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Salemi M, Ravo M, Lanza G, Schillaci FA, Ventola GM, Marchese G, Salluzzo MG, Cappelletti G, Ferri R. Gene Expression Profiling of Post Mortem Midbrain of Parkinson's Disease Patients and Healthy Controls. Int J Mol Sci 2024; 25:707. [PMID: 38255780 PMCID: PMC10815072 DOI: 10.3390/ijms25020707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Parkinson's disease (PD) stands as the most prevalent degenerative movement disorder, marked by the degeneration of dopaminergic neurons in the substantia nigra of the midbrain. In this study, we conducted a transcriptome analysis utilizing post mortem mRNA extracted from the substantia nigra of both PD patients and healthy control (CTRL) individuals. Specifically, we acquired eight samples from individuals with PD and six samples from CTRL individuals, with no discernible pathology detected in the latter group. RNA sequencing was conducted using the TapeStation 4200 system from Agilent Technologies. A total of 16,148 transcripts were identified, with 92 mRNAs displaying differential expression between the PD and control groups. Specifically, 33 mRNAs were significantly up-regulated, while 59 mRNAs were down-regulated in PD compared to the controls. The identification of statistically significant signaling pathways, with an adjusted p-value threshold of 0.05, unveiled noteworthy insights. Specifically, the enriched categories included cardiac muscle contraction (involving genes such as ATPase Na+/K+ transporting subunit beta 2 (ATP1B2), solute carrier family 8 member A1 (SLC8A1), and cytochrome c oxidase subunit II (COX2)), GABAergic synapse (involving GABA type A receptor-associated protein-like 1 (GABARAPL1), G protein subunit beta 5 (GNB5), and solute carrier family 38 member 2 (SLC38A2), autophagy (involving GABARAPL1 and tumor protein p53-inducible nuclear protein 2 (TP53INP2)), and Fc gamma receptor (FcγR) mediated phagocytosis (involving amphiphysin (AMPH)). These findings uncover new pathophysiological dimensions underlying PD, implicating genes associated with heart muscle contraction. This knowledge enhances diagnostic accuracy and contributes to the advancement of targeted therapies.
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Affiliation(s)
- Michele Salemi
- Oasi Research Institute–IRCCS, 94018 Troin, Italy; (G.L.); (F.A.S.); (M.G.S.); (R.F.)
| | - Maria Ravo
- Genomix4Life Srl, 94081 Baroniss, Italy; (M.R.); (G.M.V.); (G.M.)
- Genome Research Center for Health–CRGS, 94081 Baronissi, Italy
| | - Giuseppe Lanza
- Oasi Research Institute–IRCCS, 94018 Troin, Italy; (G.L.); (F.A.S.); (M.G.S.); (R.F.)
- Department of Surgery and Medical–Surgical Specialties, University of Catania, 95100 Catania, Italy
| | | | - Giovanna Maria Ventola
- Genomix4Life Srl, 94081 Baroniss, Italy; (M.R.); (G.M.V.); (G.M.)
- Genome Research Center for Health–CRGS, 94081 Baronissi, Italy
| | - Giovanna Marchese
- Genomix4Life Srl, 94081 Baroniss, Italy; (M.R.); (G.M.V.); (G.M.)
- Genome Research Center for Health–CRGS, 94081 Baronissi, Italy
| | - Maria Grazia Salluzzo
- Oasi Research Institute–IRCCS, 94018 Troin, Italy; (G.L.); (F.A.S.); (M.G.S.); (R.F.)
| | | | - Raffaele Ferri
- Oasi Research Institute–IRCCS, 94018 Troin, Italy; (G.L.); (F.A.S.); (M.G.S.); (R.F.)
