrial H2O2 levels. Total and mitochondria-specific lipid peroxidation was not increased in the inhibited cells as reported by the C11-BODIPY(581/591) and MitoPerOx biosensors. Also expression of the superoxide-detoxifying enzymes CuZnSOD (cytosolic) and MnSOD (mitochondrial) was not affected. Oxyblot analysis revealed that protein carbonylation was not stimulated by CI and CIII inhibition. Our findings suggest that chronic inhibition of CI and CIII: (i) increases the levels of HEt-oxidizing ROS and (ii) specifically elevates cytosolic but not mitochondrial H2O2 levels, (iii) does not induce oxidative stress or substantial cell death. We conclude that the increased ROS levels are below the stress-inducing level and might play a role in redox signaling.
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Affiliation(s)
- Marleen Forkink
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Farhan Basit
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - José Teixeira
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
| | - Herman G Swarts
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Werner J H Koopman
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
| | - Peter H G M Willems
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
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Cameron JM, MacKay N, Feigenbaum A, Tarnopolsky M, Blaser S, Robinson BH, Schulze A. Exome sequencing identifies complex I NDUFV2 mutations as a novel cause of Leigh syndrome. Eur J Paediatr Neurol 2015; 19:525-32. [PMID: 26008862 DOI: 10.1016/j.ejpn.2015.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/12/2015] [Accepted: 05/05/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Two siblings with hypertrophic cardiomyopathy and brain atrophy were diagnosed with Complex I deficiency based on low enzyme activity in muscle and high lactate/pyruvate ratio in fibroblasts. METHODS Whole exome sequencing results of fibroblast gDNA from one sibling was narrowed down to 190 SNPs or In/Dels in 185 candidate genes by selecting non-synonymous coding sequence base pair changes that were not present in the SNP database. RESULTS Two compound heterozygous mutations were identified in both siblings in NDUFV2, encoding the 24 kDa subunit of Complex I. The intronic mutation (c.IVS2 + 1delGTAA) is disease causing and has been reported before. The other mutation is novel (c.669_670insG, p.Ser224Valfs*3) and predicted to cause a pathogenic frameshift in the protein. Subsequent investigation of 10 probands with complex I deficiency from different families revealed homozygosity for the intronic c.IVS2 + 1delGTAA mutation in a second, consanguineous family. In this family three of five siblings were affected. Interestingly, they presented with Leigh syndrome but no cardiac involvement. The same genotype had been reported previously in a two families but presenting with hypertrophic cardiomyopathy, trunk hypotonia and encephalopathy. CONCLUSION We have identified NDUFV2 mutations in two families with Complex I deficiency, including a novel mutation. The diagnosis of Leigh syndrome expands the clinical phenotypes associated with the c.IVS2 + 1delGTAA mutation in this gene.
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Affiliation(s)
- Jessie M Cameron
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada.
| | - Nevena MacKay
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Annette Feigenbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada.
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada.
| | - Susan Blaser
- Department of Radiology, The Hospital for Sick Children and University of Toronto, ON M5G 1X8, Canada.
| | - Brian H Robinson
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Andreas Schulze
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada.
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Jeong JC, Chen X. A New Semantic Functional Similarity over Gene Ontology. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:322-334. [PMID: 26357220 DOI: 10.1109/tcbb.2014.2343963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Identifying functionally similar or closely related genes and gene products has significant impacts on biological and clinical studies as well as drug discovery. In this paper, we propose an effective and practically useful method measuring both gene and gene product similarity by integrating the topology of gene ontology, known functional domains and their functional annotations. The proposed method is comprehensively evaluated through statistical analysis of the similarities derived from sequence, structure and phylogenetic profiles, and clustering analysis of disease genes clusters. Our results show that the proposed method clearly outperforms other conventional methods. Furthermore, literature analysis also reveals that the proposed method is both statistically and biologically promising for identifying functionally similar genes or gene products. In particular, we demonstrate that the proposed functional similarity metric is capable of discoverying new disease related genes or gene products.
