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Lesner NP, Wang X, Chen Z, Frank A, Menezes CJ, House S, Shelton SD, Lemoff A, McFadden DG, Wansapura J, DeBerardinis RJ, Mishra P. Differential requirements for mitochondrial electron transport chain components in the adult murine liver. eLife 2022; 11:e80919. [PMID: 36154948 PMCID: PMC9648974 DOI: 10.7554/elife.80919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial electron transport chain (ETC) dysfunction due to mutations in the nuclear or mitochondrial genome is a common cause of metabolic disease in humans and displays striking tissue specificity depending on the affected gene. The mechanisms underlying tissue-specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for basal respiration and maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function, redox and oxygen status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, impaired oxygen handling, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes use alternative electron donors to fuel the mitochondrial ETC.
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Affiliation(s)
- Nicholas P Lesner
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Xun Wang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Zhenkang Chen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anderson Frank
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - Cameron J Menezes
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sara House
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Spencer D Shelton
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - David G McFadden
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Janaka Wansapura
- Advanced Imaging Research Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
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2
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Chlamydia pneumoniae can infect the central nervous system via the olfactory and trigeminal nerves and contributes to Alzheimer's disease risk. Sci Rep 2022; 12:2759. [PMID: 35177758 PMCID: PMC8854390 DOI: 10.1038/s41598-022-06749-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
Chlamydia pneumoniae is a respiratory tract pathogen but can also infect the central nervous system (CNS). Recently, the link between C. pneumoniae CNS infection and late-onset dementia has become increasingly evident. In mice, CNS infection has been shown to occur weeks to months after intranasal inoculation. By isolating live C. pneumoniae from tissues and using immunohistochemistry, we show that C. pneumoniae can infect the olfactory and trigeminal nerves, olfactory bulb and brain within 72 h in mice. C. pneumoniae infection also resulted in dysregulation of key pathways involved in Alzheimer’s disease pathogenesis at 7 and 28 days after inoculation. Interestingly, amyloid beta accumulations were also detected adjacent to the C. pneumoniae inclusions in the olfactory system. Furthermore, injury to the nasal epithelium resulted in increased peripheral nerve and olfactory bulb infection, but did not alter general CNS infection. In vitro, C. pneumoniae was able to infect peripheral nerve and CNS glia. In summary, the nerves extending between the nasal cavity and the brain constitute invasion paths by which C. pneumoniae can rapidly invade the CNS likely by surviving in glia and leading to Aβ deposition.
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3
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Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
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Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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4
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Zhu Z, Li R, Qin W, Zhang H, Cheng Y, Chen F, Chen C, Chen L, Zhao Y. Target engagement of ginsenosides in mild cognitive impairment using mass spectrometry-based drug affinity responsive target stability. J Ginseng Res 2021; 46:750-758. [DOI: 10.1016/j.jgr.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 10/31/2022] Open
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5
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Nolin SL, Napoli E, Flores A, Hagerman RJ, Giulivi C. Deficits in Prenatal Serine Biosynthesis Underlie the Mitochondrial Dysfunction Associated with the Autism-Linked FMR1 Gene. Int J Mol Sci 2021; 22:ijms22115886. [PMID: 34070950 PMCID: PMC8198117 DOI: 10.3390/ijms22115886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Fifty-five to two hundred CGG repeats (called a premutation, or PM) in the 5′-UTR of the FMR1 gene are generally unstable, often expanding to a full mutation (>200) in one generation through maternal inheritance, leading to fragile X syndrome, a condition associated with autism and other intellectual disabilities. To uncover the early mechanisms of pathogenesis, we performed metabolomics and proteomics on amniotic fluids from PM carriers, pregnant with male fetuses, who had undergone amniocentesis for fragile X prenatal diagnosis. The prenatal metabolic footprint identified mitochondrial deficits, which were further validated by using internal and external cohorts. Deficits in the anaplerosis of the Krebs cycle were noted at the level of serine biosynthesis, which was confirmed by rescuing the mitochondrial dysfunction in the carriers’ umbilical cord fibroblasts using alpha-ketoglutarate precursors. Maternal administration of serine and its precursors has the potential to decrease the risk of developing energy shortages associated with mitochondrial dysfunction and linked comorbidities.
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Affiliation(s)
- Sarah L. Nolin
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA;
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (E.N.); (A.F.)
| | - Amanda Flores
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (E.N.); (A.F.)
- Medical Sciences Campus, Department of Biochemistry, University of Puerto Rico, San Juan PR00936, Puerto Rico
| | - Randi J. Hagerman
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, CA 95817, USA;
- The MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (E.N.); (A.F.)
