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Wu J, Feng S, Luo Y, Ning Y, Qiu P, Lin Y, Ma F, Zhuo Y. Transcriptomic profile of premature ovarian insufficiency with RNA-sequencing. Front Cell Dev Biol 2024; 12:1370772. [PMID: 38655066 PMCID: PMC11035783 DOI: 10.3389/fcell.2024.1370772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction This study aimed to explore the transcriptomic profile of premature ovarian insufficiency (POI) by investigating alterations in gene expression. Methods A total of sixty-one women, comprising 31 individuals with POI in the POI group and 30 healthy women in the control group (HC group), aged between 24 and 40 years, were recruited for this study. The transcriptomic profiles of peripheral blood samples from all study subjects were analyzed using RNA-sequencing. Results The results revealed 39 differentially expressed genes in individuals with POI compared to healthy controls, with 10 upregulated and 29 downregulated genes. Correlation analysis highlighted the relationship between the expression of SLC25A39, CNIH3, and PDZK1IP1 and hormone levels. Additionally, an effective classification model was developed using SLC25A39, CNIH3, PDZK1IP1, SHISA4, and LOC389834. Functional enrichment analysis demonstrated the involvement of these differentially expressed genes in the "haptoglobin-hemoglobin complex," while KEGG pathway analysis indicated their participation in the "Proteoglycans in cancer" pathway. Conclusion The identified genes could play a crucial role in characterizing the genetic foundation of POI, potentially serving as valuable biomarkers for enhancing disease classification accuracy.
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Affiliation(s)
- Jiaman Wu
- Department of Chinese Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shiyu Feng
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan Ning
- Department of Chinese Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Pingping Qiu
- Department of Chinese Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yanting Lin
- Department of Chinese Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Fei Ma
- Department of Chinese Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuanyuan Zhuo
- Department of Acupuncture and Moxibustion, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
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2
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Kudo N, Kouno R, Shibayama Y. SLC25A40 Facilitates Anticancer Drug Resistance in Human Leukemia K562 Cells. Biol Pharm Bull 2023; 46:1304-1309. [PMID: 37407483 DOI: 10.1248/bpb.b23-00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The chronic myelogenous leukemia cell line, K562/ADM is derived from the K562 cell line, which is resistant to doxorubicin (alias, adriamycin: ADM). P-glycoprotein levels are significantly higher in K562/ADM cells than in K562 cells. The overexpression of p-glycoprotein has been shown to cause drug resistance. Therefore, the present study investigated a novel mechanism underlying the drug resistance of K562/ADM cells. A gene ontology analysis demonstrated that the expression of solute carrier (SLC)-mediated transmembrane transport genes was significantly higher in K562/ADM cells than in K562 cells. The expression level of a member of the SLC family, SLC25A40 was higher in K562/ADM cells than in K562 cells. SLC25A40 is located near the ABCB1 gene. A real-time PCR analysis showed that the expression of SLC25A40, ABCB4, and ADAM22 was up-regulated. These genes are located close to SLC25A40. The down-regulation of SLC25A40 significantly decreased the mitochondrial concentration of glutathione and cell proliferation. Collectively, the present results demonstrated that the expression of SLC25A40 was up-regulated in K562/ADM cells, which enhanced to cell proliferation, and that the expression of SLC25A40 affected drug resistance to ADM.
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Affiliation(s)
- Nodoka Kudo
- Department of Drug Formulation, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido
| | - Rikuma Kouno
- Department of Drug Formulation, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido
| | - Yoshihiko Shibayama
- Department of Drug Formulation, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido
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3
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Yang J, Wu X, Song Y. Recent advances in novel mutation genes of Parkinson's disease. J Neurol 2023:10.1007/s00415-023-11781-4. [PMID: 37222843 DOI: 10.1007/s00415-023-11781-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/25/2023]
Abstract
With increasing life expectancy, a growing number of individuals are being affected by Parkinson's Disease (PD), a Neurodegenerative Disease (ND). Approximately, 5-10% of PD is explained by genetic causes linked to known PD genes. With improvements in genetic testing and high-throughput technologies, more PD-associated susceptibility genes have been reported in recent years. However, a comprehensive review of the pathogenic mechanisms and physiological roles of these genes is still lacking. This article reviews novel genes with putative or confirmed pathogenic mutations in PD reported since 2019, summarizes the physiological functions and potential associations with PD. Newly reported PD-related genes include ANK2, DNAH1, STAB1, NOTCH2NLC, UQCRC1, ATP10B, TFG, CHMP1A, GIPC1, KIF21B, KIF24, SLC25A39, SPTBN1 and TOMM22. However, the evidence for pathogenic effects of many of these genes is inconclusive. A variety of novel PD-associated genes have been identified through clinical cases of PD patients and analysis of Genome-Wide Association Studies (GWAS). However, more evidence is needed in confirm the strong association of novel genes with disease.
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Affiliation(s)
- Jie Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, 130062, China
| | - Xinyu Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, 130062, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, 130062, China.