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Ruhoy IS, Saneto RP. The genetics of Leigh syndrome and its implications for clinical practice and risk management. APPLICATION OF CLINICAL GENETICS 2014; 7:221-34. [PMID: 25419155 PMCID: PMC4235479 DOI: 10.2147/tacg.s46176] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Leigh syndrome, also referred to as subacute necrotizing encephalomyelopathy, is a severe, early-onset neurodegenerative disorder that is relentlessly progressive and devastating to both the patient and the patient’s family. Attributed to the ultimate failure of the mitochondrial respiratory chain, once it starts, the disease often results in the regression of both mental and motor skills, leading to disability and rapid progression to death. It is a mitochondrial disorder with both phenotypic and genetic heterogeneity. The cause of death is most often respiratory failure, but there are a whole host of complications, including refractory seizures, that may further complicate morbidity and mortality. The symptoms may develop slowly or with rapid progression, usually associated with age of onset. Although the disease is usually diagnosed within the first year of life, it is important to note that recent studies reveal phenotypic heterogeneity, with some patients having evidence of in utero presentation and others having adult-onset symptoms.
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Affiliation(s)
- Ilene S Ruhoy
- Division of Pediatric Neurology, Seattle Children's Hospital/University of Washington, Seattle, WA, USA
| | - Russell P Saneto
- Division of Pediatric Neurology, Seattle Children's Hospital/University of Washington, Seattle, WA, USA
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Mitochondrial hyperpolarization during chronic complex I inhibition is sustained by low activity of complex II, III, IV and V. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1247-56. [PMID: 24769419 DOI: 10.1016/j.bbabio.2014.04.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 02/01/2023]
Abstract
The mitochondrial oxidative phosphorylation (OXPHOS) system consists of four electron transport chain (ETC) complexes (CI-CIV) and the FoF1-ATP synthase (CV), which sustain ATP generation via chemiosmotic coupling. The latter requires an inward-directed proton-motive force (PMF) across the mitochondrial inner membrane (MIM) consisting of a proton (ΔpH) and electrical charge (Δψ) gradient. CI actively participates in sustaining these gradients via trans-MIM proton pumping. Enigmatically, at the cellular level genetic or inhibitor-induced CI dysfunction has been associated with Δψ depolarization or hyperpolarization. The cellular mechanism of the latter is still incompletely understood. Here we demonstrate that chronic (24h) CI inhibition in HEK293 cells induces a proton-based Δψ hyperpolarization in HEK293 cells without triggering reverse-mode action of CV or the adenine nucleotide translocase (ANT). Hyperpolarization was associated with low levels of CII-driven O2 consumption and prevented by co-inhibition of CII, CIII or CIV activity. In contrast, chronic CIII inhibition triggered CV reverse-mode action and induced Δψ depolarization. CI- and CIII-inhibition similarly reduced free matrix ATP levels and increased the cell's dependence on extracellular glucose to maintain cytosolic free ATP. Our findings support a model in which Δψ hyperpolarization in CI-inhibited cells results from low activity of CII, CIII and CIV, combined with reduced forward action of CV and ANT.
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Rak M, Rustin P. Supernumerary subunits NDUFA3, NDUFA5 and NDUFA12 are required for the formation of the extramembrane arm of human mitochondrial complex I. FEBS Lett 2014; 588:1832-8. [PMID: 24717771 DOI: 10.1016/j.febslet.2014.03.046] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/12/2014] [Accepted: 03/23/2014] [Indexed: 12/13/2022]
Abstract
Mammalian complex I is composed of fourteen highly conserved core subunits and additional thirty subunits acquired in the course of evolution. At present, the function of the majority of these supernumerary subunits is poorly understood. In this work, we have studied NDUFA3, NDUFA5 and NDUFA12 supernumerary subunits to gain insight into their role in CI activity and biogenesis. Using human cell lines in which the expression of these subunits was knocked down with miRNAs, we showed that they are necessary for the formation of a functional holoenzyme. Analysis of the assembly intermediates in mitochondria depleted for these subunits further suggested that they are required for assembly and/or stability of the electron transferring Q module in the peripheral arm of the CI.
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Affiliation(s)
- Malgorzata Rak
- INSERM UMR 1141, Bâtiment Ecran, Hôpital Robert Debré, 48 Boulevard Serurier, 75019 Paris, France.
| | - Pierre Rustin
- INSERM UMR 1141, Bâtiment Ecran, Hôpital Robert Debré, 48 Boulevard Serurier, 75019 Paris, France
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45
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Abstract
Mitochondrial respiratory complex I is a product of both the nuclear and mitochondrial genomes. The integration of seven subunits encoded in mitochondrial DNA into the inner membrane, their association with 14 nuclear-encoded membrane subunits, the construction of the extrinsic arm from 23 additional nuclear-encoded proteins, iron-sulfur clusters, and flavin mononucleotide cofactor require the participation of assembly factors. Some are intrinsic to the complex, whereas others participate transiently. The suppression of the expression of the NDUFA11 subunit of complex I disrupted the assembly of the complex, and subcomplexes with masses of 550 and 815 kDa accumulated. Eight of the known extrinsic assembly factors plus a hydrophobic protein, C3orf1, were associated with the subcomplexes. The characteristics of C3orf1, of another assembly factor, TMEM126B, and of NDUFA11 suggest that they all participate in constructing the membrane arm of complex I.