- The MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA
- Correspondence: ; Tel.: +1-530-754-8603
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6
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Xiao W, Yang Z, Yan X, Feng L, Long L, Tu T, Deng N, Chen W, Xiao B, Long H, Zeng Y. iTRAQ-Based Proteomic Analysis of Dentate Gyrus in Temporal Lobe Epilepsy With Hippocampal Sclerosis. Front Neurol 2021; 11:626013. [PMID: 33569037 PMCID: PMC7868380 DOI: 10.3389/fneur.2020.626013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Temporal lobe epilepsy (TLE) is the most frequent type of focal epilepsy in adults, typically resistant to pharmacological treatment, and mostly presents with cognitive impairment and psychiatric comorbidities. The most common neuropathological hallmark in TLE patients is hippocampal sclerosis (HS). However, the underlying molecular mechanisms involved remain poorly characterized. The dentate gyrus (DG), one specific hippocampal subarea, structural and functional changes imply a key involvement of the DG in the development of TLE. In this study, a isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic technique was performed for the analysis of hippocampal DG obtained from patients with TLE-HS compared to control samples obtained from autopsy. Our proteomic data identified 5,583 proteins, of which 82 proteins were upregulated and 90 proteins were downregulated. Bioinformatics analysis indicated that differentially expressed proteins were enriched in "synaptic vesicle," "mitochondrion," "cell-cell adhesion," "regulation of synaptic plasticity," "ATP binding," and "oxidative phosphorylation." Protein-protein interaction network analysis found a pivotal module of 10 proteins that were related to "oxidative phosphorylation." This study has investigated proteomic alterations in the DG region of TLE-HS patients, and paved the way for the better understanding of epileptogenesis mechanisms and future therapeutic intervention.
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Affiliation(s)
- Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiquan Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxin Yan
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tian Tu
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Na Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Wenjuan Chen
- Department of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
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7
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Adult mesenchymal stem cell ageing interplays with depressed mitochondrial Ndufs6. Cell Death Dis 2020; 11:1075. [PMID: 33323934 PMCID: PMC7738680 DOI: 10.1038/s41419-020-03289-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023]
Abstract
Mesenchymal stem cell (MSC)-based therapy has emerged as a novel strategy to treat many degenerative diseases. Accumulating evidence shows that the function of MSCs declines with age, thus limiting their regenerative capacity. Nonetheless, the underlying mechanisms that control MSC ageing are not well understood. We show that compared with bone marrow-MSCs (BM-MSCs) isolated from young and aged samples, NADH dehydrogenase (ubiquinone) iron-sulfur protein 6 (Ndufs6) is depressed in aged MSCs. Similar to that of Ndufs6 knockout (Ndufs6−/−) mice, MSCs exhibited a reduced self-renewal and differentiation capacity with a tendency to senescence in the presence of an increased p53/p21 level. Downregulation of Ndufs6 by siRNA also accelerated progression of wild-type BM-MSCs to an aged state. In contrast, replenishment of Ndufs6 in Ndufs6−/−-BM-MSCs significantly rejuvenated senescent cells and restored their proliferative ability. Compared with BM-MSCs, Ndufs6−/−-BM-MSCs displayed increased intracellular and mitochondrial reactive oxygen species (ROS), and decreased mitochondrial membrane potential. Treatment of Ndufs6−/−-BM-MSCs with mitochondrial ROS inhibitor Mito-TEMPO notably reversed the cellular senescence and reduced the increased p53/p21 level. We provide direct evidence that impairment of mitochondrial Ndufs6 is a putative accelerator of adult stem cell ageing that is associated with excessive ROS accumulation and upregulation of p53/p21. It also indicates that manipulation of mitochondrial function is critical and can effectively protect adult stem cells against senescence.
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8
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Peralta S, Pinto M, Arguello T, Garcia S, Diaz F, Moraes CT. Metformin delays neurological symptom onset in a mouse model of neuronal complex I deficiency. JCI Insight 2020; 5:141183. [PMID: 33148885 PMCID: PMC7710273 DOI: 10.1172/jci.insight.141183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
Complex I (also known as NADH-ubiquinone oxidoreductase) deficiency is the most frequent mitochondrial disorder present in childhood. NADH-ubiquinone oxidoreductase iron-sulfur protein 3 (NDUFS3) is a catalytic subunit of the mitochondrial complex I; NDUFS3 is conserved from bacteria and essential for complex I function. Mutations affecting complex I, including in the Ndufs3 gene, cause fatal neurodegenerative diseases, such as Leigh syndrome. No treatment is available for these conditions. We developed and performed a detailed molecular characterization of a neuron-specific Ndufs3 conditional KO mouse model. We showed that deletion of Ndufs3 in forebrain neurons reduced complex I activity, altered brain energy metabolism, and increased locomotor activity with impaired motor coordination, balance, and stereotyped behavior. Metabolomics analyses showed an increase of glycolysis intermediates, suggesting an adaptive response to the complex I defect. Administration of metformin to these mice delayed the onset of the neurological symptoms but not of neuronal loss. This improvement was likely related to enhancement of glucose uptake and utilization, which are known effects of metformin in the brain. Despite reports that metformin inhibits complex I activity, our findings did not show worsening a complex I defect nor increases in lactic acid, suggesting that metformin should be further evaluated for use in patients with mitochondrial encephalopathies. Metformin delays onset of mitochondrial encephalopathy in a CNS model of mitochondrial oxidative phosphorylation defect.