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Mei T, Li Y, Orduña Dolado A, Li Z, Andersson R, Berliocchi L, Rasmussen LJ. Pooled analysis of frontal lobe transcriptomic data identifies key mitophagy gene changes in Alzheimer's disease brain. Front Aging Neurosci 2023; 15:1101216. [PMID: 37358952 PMCID: PMC10288858 DOI: 10.3389/fnagi.2023.1101216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Background The growing prevalence of Alzheimer's disease (AD) is becoming a global health challenge without effective treatments. Defective mitochondrial function and mitophagy have recently been suggested as etiological factors in AD, in association with abnormalities in components of the autophagic machinery like lysosomes and phagosomes. Several large transcriptomic studies have been performed on different brain regions from AD and healthy patients, and their data represent a vast source of important information that can be utilized to understand this condition. However, large integration analyses of these publicly available data, such as AD RNA-Seq data, are still missing. In addition, large-scale focused analysis on mitophagy, which seems to be relevant for the aetiology of the disease, has not yet been performed. Methods In this study, publicly available raw RNA-Seq data generated from healthy control and sporadic AD post-mortem human samples of the brain frontal lobe were collected and integrated. Sex-specific differential expression analysis was performed on the combined data set after batch effect correction. From the resulting set of differentially expressed genes, candidate mitophagy-related genes were identified based on their known functional roles in mitophagy, the lysosome, or the phagosome, followed by Protein-Protein Interaction (PPI) and microRNA-mRNA network analysis. The expression changes of candidate genes were further validated in human skin fibroblast and induced pluripotent stem cells (iPSCs)-derived cortical neurons from AD patients and matching healthy controls. Results From a large dataset (AD: 589; control: 246) based on three different datasets (i.e., ROSMAP, MSBB, & GSE110731), we identified 299 candidate mitophagy-related differentially expressed genes (DEG) in sporadic AD patients (male: 195, female: 188). Among these, the AAA ATPase VCP, the GTPase ARF1, the autophagic vesicle forming protein GABARAPL1 and the cytoskeleton protein actin beta ACTB were selected based on network degrees and existing literature. Changes in their expression were further validated in AD-relevant human in vitro models, which confirmed their down-regulation in AD conditions. Conclusion Through the joint analysis of multiple publicly available data sets, we identify four differentially expressed key mitophagy-related genes potentially relevant for the pathogenesis of sporadic AD. Changes in expression of these four genes were validated using two AD-relevant human in vitro models, primary human fibroblasts and iPSC-derived neurons. Our results provide foundation for further investigation of these genes as potential biomarkers or disease-modifying pharmacological targets.
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Affiliation(s)
- Taoyu Mei
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Anna Orduña Dolado
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zhiquan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Robin Andersson
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura Berliocchi
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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Varga VB, Keresztes F, Sigmond T, Vellai T, Kovács T. The evolutionary and functional divergence of the Atg8 autophagy protein superfamily. Biol Futur 2022; 73:375-384. [PMID: 35731422 DOI: 10.1007/s42977-022-00123-6] [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: 04/11/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023]
Abstract
Autophagy is a highly conserved self-degradation process of eukaryotic cells which is required for the effective elimination of damaged and unnecessary cytosolic constituents. Defects in the process can cause the intracellular accumulation of such damages, thereby leading to the senescence and subsequent loss of the affected cell. Defective autophagy hence is implicated in the development of various degenerative processes, including cancer, neurodegenerative diseases, diabetes, tissue atrophy and fibrosis, and immune deficiency, as well as in accelerated aging. The autophagic process is mediated by numerous autophagy-related (ATG) proteins, among which the ATG8/LC3/GABARAP (Microtubule-associated protein 1A/1B-light chain 3/Gammaaminobutyric acid receptor-associated protein) superfamily has a pivotal role in the formation and maturation of autophagosome, a key (macro) autophagic structure (the autophagosome sequesters parts of the cytoplasm which are destined for breakdown). While in the unicellular yeast there is only a single ATG8 protein, metazoan systems usually contain more ATG8 paralogs. ATG8 paralogs generally display tissue-specific expression patterns and their functions are not strictly restricted to autophagy. For example, GABARAP proteins also play a role in intracellular vesicle transport, and, in addition to autophagosome formation, ATG8 also functions in selective autophagy. In this review, we summarize the functional diversity of ATG8/LC3/GABARAP proteins, using tractable genetic models applied in autophagy research.
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Affiliation(s)
- Virginia B Varga
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Fanni Keresztes
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tímea Sigmond
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tibor Vellai
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.,ELKH-ELTE Genetics Research Group, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tibor Kovács
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
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van’t Sant LJ, White JJ, Hoeijmakers JHJ, Vermeij WP, Jaarsma D. In vivo 5-ethynyluridine (EU) labelling detects reduced transcription in Purkinje cell degeneration mouse mutants, but can itself induce neurodegeneration. Acta Neuropathol Commun 2021; 9:94. [PMID: 34020718 PMCID: PMC8139001 DOI: 10.1186/s40478-021-01200-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent staining of newly transcribed RNA via metabolic labelling with 5-ethynyluridine (EU) and click chemistry enables visualisation of changes in transcription, such as in conditions of cellular stress. Here, we tested whether EU labelling can be used to examine transcription in vivo in mouse models of nervous system disorders. We show that injection of EU directly into the cerebellum results in reproducible labelling of newly transcribed RNA in cerebellar neurons and glia, with cell type-specific differences in relative labelling intensities, such as Purkinje cells exhibiting the highest levels. We also observed EU-labelling accumulating into cytoplasmic inclusions, indicating that EU, like other modified uridines, may introduce non-physiological properties in labelled RNAs. Additionally, we found that EU induces Purkinje cell degeneration nine days after EU injection, suggesting that EU incorporation not only results in abnormal RNA transcripts, but also eventually becomes neurotoxic in highly transcriptionally-active neurons. However, short post-injection intervals of EU labelling in both a Purkinje cell-specific DNA repair-deficient mouse model and a mouse model of spinocerebellar ataxia 1 revealed reduced transcription in Purkinje cells compared to controls. We combined EU labelling with immunohistology to correlate altered EU staining with pathological markers, such as genotoxic signalling factors. These data indicate that the EU-labelling method provided here can be used to identify changes in transcription in vivo in nervous system disease models.