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4
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Ehlers JS, Bracke K, von Bohlen Und Halbach V, Siegerist F, Endlich N, von Bohlen Und Halbach O. Morphological and behavioral analysis of Slc35f1-deficient mice revealed no neurodevelopmental phenotype. Brain Struct Funct 2023; 228:895-906. [PMID: 36951990 PMCID: PMC10147817 DOI: 10.1007/s00429-023-02629-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023]
Abstract
SLC35F1 is a member of the sugar-like carrier (SLC) superfamily that is expressed in the mammalian brain. Malfunction of SLC35F1 in humans is associated with neurodevelopmental disorders. To get insight into the possible roles of Slc35f1 in the brain, we generated Slc35f1-deficient mice. The Slc35f1-deficient mice are viable and survive into adulthood, which allowed examining adult Slc35f1-deficient mice on the anatomical as well as behavioral level. In humans, mutation in the SLC35F1 gene can induce a Rett syndrome-like phenotype accompanied by intellectual disability (Fede et al. Am J Med Genet A 185:2238-2240, 2021). The Slc35f1-deficient mice, however, display only a very mild phenotype and no obvious deficits in learning and memory as, e.g., monitored with the novel object recognition test or the Morris water maze test. Moreover, neuroanatomical parameters of neuronal plasticity (as dendritic spines and adult hippocampal neurogenesis) are also unaltered. Thus, Slc35f1-deficient mice display no major alterations that resemble a neurodevelopmental phenotype.
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Affiliation(s)
- Julia Sophie Ehlers
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany
| | - Katharina Bracke
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany
| | - Viola von Bohlen Und Halbach
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany
| | - Florian Siegerist
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany
| | - Nicole Endlich
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany
| | - Oliver von Bohlen Und Halbach
- Institute for Anatomy and Cell Biology, Universitätsmedizin Greifswald, Friedrich Loeffler Str. 23C, 17487, Greifswald, Germany.
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5
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Praschberger R, Kuenen S, Schoovaerts N, Kaempf N, Singh J, Janssens J, Swerts J, Nachman E, Calatayud C, Aerts S, Poovathingal S, Verstreken P. Neuronal identity defines α-synuclein and tau toxicity. Neuron 2023; 111:1577-1590.e11. [PMID: 36948206 DOI: 10.1016/j.neuron.2023.02.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
Pathogenic α-synuclein and tau are critical drivers of neurodegeneration, and their mutations cause neuronal loss in patients. Whether the underlying preferential neuronal vulnerability is a cell-type-intrinsic property or a consequence of increased expression levels remains elusive. Here, we explore cell-type-specific α-synuclein and tau expression in human brain datasets and use deep phenotyping as well as brain-wide single-cell RNA sequencing of >200 live neuron types in fruit flies to determine which cellular environments react most to α-synuclein or tau toxicity. We detect phenotypic and transcriptomic evidence of differential neuronal vulnerability independent of α-synuclein or tau expression levels. Comparing vulnerable with resilient neurons in Drosophila enabled us to predict numerous human neuron subtypes with increased intrinsic susceptibility to pathogenic α-synuclein or tau. By uncovering synapse- and Ca2+ homeostasis-related genes as tau toxicity modifiers, our work paves the way to leverage neuronal identity to uncover modifiers of neurodegeneration-associated toxic proteins.
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Affiliation(s)
- Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| | - Sabine Kuenen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Natalie Kaempf
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Jeevanjot Singh
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Jasper Janssens
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Human Genetics, 3000 Leuven, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Eliana Nachman
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Carles Calatayud
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Human Genetics, 3000 Leuven, Belgium
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
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6
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Bademosi AT, Decet M, Kuenen S, Calatayud C, Swerts J, Gallego SF, Schoovaerts N, Karamanou S, Louros N, Martin E, Sibarita JB, Vints K, Gounko NV, Meunier FA, Economou A, Versées W, Rousseau F, Schymkowitz J, Soukup SF, Verstreken P. EndophilinA-dependent coupling between activity-induced calcium influx and synaptic autophagy is disrupted by a Parkinson-risk mutation. Neuron 2023; 111:1402-1422.e13. [PMID: 36827984 PMCID: PMC10166451 DOI: 10.1016/j.neuron.2023.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/09/2022] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Neuronal activity causes use-dependent decline in protein function. However, it is unclear how this is coupled to local quality control mechanisms. We show in Drosophila that the endocytic protein Endophilin-A (EndoA) connects activity-induced calcium influx to synaptic autophagy and neuronal survival in a Parkinson disease-relevant fashion. Mutations in the disordered loop, including a Parkinson disease-risk mutation, render EndoA insensitive to neuronal stimulation and affect protein dynamics: when EndoA is more flexible, its mobility in membrane nanodomains increases, making it available for autophagosome formation. Conversely, when EndoA is more rigid, its mobility reduces, blocking stimulation-induced autophagy. Balanced stimulation-induced autophagy is required for dopagminergic neuron survival, and a variant in the human ENDOA1 disordered loop conferring risk to Parkinson disease also blocks nanodomain protein mobility and autophagy both in vivo and in human-induced dopaminergic neurons. Thus, we reveal a mechanism that neurons use to connect neuronal activity to local autophagy and that is critical for neuronal survival.
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Affiliation(s)
- Adekunle T Bademosi
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia
| | - Marianna Decet
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Sabine Kuenen
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Carles Calatayud
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Sandra F Gallego
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Nikolaos Louros
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Ella Martin
- VIB-VUB Center for Structural Biology, Brussels 1050, Belgium; Department of Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, F-33000 Bordeaux, France
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; VIB Bio Core, KU Leuven, Leuven 3000, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; VIB Bio Core, KU Leuven, Leuven 3000, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Brussels 1050, Belgium; Department of Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium.