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Affiliation(s)
| | | | | | | | | | - Carlos T Moraes
- Department of Neurology and.,Department of Cell Biology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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9
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Liu H, Perumal N, Manicam C, Mercieca K, Prokosch V. Proteomics Reveals the Potential Protective Mechanism of Hydrogen Sulfide on Retinal Ganglion Cells in an Ischemia/Reperfusion Injury Animal Model. Pharmaceuticals (Basel) 2020; 13:ph13090213. [PMID: 32867129 PMCID: PMC7557839 DOI: 10.3390/ph13090213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Glaucoma is the leading cause of irreversible blindness and is characterized by progressive retinal ganglion cell (RGC) degeneration. Hydrogen sulfide (H2S) is a potent neurotransmitter and has been proven to protect RGCs against glaucomatous injury in vitro and in vivo. This study is to provide an overall insight of H2S’s role in glaucoma pathophysiology. Ischemia-reperfusion injury (I/R) was induced in Sprague-Dawley rats (n = 12) by elevating intraocular pressure to 55 mmHg for 60 min. Six of the animals received intravitreal injection of H2S precursor prior to the procedure and the retina was harvested 24 h later. Contralateral eyes were assigned as control. RGCs were quantified and compared within the groups. Retinal proteins were analyzed via label-free mass spectrometry based quantitative proteomics approach. The pathways of the differentially expressed proteins were identified by ingenuity pathway analysis (IPA). H2S significantly improved RGC survival against I/R in vivo (p < 0.001). In total 1115 proteins were identified, 18 key proteins were significantly differentially expressed due to I/R and restored by H2S. Another 11 proteins were differentially expressed following H2S. IPA revealed a significant H2S-mediated activation of pathways related to mitochondrial function, iron homeostasis and vasodilation. This study provides first evidence of the complex role that H2S plays in protecting RGC against I/R.
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Affiliation(s)
- Hanhan Liu
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Caroline Manicam
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Karl Mercieca
- Royal Eye Hospital, School of Medicine, University of Manchester, Manchester M13 9WH, UK;
| | - Verena Prokosch
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Correspondence: ; Tel.: +49-1703862250
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10
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Wang W, Zhao F, Ma X, Perry G, Zhu X. Mitochondria dysfunction in the pathogenesis of Alzheimer's disease: recent advances. Mol Neurodegener 2020; 15:30. [PMID: 32471464 PMCID: PMC7257174 DOI: 10.1186/s13024-020-00376-6] [Citation(s) in RCA: 521] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases, characterized by impaired cognitive function due to progressive loss of neurons in the brain. Under the microscope, neuronal accumulation of abnormal tau proteins and amyloid plaques are two pathological hallmarks in affected brain regions. Although the detailed mechanism of the pathogenesis of AD is still elusive, a large body of evidence suggests that damaged mitochondria likely play fundamental roles in the pathogenesis of AD. It is believed that a healthy pool of mitochondria not only supports neuronal activity by providing enough energy supply and other related mitochondrial functions to neurons, but also guards neurons by minimizing mitochondrial related oxidative damage. In this regard, exploration of the multitude of mitochondrial mechanisms altered in the pathogenesis of AD constitutes novel promising therapeutic targets for the disease. In this review, we will summarize recent progress that underscores the essential role of mitochondria dysfunction in the pathogenesis of AD and discuss mechanisms underlying mitochondrial dysfunction with a focus on the loss of mitochondrial structural and functional integrity in AD including mitochondrial biogenesis and dynamics, axonal transport, ER-mitochondria interaction, mitophagy and mitochondrial proteostasis.
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Affiliation(s)
- Wenzhang Wang
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
| | - Fanpeng Zhao
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - Xiaopin Ma
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
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11
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Tsai YL, Coady TH, Lu L, Zheng D, Alland I, Tian B, Shneider NA, Manley JL. ALS/FTD-associated protein FUS induces mitochondrial dysfunction by preferentially sequestering respiratory chain complex mRNAs. Genes Dev 2020; 34:785-805. [PMID: 32381627 PMCID: PMC7263147 DOI: 10.1101/gad.335836.119] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Dysregulation of the DNA/RNA-binding protein FUS causes certain subtypes of ALS/FTD by largely unknown mechanisms. Recent evidence has shown that FUS toxic gain of function due either to mutations or to increased expression can disrupt critical cellular processes, including mitochondrial functions. Here, we demonstrate that in human cells overexpressing wild-type FUS or expressing mutant derivatives, the protein associates with multiple mRNAs, and these are enriched in mRNAs encoding mitochondrial respiratory chain components. Notably, this sequestration leads to reduced levels of the encoded proteins, which is sufficient to bring about disorganized mitochondrial networks, reduced aerobic respiration and increased reactive oxygen species. We further show that mutant FUS associates with mitochondria and with mRNAs encoded by the mitochondrial genome. Importantly, similar results were also observed in fibroblasts derived from ALS patients with FUS mutations. Finally, we demonstrate that FUS loss of function does not underlie the observed mitochondrial dysfunction, and also provides a mechanism for the preferential sequestration of the respiratory chain complex mRNAs by FUS that does not involve sequence-specific binding. Together, our data reveal that respiratory chain complex mRNA sequestration underlies the mitochondrial defects characteristic of ALS/FTD and contributes to the FUS toxic gain of function linked to this disease spectrum.