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Transcriptomic Changes Associated with Loss of Cell Viability Induced by Oxysterol Treatment of a Retinal Photoreceptor-Derived Cell Line: An In Vitro Model of Smith-Lemli-Opitz Syndrome. Int J Mol Sci 2021; 22:ijms22052339. [PMID: 33652836 PMCID: PMC7956713 DOI: 10.3390/ijms22052339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/17/2022] Open
Abstract
Smith–Lemli–Opitz Syndrome (SLOS) results from mutations in the gene encoding the enzyme DHCR7, which catalyzes conversion of 7-dehydrocholesterol (7DHC) to cholesterol (CHOL). Rats treated with a DHCR7 inhibitor serve as a SLOS animal model, and exhibit progressive photoreceptor-specific cell death, with accumulation of 7DHC and oxidized sterols. To understand the basis of this cell type specificity, we performed transcriptomic analyses on a photoreceptor-derived cell line (661W), treating cells with two 7DHC-derived oxysterols, which accumulate in tissues and bodily fluids of SLOS patients and in the rat SLOS model, as well as with CHOL (negative control), and evaluated differentially expressed genes (DEGs) for each treatment. Gene enrichment analysis and compilation of DEG sets indicated that endoplasmic reticulum stress, oxidative stress, DNA damage and repair, and autophagy were all highly up-regulated pathways in oxysterol-treated cells. Detailed analysis indicated that the two oxysterols exert their effects via different molecular mechanisms. Changes in expression of key genes in highlighted pathways (Hmox1, Ddit3, Trib3, and Herpud1) were validated by immunofluorescence confocal microscopy. The results extend our understanding of the pathobiology of retinal degeneration and SLOS, identifying potential new druggable targets for therapeutic intervention into these and other related orphan diseases.
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Madruga E, Maestro I, Martínez A. Mitophagy Modulation, a New Player in the Race against ALS. Int J Mol Sci 2021; 22:ijms22020740. [PMID: 33450997 PMCID: PMC7828440 DOI: 10.3390/ijms22020740] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that usually results in respiratory paralysis in an interval of 2 to 4 years. ALS shows a multifactorial pathogenesis with an unknown etiology, and currently lacks an effective treatment. The vast majority of patients exhibit protein aggregation and a dysfunctional mitochondrial accumulation in their motoneurons. As a result, autophagy and mitophagy modulators may be interesting drug candidates that mitigate key pathological hallmarks of the disease. This work reviews the most relevant evidence that correlate mitophagy defects and ALS, and discusses the possibility of considering mitophagy as an interesting target in the search for an effective treatment for ALS.
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Affiliation(s)
- Enrique Madruga
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.M.); (I.M.)
| | - Inés Maestro
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.M.); (I.M.)
| | - Ana Martínez
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.M.); (I.M.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
- Correspondence: ; Tel.: +34-918373112
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Jara JH, Sheets PL, Nigro MJ, Perić M, Brooks C, Heller DB, Martina M, Andjus PR, Ozdinler PH. The Electrophysiological Determinants of Corticospinal Motor Neuron Vulnerability in ALS. Front Mol Neurosci 2020; 13:73. [PMID: 32508590 PMCID: PMC7248374 DOI: 10.3389/fnmol.2020.00073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
The brain is complex and heterogeneous. Even though numerous independent studies indicate cortical hyperexcitability as a potential contributor to amyotrophic lateral sclerosis (ALS) pathology, the mechanisms that are responsible for upper motor neuron (UMN) vulnerability remain elusive. To reveal the electrophysiological determinants of corticospinal motor neuron (CSMN, a.k.a UMN in mice) vulnerability, we investigated the motor cortex of hSOD1G93A mice at P30 (postnatal day 30), a presymptomatic time point. Glutamate uncaging by laser scanning photostimulation (LSPS) revealed altered dynamics especially within the inhibitory circuitry and more specifically in L2/3 of the motor cortex, whereas the excitatory microcircuits were unchanged. Observed microcircuitry changes were specific to CSMN in the motor column. Electrophysiological evaluation of the intrinsic properties in response to the microcircuit changes, as well as the exon microarray expression profiles of CSMN isolated from hSOD1G93A and healthy mice at P30, revealed the presence of a very dynamic set of events, ultimately directed to establish, maintain and retain the balance at this early stage. Also, the expression profile of key voltage-gated potassium and sodium channel subunits as well as of the inhibitory GABA receptor subunits and modulatory proteins began to suggest the challenges CSMN face at this early age. Since neurodegeneration is initiated when neurons can no longer maintain balance, the complex cellular events that occur at this critical time point help reveal how CSMN try to cope with the challenges of disease manifestation. This information is critically important for the proper modulation of UMNs and for developing effective treatment strategies.