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7
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Jacquemyn J, Kuenen S, Swerts J, Pavie B, Vijayan V, Kilic A, Chabot D, Wang YC, Schoovaerts N, Corthout N, Verstreken P. Parkinsonism mutations in DNAJC6 cause lipid defects and neurodegeneration that are rescued by Synj1. NPJ Parkinsons Dis 2023; 9:19. [PMID: 36739293 PMCID: PMC9899244 DOI: 10.1038/s41531-023-00459-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
Recent evidence links dysfunctional lipid metabolism to the pathogenesis of Parkinson's disease, but the mechanisms are not resolved. Here, we generated a new Drosophila knock-in model of DNAJC6/Auxilin and find that the pathogenic mutation causes synaptic dysfunction, neurological defects and neurodegeneration, as well as specific lipid metabolism alterations. In these mutants, membrane lipids containing long-chain polyunsaturated fatty acids, including phosphatidylinositol lipid species that are key for synaptic vesicle recycling and organelle function, are reduced. Overexpression of another protein mutated in Parkinson's disease, Synaptojanin-1, known to bind and metabolize specific phosphoinositides, rescues the DNAJC6/Auxilin lipid alterations, the neuronal function defects and neurodegeneration. Our work reveals a functional relation between two proteins mutated in Parkinsonism and implicates deregulated phosphoinositide metabolism in the maintenance of neuronal integrity and neuronal survival.
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Affiliation(s)
- Julie Jacquemyn
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium ,grid.17089.370000 0001 2190 316XPresent Address: Neuroscience and Mental Health Institute, University of Alberta, Department of Physiology, Department of Cell Biology, Group on Molecular and Cell Biology of Lipids, Edmonton, Alberta Canada
| | - Sabine Kuenen
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Jef Swerts
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Benjamin Pavie
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium ,VIB-Bioimaging Core, 3000 Leuven, Belgium
| | - Vinoy Vijayan
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Ayse Kilic
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Dries Chabot
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Yu-Chun Wang
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium ,grid.11486.3a0000000104788040Present Address: VIB Technology Watch, Technology Innovation Laboratory, VIB, Gent, Belgium
| | - Nils Schoovaerts
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
| | - Nikky Corthout
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium ,VIB-Bioimaging Core, 3000 Leuven, Belgium
| | - Patrik Verstreken
- grid.511015.1VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000 Leuven, Belgium
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8
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Lepiarczyk E, Paukszto Ł, Wiszpolska M, Łopieńska-Biernat E, Bossowska A, Majewski MK, Majewska M. Molecular Influence of Resiniferatoxin on the Urinary Bladder Wall Based on Differential Gene Expression Profiling. Cells 2023; 12:cells12030462. [PMID: 36766804 PMCID: PMC9914288 DOI: 10.3390/cells12030462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Resiniferatoxin (RTX) is a potent capsaicin analog used as a drug for experimental therapy to treat neurogenic disorders associated with enhanced nociceptive transmission, including lower urinary tract symptoms. The present study, for the first time, investigated the transcriptomic profile of control and RTX-treated porcine urinary bladder walls. We applied multistep bioinformatics and discovered 129 differentially expressed genes (DEGs): 54 upregulated and 75 downregulated. Metabolic pathways analysis revealed five significant Kyoto Encyclopedia of Genes and Genomes (KEGG) items ('folate biosynthesis', 'metabolic pathways', 'sulfur relay system', 'sulfur metabolism' and 'serotonergic synapse') that were altered after RTX intravesical administration. A thorough analysis of the detected DEGs indicated that RTX treatment influenced the signaling pathways regulating nerve growth, myelination, axon specification, and elongation. Many of the revealed DEGs are involved in the nerve degeneration process; however, some of them were implicated in the initiation of neuroprotective mechanisms. Interestingly, RTX intravesical installation was followed by changes in the expression of genes involved in synaptic plasticity and neuromodulation, including 5-HT, H2S, glutamate, and GABA transmission. The obtained results suggest that the toxin may exert a therapeutic, antinociceptive effect not only by acting on TRPV1 receptors.
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Affiliation(s)
- Ewa Lepiarczyk
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
- Correspondence: ; Tel.: +48-89-524-53-34; Fax: +48-89-524-53-07
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland
| | - Marta Wiszpolska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
| | - Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Agnieszka Bossowska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
| | - Mariusz Krzysztof Majewski
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
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Bar-Peled L, Kory N. Principles and functions of metabolic compartmentalization. Nat Metab 2022; 4:1232-1244. [PMID: 36266543 PMCID: PMC10155461 DOI: 10.1038/s42255-022-00645-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/24/2022] [Indexed: 01/20/2023]
Abstract
Metabolism has historically been studied at the levels of whole cells, whole tissues and whole organisms. As a result, our understanding of how compartmentalization-the spatial and temporal separation of pathways and components-shapes organismal metabolism remains limited. At its essence, metabolic compartmentalization fulfils three important functions or 'pillars': establishing unique chemical environments, providing protection from reactive metabolites and enabling the regulation of metabolic pathways. However, how these pillars are established, regulated and maintained at both the cellular and systemic levels remains unclear. Here we discuss how the three pillars are established, maintained and regulated within the cell and discuss the consequences of dysregulation of metabolic compartmentalization in human disease. Organelles are increasingly emerging as 'command-and-control centres' and the increased understanding of metabolic compartmentalization is revealing new aspects of metabolic homeostasis, with this knowledge being translated into therapies for the treatment of cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Nora Kory
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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10
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Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nat Commun 2022; 13:2483. [PMID: 35513392 PMCID: PMC9072411 DOI: 10.1038/s41467-022-30126-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2022] [Indexed: 12/18/2022] Open
Abstract
The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors across mitochondrial membranes. The family is highly redundant and their transport activities coupled to metabolic state. Here, we use a pooled, dual CRISPR screening strategy that knocks out pairs of transporters in four metabolic states - glucose, galactose, OXPHOS inhibition, and absence of pyruvate - designed to unmask the inter-dependence of these genes. In total, we screen 63 genes in four metabolic states, corresponding to 2016 single and pair-wise genetic perturbations. We recover 19 gene-by-environment (GxE) interactions and 9 gene-by-gene (GxG) interactions. One GxE interaction hit illustrates that the fitness defect in the mitochondrial folate carrier (SLC25A32) KO cells is genetically buffered in galactose due to a lack of substrate in de novo purine biosynthesis. GxG analysis highlights a buffering interaction between the iron transporter SLC25A37 (A37) and the poorly characterized SLC25A39 (A39). Mitochondrial metabolite profiling, organelle transport assays, and structure-guided mutagenesis identify A39 as critical for mitochondrial glutathione (GSH) import. Functional studies reveal that A39-mediated glutathione homeostasis and A37-mediated mitochondrial iron uptake operate jointly to support mitochondrial OXPHOS. Our work underscores the value of studying family-wide genetic interactions across different metabolic environments.