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Affiliation(s)
- Yueh-Lin Tsai
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Tristan H Coady
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Lei Lu
- Center for Motor Neuron Biology and Disease, Columbia University, New York, New York 10027, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Isabel Alland
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Neil A Shneider
- Center for Motor Neuron Biology and Disease, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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12
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Hamzeh O, Alkhateeb A, Zheng J, Kandalam S, Rueda L. Prediction of tumor location in prostate cancer tissue using a machine learning system on gene expression data. BMC Bioinformatics 2020; 21:78. [PMID: 32164523 PMCID: PMC7068980 DOI: 10.1186/s12859-020-3345-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Finding the tumor location in the prostate is an essential pathological step for prostate cancer diagnosis and treatment. The location of the tumor - the laterality - can be unilateral (the tumor is affecting one side of the prostate), or bilateral on both sides. Nevertheless, the tumor can be overestimated or underestimated by standard screening methods. In this work, a combination of efficient machine learning methods for feature selection and classification are proposed to analyze gene activity and select them as relevant biomarkers for different laterality samples. RESULTS A data set that consists of 450 samples was used in this study. The samples were divided into three laterality classes (left, right, bilateral). The aim of this work is to understand the genomic activity in each class and find relevant genes as indicators for each class with nearly 99% accuracy. The system identified groups of differentially expressed genes (RTN1, HLA-DMB, MRI1) that are able to differentiate samples among the three classes. CONCLUSION The proposed method was able to detect sets of genes that can identify different laterality classes. The resulting genes are found to be strongly correlated with disease progression. HLA-DMB and EIF4G2, which are detected in the set of genes can detect the left laterality, were reported earlier to be in the same pathway called Allograft rejection SuperPath.
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Affiliation(s)
- Osama Hamzeh
- School of Computer Science, University of Windsor, 401 Sunset Ave, Windsor, N9B 3P4 ON Canada
| | - Abedalrhman Alkhateeb
- School of Computer Science, University of Windsor, 401 Sunset Ave, Windsor, N9B 3P4 ON Canada
| | - Julia Zheng
- School of Computer Science, University of Windsor, 401 Sunset Ave, Windsor, N9B 3P4 ON Canada
| | - Srinath Kandalam
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave, Windsor, N9B 3P4 ON Canada
| | - Luis Rueda
- School of Computer Science, University of Windsor, 401 Sunset Ave, Windsor, N9B 3P4 ON Canada
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13
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Pereira CV, Peralta S, Arguello T, Bacman SR, Diaz F, Moraes CT. Myopathy reversion in mice after restauration of mitochondrial complex I. EMBO Mol Med 2020; 12:e10674. [PMID: 31916679 PMCID: PMC7005622 DOI: 10.15252/emmm.201910674] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 01/03/2023] Open
Abstract
Myopathies are common manifestations of mitochondrial diseases. To investigate whether gene replacement can be used as an effective strategy to treat or cure mitochondrial myopathies, we have generated a complex I conditional knockout mouse model lacking NDUFS3 subunit in skeletal muscle. NDUFS3 protein levels were undetectable in muscle of 15‐day‐old smKO mice, and myopathy symptoms could be detected by 2 months of age, worsening over time. rAAV9‐Ndufs3 delivered systemically into 15‐ to 18‐day‐old mice effectively restored NDUFS3 levels in skeletal muscle, precluding the development of the myopathy. To test the ability of rAAV9‐mediated gene replacement to revert muscle function after disease onset, we also treated post‐symptomatic, 2‐month‐old mice. The injected mice showed a remarkable improvement of the mitochondrial myopathy and biochemical parameters, which remained for the duration of the study. Our results showed that muscle pathology could be reversed after restoring complex I, which was absent for more than 2 months. These findings have far‐reaching implications for the ability of muscle to tolerate a mitochondrial defect and for the treatment of mitochondrial myopathies.
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Affiliation(s)
- Claudia V Pereira
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susana Peralta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tania Arguello
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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14
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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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15
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Vrbacký M, Kovalčíková J, Chawengsaksophak K, Beck IM, Mráček T, Nůsková H, Sedmera D, Papoušek F, Kolář F, Sobol M, Hozák P, Sedlacek R, Houštěk J. Knockout of Tmem70 alters biogenesis of ATP synthase and leads to embryonal lethality in mice. Hum Mol Genet 2018; 25:4674-4685. [PMID: 28173120 DOI: 10.1093/hmg/ddw295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 12/24/2022] Open
Abstract
TMEM70, a 21-kDa protein localized in the inner mitochondrial membrane, has been shown to facilitate the biogenesis of mammalian F1Fo ATP synthase. Mutations of the TMEM70 gene represent the most frequent cause of isolated ATP synthase deficiency resulting in a severe mitochondrial disease presenting as neonatal encephalo-cardiomyopathy (OMIM 604273). To better understand the biological role of this factor, we generated Tmem70-deficient mice and found that the homozygous Tmem70-/- knockouts exhibited profound growth retardation and embryonic lethality at ∼9.5 days post coitum. Blue-Native electrophoresis demonstrated an isolated deficiency in fully assembled ATP synthase in the Tmem70-/- embryos (80% decrease) and a marked accumulation of F1 complexes indicative of impairment in ATP synthase biogenesis that was stalled at the early stage, following the formation of F1 oligomer. Consequently, a decrease in ADP-stimulated State 3 respiration, respiratory control ratio and ATP/ADP ratios, indicated compromised mitochondrial ATP production. Tmem70-/- embryos exhibited delayed development of the cardiovascular system and a disturbed heart mitochondrial ultrastructure, with concentric or irregular cristae structures. Tmem70+/- heterozygous mice were fully viable and displayed normal postnatal growth and development of the mitochondrial oxidative phosphorylation system. Nevertheless, they presented with mild deterioration of heart function. Our results demonstrated that Tmem70 knockout in the mouse results in embryonic lethality due to the lack of ATP synthase and impairment of mitochondrial energy provision. This is analogous to TMEM70 dysfunction in humans and verifies the crucial role of this factor in the biosynthesis and assembly of mammalian ATP synthase.