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Affiliation(s)
- Javier H Jara
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Patrick L Sheets
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Maximiliano José Nigro
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Mina Perić
- Institute for Physiology and Biochemistry "Ivan Djaja", Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Carolyn Brooks
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Daniel B Heller
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Marco Martina
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Pavle R Andjus
- Institute for Physiology and Biochemistry "Ivan Djaja", Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - P Hande Ozdinler
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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Ortega-Martínez M, Gutiérrez-Dávila V, Niderhauser-García A, Salazar-Aranda R, Solís-Soto JM, Montes-de-Oca-Luna R, Jaramillo-Rangel G. Peroxisomicine A1, a potential antineoplastic agent, causes micropexophagy in addition to macropexophagy. Cell Biol Int 2020; 44:918-923. [PMID: 31814220 DOI: 10.1002/cbin.11280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Peroxisomicine A1 (PA1) is a potential antineoplastic agent with high and selective toxicity toward peroxisomes of tumor cells. Pexophagy is a selective autophagy process that degrades damaged peroxisomes; this process has been studied mainly in methylotrophic yeasts. There are two main modes of pexophagy in yeast: macropexophagy and micropexophagy. Previous studies showed that peroxisomes damaged by a prolonged exposition to PA1 are eliminated by macropexophagy. In this work, Candida boidinii was grown in methanol-containing media, and PA1 was added to the cultures at 2 µg/mL after they reached the mid-exponential growth phase. Samples were taken at 5, 10, 15, 20, and 25 min after the addition of PA1 and processed for ultrastructural analysis. Typical morphological characteristics of micropexophagy were observed: the direct engulfment of peroxisomes by the vacuolar membrane and the presence of the micropexophagic membrane apparatus (MIPA), which mediates the fusion between the opposing tips of the vacuole to complete sequestration of peroxisomes from the cytosol. In conclusion, here we report that, in addition to macropexophagy, peroxisomes damaged by PA1 can be eliminated by micropexophagy. This information is useful to deepen the knowledge of the mechanism of action of PA1 and of that of pexophagy per se.
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Affiliation(s)
- Marta Ortega-Martínez
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Vanessa Gutiérrez-Dávila
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Alberto Niderhauser-García
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Ricardo Salazar-Aranda
- Department of Analytical Chemistry, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Juan M Solís-Soto
- Department of Physiology, School of Dentistry, Autonomous University of Nuevo Leon, Dr. Eduardo Aguirre P. y Silao, Monterrey, Nuevo León, 64460, Mexico
| | - Roberto Montes-de-Oca-Luna
- Department of Histology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Gilberto Jaramillo-Rangel
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
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Transcriptomic Analysis of MAPK Signaling in NSC-34 Motor Neurons Treated with Vitamin E. Nutrients 2019; 11:nu11051081. [PMID: 31096690 PMCID: PMC6566669 DOI: 10.3390/nu11051081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Vitamin E family is composed of different tocopherols and tocotrienols that are well-known as antioxidants but that exert also non-antioxidant effects. Oxidative stress may be involved in the progression of neurodegenerative disorders including amyotrophic lateral sclerosis (ALS), characterized by motor neuron death. The aim of the study was the evaluation of the changes induced in the transcriptional profile of NSC-34 motor neurons treated with α-tocopherol. In particular, cells were treated for 24 h with 10 µM α-tocopherol, RNA was extracted and transcriptomic analysis was performed using Next Generation Sequencing. Vitamin E treatment modulated MAPK signaling pathway. The evaluation revealed that 34 and 12 genes, respectively belonging to “Classical MAP kinase pathway” and “JNK and p38 MAP kinase pathway”, were involved. In particular, a downregulation of the genes encoding for p38 (Log2 fold change −0.87 and −0.67) and JNK (Log2 fold change −0.16) was found. On the contrary, the gene encoding for ERK showed a higher expression in cells treated with vitamin E (Log2 fold change 0.30). Since p38 and JNK seem more involved in cell death, while ERK in cell survival, the data suggested that vitamin E treatment may exert a protective role in NSC-34 motor neurons. Moreover, Vitamin E treatment reduced the expression of the genes which encode proteins involved in mitophagy. These results indicate that vitamin E may be an efficacious therapy in preventing motor neuron death, opening new strategies for those diseases that involve motor neurons, including ALS.