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Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hardik Shah
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Katie Byrne
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Luanna Summer
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA.
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
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11
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von Bohlen Und Halbach O. Controlling glutathione entry into mitochondria: potential roles for SLC25A39 in health and (treatment of) disease. Signal Transduct Target Ther 2022; 7:75. [PMID: 35264552 PMCID: PMC8907158 DOI: 10.1038/s41392-022-00928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
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12
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Ceder MM, Fredriksson R. A phylogenetic analysis between humans and D. melanogaster: A repertoire of solute carriers in humans and flies. Gene 2022; 809:146033. [PMID: 34673204 DOI: 10.1016/j.gene.2021.146033] [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: 04/06/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/04/2022]
Abstract
The solute carrier (SLC) superfamily is the largest group of transporters in humans, with the role to transport solutes across plasma membranes. The SLCs are currently divided into 65 families with 430 members. Here, we performed a detailed mining of the SLC superfamily and the recent annotated family of "atypical" SLCs in human and D. melanogaster using Hidden Markov Models and PSI-BLAST. Our analyses identified 381 protein sequences in D. melanogaster and of those, 55 proteins have not been previously identified in flies. In total, 11 of the 65 human SLC families were found to not be conserved in flies, while a few families are highly conserved, which perhaps reflects the families' functions and roles in cellular pathways. This study provides the first collection of all SLC sequences in D. melanogaster and can serve as a SLC database to be used for classification of SLCs in other phyla.
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Affiliation(s)
- Mikaela M Ceder
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden; Sensory Circuits, Department of Neuroscience, Uppsala University, Uppsala, Sweden, Mikaela.
| | - Robert Fredriksson
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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13
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Wang Y, Yen FS, Zhu XG, Timson RC, Weber R, Xing C, Liu Y, Allwein B, Luo H, Yeh HW, Heissel S, Unlu G, Gamazon ER, Kharas MG, Hite R, Birsoy K. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells. Nature 2021; 599:136-140. [PMID: 34707288 PMCID: PMC10981497 DOI: 10.1038/s41586-021-04025-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/09/2021] [Indexed: 01/20/2023]
Abstract
Glutathione (GSH) is a small-molecule thiol that is abundant in all eukaryotes and has key roles in oxidative metabolism1. Mitochondria, as the major site of oxidative reactions, must maintain sufficient levels of GSH to perform protective and biosynthetic functions2. GSH is synthesized exclusively in the cytosol, yet the molecular machinery involved in mitochondrial GSH import remains unknown. Here, using organellar proteomics and metabolomics approaches, we identify SLC25A39, a mitochondrial membrane carrier of unknown function, as a regulator of GSH transport into mitochondria. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of proteins containing iron-sulfur clusters. We find that mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. Heterologous expression of an engineered bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria enables mitochondrial GSH production and ameliorates the metabolic and proliferative defects caused by its depletion. Finally, GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import in mammalian cells. Our work identifies SLC25A39 as an essential and regulated component of the mitochondrial GSH-import machinery.
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Affiliation(s)
- Ying Wang
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Frederick S Yen
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Xiphias Ge Zhu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Rebecca C Timson
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Ross Weber
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Changrui Xing
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin Allwein
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hsi-Wen Yeh
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Clare Hall and MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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14
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Missirlis F. Regulation and biological function of metal ions in Drosophila. CURRENT OPINION IN INSECT SCIENCE 2021; 47:18-24. [PMID: 33581350 DOI: 10.1016/j.cois.2021.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
A conceptual framework is offered for critically approaching the formidable ability of insects to segregate metal ions to their multiple destinations in proteins and subcellular compartments. New research in Drosophila melanogaster suggests that nuclear iron regulatory proteins and oxidative stress transcription factors mediate metal-responsive gene expression. Identification of a zinc-regulated chaperone in the endoplasmic reticulum potentially explains membrane protein trafficking defects observed in zinc transporter mutants. Compartmentalized zinc is utilized in fertilization, embryogenesis and for the activation of zinc-finger transcription factors - the latter function demonstrated during muscle development, while dietary zinc is sensed through gating of a chloride channel. Another emerging theme in cellular metal homeostasis is that transporters and related proteins meet at endoplasmic reticulum-mitochondria associated membranes with physiologically relevant consequences during aging.