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Affiliation(s)
- Marek Vrbacký
- Department of Bioenergetics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Kovalčíková
- Department of Bioenergetics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Inken M Beck
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Mráček
- Department of Bioenergetics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Nůsková
- Department of Bioenergetics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Sedmera
- Department of Cardiovascular Morphogenesis, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic,Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - František Papoušek
- Department of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - František Kolář
- Department of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Margarita Sobol
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Hozák
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Josef Houštěk
- Department of Bioenergetics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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16
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Hunt RJ, Bateman JM. Mitochondrial retrograde signaling in the nervous system. FEBS Lett 2017; 592:663-678. [PMID: 29086414 DOI: 10.1002/1873-3468.12890] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]
Abstract
Mitochondria generate the majority of cellular ATP and are essential for neuronal function. Loss of mitochondrial activity leads to primary mitochondrial diseases and may contribute to neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Mitochondria communicate with the cell through mitochondrial retrograde signaling pathways. These signaling pathways are triggered by mitochondrial dysfunction and allow the organelle to control nuclear gene transcription. Neuronal mitochondrial retrograde signaling pathways have been identified in disease model systems and targeted to restore neuronal function and prevent neurodegeneration. In this review, we describe yeast and mammalian cellular models that have paved the way in the investigation of mitochondrial retrograde mechanisms. We then discuss the evidence for retrograde signaling in neurons and our current knowledge of retrograde signaling mechanisms in neuronal model systems. We argue that targeting mitochondrial retrograde pathways has the potential to lead to novel treatments for neurological diseases.
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Affiliation(s)
- Rachel J Hunt
- Wolfson Centre for Age-Related Diseases, King's College London, UK
| | - Joseph M Bateman
- Wolfson Centre for Age-Related Diseases, King's College London, UK
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17
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Kim C, Potluri P, Khalil A, Gaut D, McManus M, Compton S, Wallace DC, Yadava N. An X-chromosome linked mouse model (Ndufa1 S55A) for systemic partial Complex I deficiency for studying predisposition to neurodegeneration and other diseases. Neurochem Int 2017; 109:78-93. [PMID: 28506826 DOI: 10.1016/j.neuint.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/07/2017] [Accepted: 05/08/2017] [Indexed: 01/19/2023]
Abstract
The respiratory chain Complex I deficiencies are the most common cause of mitochondrial diseases. Complex I biogenesis is controlled by 58 genes and at least 47 of these cause mitochondrial disease in humans. Two of these are X-chromosome linked nuclear (nDNA) genes (NDUFA1 and NDUFB11), and 7 are mitochondrial (mtDNA, MT-ND1-6, -4L) genes, which may be responsible for sex-dependent variation in the presentation of mitochondrial diseases. In this study, we describe an X-chromosome linked mouse model (Ndufa1S55A) for systemic partial Complex I deficiency. By homologous recombination, a point mutation T > G within 55th codon of the Ndufa1 gene was introduced. The resulting allele Ndufa1S55A introduced systemic serine-55-alanine (S55A) mutation within the MWFE protein, which is essential for Complex I assembly and stability. The S55A mutation caused systemic partial Complex I deficiency of ∼50% in both sexes. The mutant males (Ndufa1S55A/Y) displayed reduced respiratory exchange ratio (RER) and produced less body heat. They were also hypoactive and ate less. They showed age-dependent Purkinje neurons degeneration. Metabolic profiling of brain, liver and serum from males showed reduced heme levels in mutants, which correlated with altered expressions of Fech and Hmox1 mRNAs in tissues. This is the first genuine X-chromosome linked mouse model for systemic partial Complex I deficiency, which shows age-dependent neurodegeneration. The effect of Complex I deficiency on survival patterns of males vs. females was different. We believe this model will be very useful for studying sex-dependent predisposition to both spontaneous and stress-induced neurodegeneration, cancer, diabetes and other diseases.
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Affiliation(s)
- Chul Kim
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, USA
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine at the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ahmed Khalil
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, USA
| | - Daria Gaut
- Center for Mitochondrial and Epigenomic Medicine at the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Meagan McManus
- Center for Mitochondrial and Epigenomic Medicine at the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shannon Compton
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine at the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nagendra Yadava
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, USA; Division of Endocrinology, Diabetes & Metabolism at Baystate Medical Center, Tufts University School of Medicine, Springfield, MA 01199, USA.