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Nouws J, te Brinke H, Nijtmans LG, Houten SM. ACAD9, a complex I assembly factor with a moonlighting function in fatty acid oxidation deficiencies. Hum Mol Genet 2013; 23:1311-9. [DOI: 10.1093/hmg/ddt521] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rhein VF, Carroll J, Ding S, Fearnley IM, Walker JE. NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I. J Biol Chem 2013; 288:33016-26. [PMID: 24089531 PMCID: PMC3829151 DOI: 10.1074/jbc.m113.518803] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ∼100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-β-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ω-NG,NG′ atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm.
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Affiliation(s)
- Virginie F Rhein
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
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Abstract
Mitochondrial complex I has a molecular mass of almost 1 MDa and comprises more than 40 polypeptides. Fourteen central subunits harbour the bioenergetic core functions. We are only beginning to understand the significance of the numerous accessory subunits. The present review addresses the role of accessory subunits for assembly, stability and regulation of complex I and for cellular functions not directly associated with redox-linked proton translocation.
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Nouws J, Wibrand F, van den Brand M, Venselaar H, Duno M, Lund AM, Trautner S, Nijtmans L, Ostergard E. A Patient with Complex I Deficiency Caused by a Novel ACAD9 Mutation Not Responding to Riboflavin Treatment. JIMD Rep 2013; 12:37-45. [PMID: 23996478 DOI: 10.1007/8904_2013_242] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/31/2022] Open
Abstract
Here we report a patient with a new pathogenic mutation in ACAD9. Shortly after birth she presented with respiratory insufficiency and a high lactate level. At age 7 weeks, she was diagnosed with severe hypertrophic cardiomyopathy and she suffered from muscle weakness and hypotonia. Her condition deteriorated during intercurrent illnesses and she died at 6 months of age in cardiogenic shock. Analysis of respiratory chain activities in muscle and fibroblasts revealed an isolated complex I deficiency. A genome-wide screen for homozygosity revealed several homozygous regions. Four candidate genes were found and sequencing revealed a homozygous missense mutation in ACAD9. The mutation results in an Ala220Val amino acid substitution located near the catalytic core of ACAD9. SDS and BN-PAGE analysis showed severely decreased ACAD9 and complex I protein levels, and lentiviral complementation of patient fibroblasts partially rescued the complex I deficiency. Riboflavin supplementation did not ameliorate the complex I deficiency in patient fibroblasts. More than a dozen ACAD9 patients with complex I deficiency have been identified in the last 3 years, indicating that ACAD9 is important for complex I assembly, and that ACAD9 mutations are a relatively frequent cause of complex I deficiency.
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Affiliation(s)
- Jessica Nouws
- Nijmegen Centre for Mitochondrial Disorders at the Department of Pediatrics, Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
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Abstract
INTRODUCTION In the last 10 years the field of mitochondrial genetics has widened, shifting the focus from rare sporadic, metabolic disease to the effects of mitochondrial DNA (mtDNA) variation in a growing spectrum of human disease. The aim of this review is to guide the reader through some key concepts regarding mitochondria before introducing both classic and emerging mitochondrial disorders. SOURCES OF DATA In this article, a review of the current mitochondrial genetics literature was conducted using PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). In addition, this review makes use of a growing number of publically available databases including MITOMAP, a human mitochondrial genome database (www.mitomap.org), the Human DNA polymerase Gamma Mutation Database (http://tools.niehs.nih.gov/polg/) and PhyloTree.org (www.phylotree.org), a repository of global mtDNA variation. AREAS OF AGREEMENT The disruption in cellular energy, resulting from defects in mtDNA or defects in the nuclear-encoded genes responsible for mitochondrial maintenance, manifests in a growing number of human diseases. AREAS OF CONTROVERSY The exact mechanisms which govern the inheritance of mtDNA are hotly debated. GROWING POINTS Although still in the early stages, the development of in vitro genetic manipulation could see an end to the inheritance of the most severe mtDNA disease.
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Affiliation(s)
| | - Gavin Hudson
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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