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Affiliation(s)
- Fanis Missirlis
- Department of Physiology, Biophysics & Neuroscience, Cinvestav, Mexico.
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15
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Gialluisi A, Reccia MG, Modugno N, Nutile T, Lombardi A, Di Giovannantonio LG, Pietracupa S, Ruggiero D, Scala S, Gambardella S, Iacoviello L, Gianfrancesco F, Acampora D, D’Esposito M, Simeone A, Ciullo M, Esposito T. Identification of sixteen novel candidate genes for late onset Parkinson's disease. Mol Neurodegener 2021; 16:35. [PMID: 34148545 PMCID: PMC8215754 DOI: 10.1186/s13024-021-00455-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a neurodegenerative movement disorder affecting 1-5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. METHODS The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). RESULTS Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10- 5). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. CONCLUSIONS Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment.
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Affiliation(s)
- Alessandro Gialluisi
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Mafalda Giovanna Reccia
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Nicola Modugno
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Teresa Nutile
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Alessia Lombardi
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Luca Giovanni Di Giovannantonio
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Sara Pietracupa
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Daniela Ruggiero
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Simona Scala
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Stefano Gambardella
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- grid.12711.340000 0001 2369 7670Department of Biomolecular Science, University of Urbino Carlo Bò, Urbino, Italy
| | | | - Licia Iacoviello
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- grid.18147.3b0000000121724807Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Fernando Gianfrancesco
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Dario Acampora
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Maurizio D’Esposito
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Antonio Simeone
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Marina Ciullo
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
| | - Teresa Esposito
- grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- grid.419869.b0000 0004 1758 2860National Research Council, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples, Italy
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16
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Yang JO, Choi MH, Yoon JY, Lee JJ, Nam SO, Jun SY, Kwon HH, Yun S, Jeon SJ, Byeon I, Halder D, Kong J, Lee B, Lee J, Kang JW, Kim NS. Characteristics of Genetic Variations Associated With Lennox-Gastaut Syndrome in Korean Families. Front Genet 2021; 11:590924. [PMID: 33584793 PMCID: PMC7874053 DOI: 10.3389/fgene.2020.590924] [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: 08/03/2020] [Accepted: 12/31/2020] [Indexed: 12/21/2022] Open
Abstract
Lennox-Gastaut syndrome (LGS) is a severe type of childhood-onset epilepsy characterized by multiple types of seizures, specific discharges on electroencephalography, and intellectual disability. Most patients with LGS do not respond well to drug treatment and show poor long-term prognosis. Approximately 30% of patients without brain abnormalities have unidentifiable causes. Therefore, accurate diagnosis and treatment of LGS remain challenging. To identify causative mutations of LGS, we analyzed the whole-exome sequencing data of 17 unrelated Korean families, including patients with LGS and LGS-like epilepsy without brain abnormalities, using the Genome Analysis Toolkit. We identified 14 mutations in 14 genes as causes of LGS or LGS-like epilepsy. 64 percent of the identified genes were reported as LGS or epilepsy-related genes. Many of these variations were novel and considered as pathogenic or likely pathogenic. Network analysis was performed to classify the identified genes into two network clusters: neuronal signal transmission or neuronal development. Additionally, knockdown of two candidate genes with insufficient evidence of neuronal functions, SLC25A39 and TBC1D8, decreased neurite outgrowth and the expression level of MAP2, a neuronal marker. These results expand the spectrum of genetic variations and may aid the diagnosis and management of individuals with LGS.
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Affiliation(s)
- Jin Ok Yang
- Korea BioInformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Min-Hyuk Choi
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, South Korea
| | - Ji-Yong Yoon
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jeong-Ju Lee
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, South Korea
| | - Soo Young Jun
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hyeok Hee Kwon
- Department of Medical Science and Anatomy, Chungnam National University, Daejeon, South Korea
| | - Sohyun Yun
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Su-Jin Jeon
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, South Korea
| | - Iksu Byeon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Debasish Halder
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Juhyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, South Korea
| | - Byungwook Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joon-Won Kang
- Department of Pediatrics and Medical Science, Chungnam National University Hospital, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Nam-Soon Kim
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, South Korea
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17
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Rosenthal EA, Crosslin DR, Gordon AS, Carrell DS, Stanaway IB, Larson EB, Grafton J, Wei WQ, Denny JC, Feng QP, Shah AS, Sturm AC, Ritchie MD, Pacheco JA, Hakonarson H, Rasmussen-Torvik LJ, Connolly JJ, Fan X, Safarova M, Kullo IJ, Jarvik GP. Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort. BMC Med Genomics 2021; 14:11. [PMID: 33407432 PMCID: PMC7789246 DOI: 10.1186/s12920-020-00854-2] [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: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
Background Elevated triglycerides (TG) are associated with, and may be causal for, cardiovascular disease (CVD), and co-morbidities such as type II diabetes and metabolic syndrome. Pathogenic variants in APOA5 and APOC3 as well as risk SNVs in other genes [APOE (rs429358, rs7412), APOA1/C3/A4/A5 gene cluster (rs964184), INSR (rs7248104), CETP (rs7205804), GCKR (rs1260326)] have been shown to affect TG levels. Knowledge of genetic causes for elevated TG may lead to early intervention and targeted treatment for CVD. We previously identified linkage and association of a rare, highly conserved missense variant in SLC25A40, rs762174003, with hypertriglyceridemia (HTG) in a single large family, and replicated this association with rare, highly conserved missense variants in a European American and African American sample. Methods Here, we analyzed a longitudinal mixed-ancestry cohort (European, African and Asian ancestry, N = 8966) from the Electronic Medical Record and Genomics (eMERGE) Network. We tested associations between median TG and the genes of interest, using linear regression, adjusting for sex, median age, median BMI, and the first two principal components of ancestry. Results We replicated the association between TG and APOC3, APOA5, and risk variation at APOE, APOA1/C3/A4/A5 gene cluster, and GCKR. We failed to replicate the association between rare, highly conserved variation at SLC25A40 and TG, as well as for risk variation at INSR and CETP. Conclusions Analysis using data from electronic health records presents challenges that need to be overcome. Although large amounts of genotype data is becoming increasingly accessible, usable phenotype data can be challenging to obtain. We were able to replicate known, strong associations, but were unable to replicate moderate associations due to the limited sample size and missing drug information.