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Lee JH, Rao MV, Yang DS, Stavrides P, Im E, Pensalfini A, Huo C, Sarkar P, Yoshimori T, Nixon RA. Transgenic expression of a ratiometric autophagy probe specifically in neurons enables the interrogation of brain autophagy in vivo. Autophagy 2019; 15:543-557. [PMID: 30269645 PMCID: PMC6351128 DOI: 10.1080/15548627.2018.1528812] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022] Open
Abstract
Autophagy-lysosome pathway (ALP) disruption is considered pathogenic in multiple neurodegenerative diseases; however, current methods are inadequate to investigate macroautophagy/autophagy flux in brain in vivo and its therapeutic modulation. Here, we describe a novel autophagy reporter mouse (TRGL6) stably expressing a dual-fluorescence-tagged LC3 (tfLC3, mRFP-eGFP-LC3) by transgenesis selectively in neurons. The tfLC3 probe distributes widely in the central nervous system, including spinal cord. Expression levels were similar to endogenous LC3 and induced no detectable ALP changes. This ratiometric reporter registers differential pH-dependent changes in color as autophagosomes form, fuse with lysosomes, acidify, and degrade substrates within autolysosomes. We confirmed predicted changes in neuronal autophagy flux following specific experimental ALP perturbations. Furthermore, using a third fluorescence label in TRGL6 brains to identify lysosomes by immunocytochemistry, we validated a novel procedure to detect defective autolysosomal acidification in vivo. Thus, TRGL6 mice represent a unique tool to investigate in vivo ALP dynamics in specific neuron populations in relation to neurological diseases, aging, and disease modifying agents. Abbreviations: ACTB: actin, beta; AD: Alzheimer disease; AL: autolysosomes; ALP: autophagy-lysosome pathway; AP: autophagosome; APP: amyloid beta (Abeta) precursor protein; ATG5: autophagy related 5; ATG7: autophagy related 7; AV: autophagic vacuoles; CNS: central nervous system; CTSD: cathepsin D; CQ: chloroquine; DMEM: Dulbecco's modified Eagle's medium; GFP: green fluorescent protein; GABARAP: gamma-aminobutyric acid receptor associated protein; GABARAPL2/GATE16: gamma-aminobutyric acid (GABA) receptor-associated protein-like 2; ICC: immunocytochemistry; ICV: intra-cerebroventricular; LAMP2: lysosomal-associated membrane protein 2; Leup: leupeptin; LY: lysosomes; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; RBFOX3/NeuN: RNA binding protein, fox-1 homolog (C. elegans) 3; RFP: red fluorescent protein; RPS6KB1: ribosomal protein S6 kinase, polypeptide 1; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SQSTM1: sequestosome 1; tfLC3: mRFP-eGFP-LC3; TRGL6: Thy1 mRFP eGFP LC3-line 6; PCR: polymerase chain reaction; PD: Parkinson disease.
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Affiliation(s)
- Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
| | - Mala V. Rao
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
| | - Dun-Sheng Yang
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
| | - Philip Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
| | - Eunju Im
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
| | - Anna Pensalfini
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
| | - Chunfeng Huo
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
| | - Pallabi Sarkar
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
| | | | - Ralph A. Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University, New York, NY, USA
- Department of Cell Biology, New York University, New York, NY, USA
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11
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Brenner D, Sieverding K, Bruno C, Lüningschrör P, Buck E, Mungwa S, Fischer L, Brockmann SJ, Ulmer J, Bliederhäuser C, Philibert CE, Satoh T, Akira S, Boillée S, Mayer B, Sendtner M, Ludolph AC, Danzer KM, Lobsiger CS, Freischmidt A, Weishaupt JH. Heterozygous Tbk1 loss has opposing effects in early and late stages of ALS in mice. J Exp Med 2019; 216:267-278. [PMID: 30635357 PMCID: PMC6363427 DOI: 10.1084/jem.20180729] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/24/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Heterozygous loss-of-function mutations of TANK-binding kinase 1 (TBK1 ) cause familial ALS, yet downstream mechanisms of TBK1 mutations remained elusive. TBK1 is a pleiotropic kinase involved in the regulation of selective autophagy and inflammation. We show that heterozygous Tbk1 deletion alone does not lead to signs of motoneuron degeneration or disturbed autophagy in mice during a 200-d observation period. Surprisingly, however, hemizygous deletion of Tbk1 inversely modulates early and late disease phases in mice additionally overexpressing ALS-linked SOD1G93A , which represents a "second hit" that induces both neuroinflammation and proteostatic dysregulation. At the early stage, heterozygous Tbk1 deletion impairs autophagy in motoneurons and prepones both the clinical onset and muscular denervation in SOD1G93A/Tbk1+/- mice. At the late disease stage, however, it significantly alleviates microglial neuroinflammation, decelerates disease progression, and extends survival. Our results indicate a profound effect of TBK1 on brain inflammatory cells under pro-inflammatory conditions and point to a complex, two-edged role of TBK1 in SOD1-linked ALS.