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18
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Feng Y, Wang X. Systematic analysis of microarray datasets to identify Parkinson's disease‑associated pathways and genes. Mol Med Rep 2017; 15:1252-1262. [PMID: 28098893 PMCID: PMC5367356 DOI: 10.3892/mmr.2017.6124] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/21/2016] [Indexed: 01/20/2023] Open
Abstract
In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co-expression networks and clinical information was adopted, using weighted gene co-expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD. Functional enrichment analysis of commonly disturbed genes was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Co-pathway relationships were identified with Pearson's correlation coefficient tests and a hypergeometric distribution-based test. Common genes in pathway pairs were selected out and regarded as risk genes. A total of 17 microarray datasets from 7 platforms were retained for further analysis. Five gene coexpression modules were identified, containing 9,745, 736, 233, 101 and 93 genes, respectively. One module was significantly correlated with PD samples and thus the 736 genes it contained were considered to be candidate PD-associated genes. Functional enrichment analysis demonstrated that these genes were implicated in oxidative phosphorylation and PD. A total of 44 pathway pairs and 52 risk genes were revealed, and a risk gene pathway relationship network was constructed. Eight modules were identified and were revealed to be associated with PD, cancers and metabolism. A number of disturbed pathways and risk genes were unveiled in PD, and these findings may help advance understanding of PD pathogenesis.
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Affiliation(s)
- Yinling Feng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Sichuan 400016, P.R. China
| | - Xuefeng Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Sichuan 400016, P.R. China
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19
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Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT. Accessory subunits are integral for assembly and function of human mitochondrial complex I. Nature 2016; 538:123-126. [PMID: 27626371 DOI: 10.1038/nature19754] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans, making it one of the largest known multi-subunit membrane protein complexes. Complex I exists in supercomplex forms with respiratory chain complexes III and IV, which are together required for the generation of a transmembrane proton gradient used for the synthesis of ATP. Complex I is also a major source of damaging reactive oxygen species and its dysfunction is associated with mitochondrial disease, Parkinson's disease and ageing. Bacterial and human complex I share 14 core subunits that are essential for enzymatic function; however, the role and necessity of the remaining 31 human accessory subunits is unclear. The incorporation of accessory subunits into the complex increases the cellular energetic cost and has necessitated the involvement of numerous assembly factors for complex I biogenesis. Here we use gene editing to generate human knockout cell lines for each accessory subunit. We show that 25 subunits are strictly required for assembly of a functional complex and 1 subunit is essential for cell viability. Quantitative proteomic analysis of cell lines revealed that loss of each subunit affects the stability of other subunits residing in the same structural module. Analysis of proteomic changes after the loss of specific modules revealed that ATP5SL and DMAC1 are required for assembly of the distal portion of the complex I membrane arm. Our results demonstrate the broad importance of accessory subunits in the structure and function of human complex I. Coupling gene-editing technology with proteomics represents a powerful tool for dissecting large multi-subunit complexes and enables the study of complex dysfunction at a cellular level.
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Affiliation(s)
- David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Elliot E Surgenor
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Marris G Dibley
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Laura D Osellame
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Tegan Stait
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital 3052, Melbourne, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University 3086, Melbourne Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
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20
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Lax NZ, Gorman GS, Turnbull DM. Review: Central nervous system involvement in mitochondrial disease. Neuropathol Appl Neurobiol 2016; 43:102-118. [PMID: 27287935 PMCID: PMC5363248 DOI: 10.1111/nan.12333] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/03/2016] [Accepted: 06/11/2016] [Indexed: 12/13/2022]
Abstract
Mitochondrial respiratory chain defects are an important cause of inherited disorders affecting approximately 1 in 5000 people in the UK population. Collectively these disorders are termed ‘mitochondrial diseases’ and they result from either mitochondrial DNA mutations or defects in nuclear DNA. Although they are frequently multisystem disorders, neurological deficits are particularly common, wide‐ranging and disabling for patients. This review details the manifold neurological impairments associated with mitochondrial disease, and describes the efforts to understand how they arise and progressively worsen in patients with mitochondrial disease. We describe advances in our understanding of disease pathogenesis through detailed neuropathological studies and how this has spurred the development of cellular and animal models of disease. We underscore the importance of continued clinical, molecular genetic, neuropathological and animal model studies to fully characterize mitochondrial diseases and understand mechanisms of neurodegeneration. These studies are instrumental for the next phase of mitochondrial research that has a particular emphasis on finding novel ways to treat mitochondrial disease to improve patient care and quality of life.
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Affiliation(s)
- N Z Lax
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - G S Gorman
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - D M Turnbull
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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21
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Huang YP, Chang NW. PPARα modulates gene expression profiles of mitochondrial energy metabolism in oral tumorigenesis. Biomedicine (Taipei) 2016; 6:3. [PMID: 26869356 PMCID: PMC4751096 DOI: 10.7603/s40681-016-0003-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/15/2015] [Indexed: 11/16/2022] Open
Abstract
Metabolic reprogramming plays a crucial role in the development of cancer. The aim of this study was to explore the effect of fenofibrate, an agonist of peroxisome proliferator-activated receptor alpha (PPARα), on gene expression profiles of mitochondrial energy metabolism. Our results showed that PPARα expression was negatively correlated with tumor progression in an oral cancer mouse model. Activation of PPARα through fenofibrate suppressed migration of oral cancer cells. Differential protein profiling demonstrated that expressions of genes related to mitochondrial energy metabolism were either up-regulated (Atp5g3, Cyc1, Ndufa5, Ndufa10, and Sdhd) or down-regulated (Cox5b, Ndufa1, Ndufb7, and Uqcrh) through PPARα activation and response. Our results indicate that PPARα exhibits a great potential for anti-oral cancer therapies by modulating cancer cell mitochondrial energy metabolism.