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Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, 1705 NE Pacific St, Box 357720, Seattle, WA, 98195, USA.
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam S Gordon
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jane Grafton
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi-Ping Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy S Shah
- Division of Endocrinology, Department of Pediatrics, Cincinnati Children's Hospital and the University of Cincinnati, Cincinnati, OH, USA
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Fan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Maya Safarova
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.,Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, 1705 NE Pacific St, Box 357720, Seattle, WA, 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
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18
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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19
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Drosophila melanogaster Mitochondrial Carriers: Similarities and Differences with the Human Carriers. Int J Mol Sci 2020; 21:ijms21176052. [PMID: 32842667 PMCID: PMC7504413 DOI: 10.3390/ijms21176052] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial carriers are a family of structurally related proteins responsible for the exchange of metabolites, cofactors and nucleotides between the cytoplasm and mitochondrial matrix. The in silico analysis of the Drosophila melanogaster genome has highlighted the presence of 48 genes encoding putative mitochondrial carriers, but only 20 have been functionally characterized. Despite most Drosophila mitochondrial carrier genes having human homologs and sharing with them 50% or higher sequence identity, D. melanogaster genes display peculiar differences from their human counterparts: (1) in the fruit fly, many genes encode more transcript isoforms or are duplicated, resulting in the presence of numerous subfamilies in the genome; (2) the expression of the energy-producing genes in D. melanogaster is coordinated from a motif known as Nuclear Respiratory Gene (NRG), a palindromic 8-bp sequence; (3) fruit-fly duplicated genes encoding mitochondrial carriers show a testis-biased expression pattern, probably in order to keep a duplicate copy in the genome. Here, we review the main features, biological activities and role in the metabolism of the D. melanogaster mitochondrial carriers characterized to date, highlighting similarities and differences with their human counterparts. Such knowledge is very important for obtaining an integrated view of mitochondrial function in D. melanogaster metabolism.
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20
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Lüthy K, Mei D, Fischer B, De Fusco M, Swerts J, Paesmans J, Parrini E, Lubarr N, Meijer IA, Mackenzie KM, Lee WT, Cittaro D, Aridon P, Schoovaerts N, Versées W, Verstreken P, Casari G, Guerrini R. TBC1D24-TLDc-related epilepsy exercise-induced dystonia: rescue by antioxidants in a disease model. Brain 2020; 142:2319-2335. [PMID: 31257402 DOI: 10.1093/brain/awz175] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/08/2019] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
Genetic mutations in TBC1D24 have been associated with multiple phenotypes, with epilepsy being the main clinical manifestation. The TBC1D24 protein consists of the unique association of a Tre2/Bub2/Cdc16 (TBC) domain and a TBC/lysin motif domain/catalytic (TLDc) domain. More than 50 missense and loss-of-function mutations have been described and are spread over the entire protein. Through whole genome/exome sequencing we identified compound heterozygous mutations, R360H and G501R, within the TLDc domain, in an index family with a Rolandic epilepsy exercise-induced dystonia phenotype (http://omim.org/entry/608105). A 20-year long clinical follow-up revealed that epilepsy was self-limited in all three affected patients, but exercise-induced dystonia persisted into adulthood in two. Furthermore, we identified three additional sporadic paediatric patients with a remarkably similar phenotype, two of whom had compound heterozygous mutations consisting of an in-frame deletion I81_K84 and an A500V mutation, and the third carried T182M and G511R missense mutations, overall revealing that all six patients harbour a missense mutation in the subdomain of TLDc between residues 500 and 511. We solved the crystal structure of the conserved Drosophila TLDc domain. This allowed us to predict destabilizing effects of the G501R and G511R mutations and, to a lesser degree, of R360H and potentially A500V. Next, we characterized the functional consequences of a strong and a weak TLDc mutation (TBC1D24G501R and TBC1D24R360H) using Drosophila, where TBC1D24/Skywalker regulates synaptic vesicle trafficking. In a Drosophila model neuronally expressing human TBC1D24, we demonstrated that the TBC1D24G501R TLDc mutation causes activity-induced locomotion and synaptic vesicle trafficking defects, while TBC1D24R360H is benign. The neuronal phenotypes of the TBC1D24G501R mutation are consistent with exacerbated oxidative stress sensitivity, which is rescued by treating TBC1D24G501R mutant animals with antioxidants N-acetylcysteine amide or α-tocopherol as indicated by restored synaptic vesicle trafficking levels and sustained behavioural activity. Our data thus show that mutations in the TLDc domain of TBC1D24 cause Rolandic-type focal motor epilepsy and exercise-induced dystonia. The humanized TBC1D24G501R fly model exhibits sustained activity and vesicle transport defects. We propose that the TBC1D24/Sky TLDc domain is a reactive oxygen species sensor mediating synaptic vesicle trafficking rates that, when dysfunctional, causes a movement disorder in patients and flies. The TLDc and TBC domain mutations' response to antioxidant treatment we observed in the animal model suggests a potential for combining antioxidant-based therapeutic approaches to TBC1D24-associated disorders with previously described lipid-altering strategies for TBC domain mutations.