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Affiliation(s)
- David Brenner
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Clara Bruno
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Patrick Lüningschrör
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Eva Buck
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Simon Mungwa
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Lena Fischer
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Johannes Ulmer
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Clémentine E Philibert
- Institut du Cerveau et de la Moelle Épinière, Institut National de la Santé et de la Recherche Médicale Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225, Sorbonne Université, Paris, France
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Séverine Boillée
- Institut du Cerveau et de la Moelle Épinière, Institut National de la Santé et de la Recherche Médicale Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225, Sorbonne Université, Paris, France
| | - Benjamin Mayer
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Wuerzburg, Germany
| | | | - Karin M Danzer
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Christian S Lobsiger
- Institut du Cerveau et de la Moelle Épinière, Institut National de la Santé et de la Recherche Médicale Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225, Sorbonne Université, Paris, France
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12
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Fu H, Hardy J, Duff KE. Selective vulnerability in neurodegenerative diseases. Nat Neurosci 2018; 21:1350-1358. [PMID: 30250262 DOI: 10.1038/s41593-018-0221-2] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases have two general characteristics that are so fundamental we usually take them for granted. The first is that the pathology associated with the disease only affects particular neurons ('selective neuronal vulnerability'); the second is that the pathology worsens with time and impacts more regions in a stereotypical and predictable fashion. The mechanisms underpinning selective neuronal and regional vulnerability have been difficult to dissect, but the recent application of whole-genome technologies, the development of mouse models that reproduce spatial and temporal features of the pathology, and the identification of intrinsic morphological, electrophysiological, and biochemical properties of vulnerable neurons are beginning to shed some light on these fundamental features of neurodegenerative diseases. Here we detail our emerging understanding of the underlying biology of selective neuronal vulnerability and outline some of the areas in which our understanding is incomplete.
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Affiliation(s)
- Hongjun Fu
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain; and Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.,Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lilla Weston Laboratories, Institute of Neurology, London, UK
| | - Karen E Duff
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain; and Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA. .,Department of Psychiatry, Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, NY, USA.
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13
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Zientara-Rytter K, Subramani S. AIM/LIR-based fluorescent sensors-new tools to monitor mAtg8 functions. Autophagy 2018; 14:1074-1078. [PMID: 29749795 DOI: 10.1080/15548627.2018.1454238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Macroautophagy/autophagy, a catabolic process by which cytoplasmic materials are degraded and recycled in lysosomes/vacuoles, remains a rapidly expanding research topic with the need for constantly improved methodologies to study each step of this pathway. Recently Lee and colleagues, as well as Stolz et al., independently reported the development of new AIM/LIR-based fluorescent sensors, which mark individual endogenous mammalian Atg8-family (mAtg8) proteins without affecting the autophagic flux. When expressed in cells, each sensor selectively recognizes individual mAtg8 isoforms and distinguishes mammalian MAP1LC3/LC3 proteins from the related GABARAPs. Such selectivity was achieved by using various LC3-interacting regions with high binding affinity to either a subgroup, or a specific, mAtg8 isoform as part of the sensor. Here we discuss the utility of these sensors in autophagy research and highlight their strengths, weaknesses and future directions.