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Affiliation(s)
- Yi-Ping Huang
- Department of Physiology, College of Medicine, China Medical University, 404, Taichung, Taiwan
| | - Nai Wen Chang
- Department of Biochemistry, College of Medicine,, China Medical University, 404, No. 91, Hsueh-Shih Road, Taichung, Taiwan.
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22
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Nechiporuk T, McGann J, Mullendorff K, Hsieh J, Wurst W, Floss T, Mandel G. The REST remodeling complex protects genomic integrity during embryonic neurogenesis. eLife 2016; 5:e09584. [PMID: 26745185 PMCID: PMC4728133 DOI: 10.7554/elife.09584] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/20/2015] [Indexed: 01/01/2023] Open
Abstract
The timely transition from neural progenitor to post-mitotic neuron requires down-regulation and loss of the neuronal transcriptional repressor, REST. Here, we have used mice containing a gene trap in the Rest gene, eliminating transcription from all coding exons, to remove REST prematurely from neural progenitors. We find that catastrophic DNA damage occurs during S-phase of the cell cycle, with long-term consequences including abnormal chromosome separation, apoptosis, and smaller brains. Persistent effects are evident by latent appearance of proneural glioblastoma in adult mice deleted additionally for the tumor suppressor p53 protein (p53). A previous line of mice deleted for REST in progenitors by conventional gene targeting does not exhibit these phenotypes, likely due to a remaining C-terminal peptide that still binds chromatin and recruits co-repressors. Our results suggest that REST-mediated chromatin remodeling is required in neural progenitors for proper S-phase dynamics, as part of its well-established role in repressing neuronal genes until terminal differentiation. DOI:http://dx.doi.org/10.7554/eLife.09584.001 In the brain, cells called neurons connect to each other to form complex networks through which information is rapidly processed. These cells start to form in the developing brains of animal embryos when “neural” stem cells divide in a process called neurogenesis. For this process to proceed normally, particular genes in the stem cells have to be switched on or off at different times. This ensures that the protein products of the genes are only made when they are needed. Proteins called transcription factors can bind to DNA to activate or inactivate particular genes; for example, a transcription factor called REST inactivates thousands of genes that are needed by neurons. During neurogenesis, the production of REST normally declines, and some studies have shown that if the production of this protein is artificially increased, the formation of neurons is delayed. However, other studies suggest that REST may not play a major role in neurogenesis. Here, Nechiporuk et al. re-examine the role of REST in mice. The experiments used genetically modified mice in which the gene that encodes REST was prematurely switched off in neural stem cells. Compared with normal mice, these mutant mice had much smaller brains that contained fewer neurons because the stem cells stopped dividing earlier than normal. Unexpectedly, many genes that are normally switched off by REST, were not significantly changed, while genes that are not normally regulated by REST – such as the gene that encodes a protein called p53 – were active. It is known from previous work that p53 is expressed when cells are exposed to harmful conditions that can damage DNA. This helps to prevent cells from becoming cancerous. Nechiporuk et al. found that cells that lacked REST had higher levels of DNA damage than normal cells due to errors during the process of copying DNA before a cell divides. Furthermore, when both REST and p53 were absent, the neural stem cells became cancerous and formed tumors in the mice. Nechiporuk et al.’s findings suggest that REST protects the DNA of genes that are needed for neurons to form and work properly. The new challenge is to understand where in the genome the damage is occurring. DOI:http://dx.doi.org/10.7554/eLife.09584.002
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Affiliation(s)
- Tamilla Nechiporuk
- Vollum Institute, Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
| | - James McGann
- Vollum Institute, Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
| | - Karin Mullendorff
- Vollum Institute, Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
| | - Jenny Hsieh
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Technische Universität München, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Floss
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gail Mandel
- Vollum Institute, Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
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23
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Abstract
Since the discovery of the existence of superassemblies between mitochondrial respiratory complexes, such superassemblies have been the object of a passionate debate. It is accepted that respiratory supercomplexes are structures that occur in vivo, although which superstructures are naturally occurring and what could be their functional role remain open questions. The main difficulty is to make compatible the existence of superassemblies with the corpus of data that drove the field to abandon the early understanding of the physical arrangement of the mitochondrial respiratory chain as a compact physical entity (the solid model). This review provides a nonexhaustive overview of the evolution of our understanding of the structural organization of the electron transport chain from the original idea of a compact organization to a view of freely moving complexes connected by electron carriers. Today supercomplexes are viewed not as a revival of the old solid model but rather as a refined revision of the fluid model, which incorporates a new layer of structural and functional complexity.