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Affiliation(s)
- Kevin Lüthy
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Baptiste Fischer
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Vrije Universiteit Brussel, Structural Biology Brussels, Brussels, Belgium
| | | | - Jef Swerts
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Jone Paesmans
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Vrije Universiteit Brussel, Structural Biology Brussels, Brussels, Belgium
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Naomi Lubarr
- Mount Sinai Beth Israel, Department of Neurology, New York, NY, USA
| | - Inge A Meijer
- Department of Pediatrics and Neurosciences, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | | | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Paolo Aridon
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Vrije Universiteit Brussel, Structural Biology Brussels, Brussels, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Giorgio Casari
- San Raffaele University, Milan, Italy.,Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy.,IRCCS Fondazione Stella Maris, Pisa, Italy
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21
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Cunningham CN, Rutter J. 20,000 picometers under the OMM: diving into the vastness of mitochondrial metabolite transport. EMBO Rep 2020; 21:e50071. [PMID: 32329174 DOI: 10.15252/embr.202050071] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
The metabolic compartmentalization enabled by mitochondria is key feature of many cellular processes such as energy conversion to ATP production, redox balance, and the biosynthesis of heme, urea, nucleotides, lipids, and others. For a majority of these functions, metabolites need to be transported across the impermeable inner mitochondrial membrane by dedicated carrier proteins. Here, we examine the substrates, structural features, and human health implications of four mitochondrial metabolite carrier families: the SLC25A family, the mitochondrial ABCB transporters, the mitochondrial pyruvate carrier (MPC), and the sideroflexin proteins.
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Affiliation(s)
- Corey N Cunningham
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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22
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Vásquez-Procopio J, Osorio B, Cortés-Martínez L, Hernández-Hernández F, Medina-Contreras O, Ríos-Castro E, Comjean A, Li F, Hu Y, Mohr S, Perrimon N, Missirlis F. Intestinal response to dietary manganese depletion inDrosophila. Metallomics 2020; 12:218-240. [DOI: 10.1039/c9mt00218a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metabolic adaptations to manganese deficiency.
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23
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Ugur B, Bao H, Stawarski M, Duraine LR, Zuo Z, Lin YQ, Neely GG, Macleod GT, Chapman ER, Bellen HJ. The Krebs Cycle Enzyme Isocitrate Dehydrogenase 3A Couples Mitochondrial Metabolism to Synaptic Transmission. Cell Rep 2019; 21:3794-3806. [PMID: 29281828 DOI: 10.1016/j.celrep.2017.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022] Open
Abstract
Neurotransmission is a tightly regulated Ca2+-dependent process. Upon Ca2+ influx, Synaptotagmin1 (Syt1) promotes fusion of synaptic vesicles (SVs) with the plasma membrane. This requires regulation at multiple levels, but the role of metabolites in SV release is unclear. Here, we uncover a role for isocitrate dehydrogenase 3a (idh3a), a Krebs cycle enzyme, in neurotransmission. Loss of idh3a leads to a reduction of the metabolite, alpha-ketoglutarate (αKG), causing defects in synaptic transmission similar to the loss of syt1. Supplementing idh3a flies with αKG suppresses these defects through an ATP or neurotransmitter-independent mechanism. Indeed, αKG, but not glutamate, enhances Syt1-dependent fusion in a reconstitution assay. αKG promotes interaction between the C2-domains of Syt1 and phospholipids. The data reveal conserved metabolic regulation of synaptic transmission via αKG. Our studies provide a synaptic role for αKG, a metabolite that has been proposed as a treatment for aging and neurodegenerative disorders.
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Affiliation(s)
- Berrak Ugur
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Huan Bao
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA; Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53705, USA
| | - Michal Stawarski
- Department of Biological Sciences and Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Lita R Duraine
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Qi Lin
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - G Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory T Macleod
- Department of Biological Sciences and Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Edwin R Chapman
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA; Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53705, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
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24
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Abstract
Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait. Because stringent genome-wide significance thresholds are applied to control the false positive rate, many true causal variants can remain undetected. To ameliorate this problem, many alternative approaches have been developed, such as genomic feature models (GFM). The GFM approach tests for association of set of genomic markers, and predicts genomic values from genomic data utilizing prior biological knowledge. We investigated to what degree the findings from GFM have biological relevance. We used the Drosophila Genetic Reference Panel to investigate locomotor activity, and applied genomic feature prediction models to identify gene ontology (GO) categories predictive of this phenotype. Next, we applied the covariance association test to partition the genomic variance of the predictive GO terms to the genes within these terms. We then functionally assessed whether the identified candidate genes affected locomotor activity by reducing gene expression using RNA interference. In five of the seven candidate genes tested, reduced gene expression altered the phenotype. The ranking of genes within the predictive GO term was highly correlated with the magnitude of the phenotypic consequence of gene knockdown. This study provides evidence for five new candidate genes for locomotor activity, and provides support for the reliability of the GFM approach.