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Affiliation(s)
- Katarzyna Zientara-Rytter
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
| | - Suresh Subramani
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
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14
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Distinct roles for motor neuron autophagy early and late in the SOD1 G93A mouse model of ALS. Proc Natl Acad Sci U S A 2017; 114:E8294-E8303. [PMID: 28904095 DOI: 10.1073/pnas.1704294114] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutations in autophagy genes can cause familial and sporadic amyotrophic lateral sclerosis (ALS). However, the role of autophagy in ALS pathogenesis is poorly understood, in part due to the lack of cell type-specific manipulations of this pathway in animal models. Using a mouse model of ALS expressing mutant superoxide dismutase 1 (SOD1G93A), we show that motor neurons form large autophagosomes containing ubiquitinated aggregates early in disease progression. To investigate whether this response is protective or detrimental, we generated mice in which the critical autophagy gene Atg7 was specifically disrupted in motor neurons (Atg7 cKO). Atg7 cKO mice were viable but exhibited structural and functional defects at a subset of vulnerable neuromuscular junctions. By crossing Atg7 cKO mice to the SOD1G93A mouse model, we found that autophagy inhibition accelerated early neuromuscular denervation of the tibialis anterior muscle and the onset of hindlimb tremor. Surprisingly, however, lifespan was extended in Atg7 cKO; SOD1G93A double-mutant mice. Autophagy inhibition did not prevent motor neuron cell death, but it reduced glial inflammation and blocked activation of the stress-related transcription factor c-Jun in spinal interneurons. We conclude that motor neuron autophagy is required to maintain neuromuscular innervation early in disease but eventually acts in a non-cell-autonomous manner to promote disease progression.
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15
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Mitophagy in neurodegenerative diseases. Neurochem Int 2017; 117:156-166. [PMID: 28797885 DOI: 10.1016/j.neuint.2017.08.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/19/2017] [Accepted: 08/05/2017] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), and Amyotrophic Lateral Sclerosis (ALS), are a complex "family" of pathologies, characterised by the progressive loss of neurons and/or neuronal functions, leading to severe physical and cognitive inabilities in affected patients. These syndromes, despite differences in the causative events, the onset, and the progression of the disease, share as common features the presence of aggregate-prone neuro-toxic proteins, in the form of aggresomes and/or inclusion bodies, perturbing cellular homeostasis and neuronal function (Popovic et al., 2014), and the presence of dysfunctional mitochondria. The removal of protein aggregates and of damaged organelles, through the ubiquitin-proteasome system (UPS) and/or the autophagy/lysosome machinery, is a crucial step for the maintenance of neuronal homeostasis. Indeed, their impairment has been reported as associated with the development of these diseases. In this review, we focus on the role played by mitophagy, a specialised form of autophagy, in the onset and progression of major neurodegenerative diseases, as well as on possible therapeutic approaches involving mitophagy modulation.
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16
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Stolz A, Putyrski M, Kutle I, Huber J, Wang C, Major V, Sidhu SS, Youle RJ, Rogov VV, Dötsch V, Ernst A, Dikic I. Fluorescence-based ATG8 sensors monitor localization and function of LC3/GABARAP proteins. EMBO J 2016; 36:549-564. [PMID: 28028054 DOI: 10.15252/embj.201695063] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a cellular surveillance pathway that balances metabolic and energy resources and transports specific cargos, including damaged mitochondria, other broken organelles, or pathogens for degradation to the lysosome. Central components of autophagosomal biogenesis are six members of the LC3 and GABARAP family of ubiquitin-like proteins (mATG8s). We used phage display to isolate peptides that possess bona fide LIR (LC3-interacting region) properties and are selective for individual mATG8 isoforms. Sensitivity of the developed sensors was optimized by multiplication, charge distribution, and fusion with a membrane recruitment (FYVE) or an oligomerization (PB1) domain. We demonstrate the use of the engineered peptides as intracellular sensors that recognize specifically GABARAP, GABL1, GABL2, and LC3C, as well as a bispecific sensor for LC3A and LC3B. By using an LC3C-specific sensor, we were able to monitor recruitment of endogenous LC3C to Salmonella during xenophagy, as well as to mitochondria during mitophagy. The sensors are general tools to monitor the fate of mATG8s and will be valuable in decoding the biological functions of the individual LC3/GABARAPs.
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Affiliation(s)
- Alexandra Stolz
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivana Kutle
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Viktória Major
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Andreas Ernst
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
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17
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Guedes-Dias P, Pinho BR, Soares TR, de Proença J, Duchen MR, Oliveira JMA. Mitochondrial dynamics and quality control in Huntington's disease. Neurobiol Dis 2015; 90:51-7. [PMID: 26388396 DOI: 10.1016/j.nbd.2015.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by polyglutamine expansion mutations in the huntingtin protein. Despite its ubiquitous distribution, expression of mutant huntingtin (mHtt) is particularly detrimental to medium spiny neurons within the striatum. Mitochondrial dysfunction has been associated with HD pathogenesis. Here we review the current evidence for mHtt-induced abnormalities in mitochondrial dynamics and quality control, with a particular focus on brain and neuronal data pertaining to striatal vulnerability. We address mHtt effects on mitochondrial biogenesis, protein import, complex assembly, fission and fusion, mitochondrial transport, and on the degradation of damaged mitochondria via autophagy (mitophagy). For an integrated perspective on potentially converging pathogenic mechanisms, we also address impaired autophagosomal transport and abnormal mHtt proteostasis in HD.