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Affiliation(s)
- José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain;
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24
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Cardiac metabolic pathways affected in the mouse model of barth syndrome. PLoS One 2015; 10:e0128561. [PMID: 26030409 PMCID: PMC4451073 DOI: 10.1371/journal.pone.0128561] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/31/2022] Open
Abstract
Cardiolipin (CL) is a mitochondrial phospholipid essential for electron transport chain (ETC) integrity. CL-deficiency in humans is caused by mutations in the tafazzin (Taz) gene and results in a multisystem pediatric disorder, Barth syndrome (BTHS). It has been reported that tafazzin deficiency destabilizes mitochondrial respiratory chain complexes and affects supercomplex assembly. The aim of this study was to investigate the impact of Taz-knockdown on the mitochondrial proteomic landscape and metabolic processes, such as stability of respiratory chain supercomplexes and their interactions with fatty acid oxidation enzymes in cardiac muscle. Proteomic analysis demonstrated reduction of several polypeptides of the mitochondrial respiratory chain, including Rieske and cytochrome c1 subunits of complex III, NADH dehydrogenase alpha subunit 5 of complex I and the catalytic core-forming subunit of F0F1-ATP synthase. Taz gene knockdown resulted in upregulation of enzymes of folate and amino acid metabolic pathways in heart mitochondria, demonstrating that Taz-deficiency causes substantive metabolic remodeling in cardiac muscle. Mitochondrial respiratory chain supercomplexes are destabilized in CL-depleted mitochondria from Taz knockdown hearts resulting in disruption of the interactions between ETC and the fatty acid oxidation enzymes, very long-chain acyl-CoA dehydrogenase and long-chain 3-hydroxyacyl-CoA dehydrogenase, potentially affecting the metabolic channeling of reducing equivalents between these two metabolic pathways. Mitochondria-bound myoglobin was significantly reduced in Taz-knockdown hearts, potentially disrupting intracellular oxygen delivery to the oxidative phosphorylation system. Our results identify the critical pathways affected by the Taz-deficiency in mitochondria and establish a future framework for development of therapeutic options for BTHS.
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25
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Modulation of mitochondrial complex I activity averts cognitive decline in multiple animal models of familial Alzheimer's Disease. EBioMedicine 2015; 2:294-305. [PMID: 26086035 PMCID: PMC4465115 DOI: 10.1016/j.ebiom.2015.03.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Development of therapeutic strategies to prevent Alzheimer's Disease (AD) is of great importance. We show that mild inhibition of mitochondrial complex I with small molecule CP2 reduces levels of amyloid beta and phospho-Tau and averts cognitive decline in three animal models of familial AD. Low-mass molecular dynamics simulations and biochemical studies confirmed that CP2 competes with flavin mononucleotide for binding to the redox center of complex I leading to elevated AMP/ATP ratio and activation of AMP-activated protein kinase in neurons and mouse brain without inducing oxidative damage or inflammation. Furthermore, modulation of complex I activity augmented mitochondrial bioenergetics increasing coupling efficiency of respiratory chain and neuronal resistance to stress. Concomitant reduction of glycogen synthase kinase 3β activity and restoration of axonal trafficking resulted in elevated levels of neurotrophic factors and synaptic proteins in adult AD mice. Our results suggest metabolic reprogramming induced by modulation of mitochondrial complex I activity represents promising therapeutic strategy for AD.
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26
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Torraco A, Peralta S, Iommarini L, Diaz F. Mitochondrial Diseases Part I: mouse models of OXPHOS deficiencies caused by defects in respiratory complex subunits or assembly factors. Mitochondrion 2015; 21:76-91. [PMID: 25660179 DOI: 10.1016/j.mito.2015.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/22/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
Abstract
Mitochondrial disorders are the most common inborn errors of metabolism affecting the oxidative phosphorylation system (OXPHOS). Because of the poor knowledge of the pathogenic mechanisms, a cure for these disorders is still unavailable and all the treatments currently in use are supportive more than curative. Therefore, in the past decade a great variety of mouse models have been developed to assess the in vivo function of several mitochondrial proteins involved in human diseases. Due to the genetic and physiological similarity to humans, mice represent reliable models to study the pathogenic mechanisms of mitochondrial disorders and are precious to test new therapeutic approaches. Here we summarize the features of several mouse models of mitochondrial diseases directly related to defects in subunits of the OXPHOS complexes or in assembly factors. We discuss how these models recapitulate many human conditions and how they have contributed to the understanding of mitochondrial function in health and disease.
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Affiliation(s)
- Alessandra Torraco
- Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Viale di San Paolo, 15-00146 Rome, Italy.
| | - Susana Peralta
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - Francisca Diaz
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
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27
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Moderate hypoxia induces β-cell dysfunction with HIF-1-independent gene expression changes. PLoS One 2014; 9:e114868. [PMID: 25503986 PMCID: PMC4264765 DOI: 10.1371/journal.pone.0114868] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/14/2014] [Indexed: 01/09/2023] Open
Abstract
Pancreatic β-cell failure is central to the development and progression of type 2 diabetes. We recently demonstrated that β-cells become hypoxic under high glucose conditions due to increased oxygen consumption and that the pancreatic islets of diabetic mice but not those of control mice are moderately hypoxic. However, the impact of moderate hypoxia on β-cell number and function is unknown. In the present study, moderate hypoxia induced a hypoxic response in MIN6 cells, as evidenced by increased levels of HIF-1α protein and target genes. Under these conditions, a selective downregulation of Mafa, Pdx1, Slc2a2, Ndufa5, Kcnj11, Ins1, Wfs1, Foxa2, and Neurod1, which play important roles in β-cells, was also observed in both MIN6 cells and isolated pancreatic islets. Consistent with the altered expression of these genes, abnormal insulin secretion was detected in hypoxic MIN6 cells. Most of the hypoxia-induced gene downregulation in MIN6 cells was not affected by the suppression of HIF-1α, suggesting a HIF-1–independent mechanism. Moderate hypoxia also induced apoptosis in MIN6 cells. These results suggest that hypoxia is a novel stressor of β-cells and that hypoxic stress may play a role in the deterioration of β-cell function.
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28
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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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