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25
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Vanhauwaert R, Kuenen S, Masius R, Bademosi A, Manetsberger J, Schoovaerts N, Bounti L, Gontcharenko S, Swerts J, Vilain S, Picillo M, Barone P, Munshi ST, de Vrij FM, Kushner SA, Gounko NV, Mandemakers W, Bonifati V, Meunier FA, Soukup SF, Verstreken P. The SAC1 domain in synaptojanin is required for autophagosome maturation at presynaptic terminals. EMBO J 2017; 36:1392-1411. [PMID: 28331029 DOI: 10.15252/embj.201695773] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/25/2017] [Accepted: 03/01/2017] [Indexed: 11/09/2022] Open
Abstract
Presynaptic terminals are metabolically active and accrue damage through continuous vesicle cycling. How synapses locally regulate protein homeostasis is poorly understood. We show that the presynaptic lipid phosphatase synaptojanin is required for macroautophagy, and this role is inhibited by the Parkinson's disease mutation R258Q. Synaptojanin drives synaptic endocytosis by dephosphorylating PI(4,5)P2, but this function appears normal in SynaptojaninRQ knock-in flies. Instead, R258Q affects the synaptojanin SAC1 domain that dephosphorylates PI(3)P and PI(3,5)P2, two lipids found in autophagosomal membranes. Using advanced imaging, we show that SynaptojaninRQ mutants accumulate the PI(3)P/PI(3,5)P2-binding protein Atg18a on nascent synaptic autophagosomes, blocking autophagosome maturation at fly synapses and in neurites of human patient induced pluripotent stem cell-derived neurons. Additionally, we observe neurodegeneration, including dopaminergic neuron loss, in SynaptojaninRQ flies. Thus, synaptojanin is essential for macroautophagy within presynaptic terminals, coupling protein turnover with synaptic vesicle cycling and linking presynaptic-specific autophagy defects to Parkinson's disease.
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Affiliation(s)
- Roeland Vanhauwaert
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Sabine Kuenen
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Roy Masius
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Adekunle Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Julia Manetsberger
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Nils Schoovaerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Laura Bounti
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Serguei Gontcharenko
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Jef Swerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Sven Vilain
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Marina Picillo
- Department of Medicine and Surgery, Center for Neurodegenerative Diseases (CEMAND), University of Salerno, Salerno, Italy
| | - Paolo Barone
- Department of Medicine and Surgery, Center for Neurodegenerative Diseases (CEMAND), University of Salerno, Salerno, Italy
| | | | - Femke Ms de Vrij
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Natalia V Gounko
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium.,Electron Microscopy Platform, VIB Bio-Imaging Core, Leuven, Belgium
| | - Wim Mandemakers
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Frederic A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Sandra-Fausia Soukup
- VIB Center for Brain & Disease Research, Leuven, Belgium .,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, Leuven, Belgium .,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
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26
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Dejonghe W, Kuenen S, Mylle E, Vasileva M, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz-Morea FA, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen LSL, Drozdzecki A, Van Houtte I, Szatmári AM, Majda M, Baisa G, Bednarek SY, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nat Commun 2016; 7:11710. [PMID: 27271794 PMCID: PMC4899852 DOI: 10.1038/ncomms11710] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 04/21/2016] [Indexed: 11/27/2022] Open
Abstract
ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane. Plant cells maintain strict proton gradients over different membranes. Here, Dejonghe et al. show that several protonophores, including the known tyrosine kinase inhibitor TyrphostinA23, inhibit clathrin-mediated endocytosis by disturbing these gradients and causing cytoplasmic acidification.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Sabine Kuenen
- VIB Center for the Biology of Disease, Laboratory of Neuronal Communication, 3000 Leuven, Belgium.,Department for Human Genetics, and Leuven Institute for Neurodegenerative Diseases, KU Leuven, 3000 Leuven, Belgium
| | - Evelien Mylle
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Mina Vasileva
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Corrado Viotti
- Department of Plant Physiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Jef Swerts
- VIB Center for the Biology of Disease, Laboratory of Neuronal Communication, 3000 Leuven, Belgium.,Department for Human Genetics, and Leuven Institute for Neurodegenerative Diseases, KU Leuven, 3000 Leuven, Belgium
| | - Matyáš Fendrych
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Fausto Andres Ortiz-Morea
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Kiril Mishev
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Simon Delang
- Developmental Biology of Plants, Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Scholl
- Developmental Biology of Plants, Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Xavier Zarza
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Mareike Heilmann
- Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University, 06120 Halle, Germany
| | - Jiorgos Kourelis
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Jaroslaw Kasprowicz
- VIB Center for the Biology of Disease, Laboratory of Neuronal Communication, 3000 Leuven, Belgium.,Department for Human Genetics, and Leuven Institute for Neurodegenerative Diseases, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Isabelle Van Houtte
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Anna-Mária Szatmári
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Mateusz Majda
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Gary Baisa
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Stéphanie Robert
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | | | - Christa Testerink
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Teun Munnik
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Daniël Van Damme
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Ingo Heilmann
- Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University, 06120 Halle, Germany
| | - Karin Schumacher
- Developmental Biology of Plants, Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Johan Winne
- Laboratory for Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Gent, Belgium
| | - Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Patrik Verstreken
- VIB Center for the Biology of Disease, Laboratory of Neuronal Communication, 3000 Leuven, Belgium.,Department for Human Genetics, and Leuven Institute for Neurodegenerative Diseases, KU Leuven, 3000 Leuven, Belgium
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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