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Affiliation(s)
- Pedro Guedes-Dias
- REQUIMTE/LAQV, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal; Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Brígida R Pinho
- REQUIMTE/LAQV, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Tânia R Soares
- REQUIMTE/LAQV, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - João de Proença
- REQUIMTE/LAQV, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Michael R Duchen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Jorge M A Oliveira
- REQUIMTE/LAQV, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.
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18
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Capurro A, Bodea LG, Schaefer P, Luthi-Carter R, Perreau VM. Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. Front Neurosci 2015; 8:441. [PMID: 25620908 PMCID: PMC4288238 DOI: 10.3389/fnins.2014.00441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/15/2014] [Indexed: 01/09/2023] Open
Abstract
The characterization of molecular changes in diseased tissues gives insight into pathophysiological mechanisms and is important for therapeutic development. Genome-wide gene expression analysis has proven valuable for identifying biological processes in neurodegenerative diseases using post mortem human brain tissue and numerous datasets are publically available. However, many studies utilize heterogeneous tissue samples consisting of multiple cell types, all of which contribute to global gene expression values, confounding biological interpretation of the data. In particular, changes in numbers of neuronal and glial cells occurring in neurodegeneration confound transcriptomic analyses, particularly in human brain tissues where sample availability and controls are limited. To identify cell specific gene expression changes in neurodegenerative disease, we have applied our recently published computational deconvolution method, population specific expression analysis (PSEA). PSEA estimates cell-type-specific expression values using reference expression measures, which in the case of brain tissue comprises mRNAs with cell-type-specific expression in neurons, astrocytes, oligodendrocytes and microglia. As an exercise in PSEA implementation and hypothesis development regarding neurodegenerative diseases, we applied PSEA to Parkinson's and Huntington's disease (PD, HD) datasets. Genes identified as differentially expressed in substantia nigra pars compacta neurons by PSEA were validated using external laser capture microdissection data. Network analysis and Annotation Clustering (DAVID) identified molecular processes implicated by differential gene expression in specific cell types. The results of these analyses provided new insights into the implementation of PSEA in brain tissues and additional refinement of molecular signatures in human HD and PD.
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Affiliation(s)
- Alberto Capurro
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Liviu-Gabriel Bodea
- Neural Regeneration Unit, Institute of Reconstructive Neurobiology, University of Bonn Bonn, Germany ; Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland St Lucia, QLD, Australia
| | | | - Ruth Luthi-Carter
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Victoria M Perreau
- The Bioinformatics Core and The Synaptic Neurobiology Laboratory, The Florey Institute of Neuroscience and Mental Health Parkville, VIC, Australia
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19
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Flores Fernández JM, Gutiérrez Ortega A, Rosario Cruz R, Padilla Camberos E, Alvarez AH, Martínez Velázquez M. Molecular cloning and characterization of two novel autophagy-related genes belonging to the ATG8 family from the cattle tick Rhipicephalus (Boophilus) microplus (Acari: Ixodidae). EXPERIMENTAL & APPLIED ACAROLOGY 2014; 64:533-542. [PMID: 25039003 DOI: 10.1007/s10493-014-9838-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
Rhipicephalus (Boophilus) microplus is an obligate haematophagous arthropod and the major problem for cattle industry due to economic losses it causes. The parasite shows a remarkable adaptability to changing environmental conditions as well as an exceptional ability to survive long-term starvation. This ability has been related to a process of intracellular protein degradation called autophagy. This process in ticks is still poorly understood and only few autophagy-related (ATG) genes have been characterized. The aim of the present study was to examine the ESTs database, BmiGI, of R. microplus searching for ATG homologues. We predicted five putative ATG genes, ATG3, ATG4, ATG6 and two ATG8s. Further characterization led to the identification of RmATG8a and RmATG8b, homologues of GABARAP and MAP1LC3, respectively, and both of them belonging to the ATG8 family. PCR analyses showed that the expression level of RmATG8a and RmATG8b was higher in egg and larval stages when compared to ovary and midgut from adult ticks. This up-regulation coincides with the period in which ticks are in a starvation state, suggesting that autophagy is active in R. microplus.
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Affiliation(s)
- José Miguel Flores Fernández
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, AC, Av. Normalistas 800, Col. Colinas de la Normal, 44270, Guadalajara, JAL, Mexico
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20
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Margulis J, Finkbeiner S. Proteostasis in striatal cells and selective neurodegeneration in Huntington's disease. Front Cell Neurosci 2014; 8:218. [PMID: 25147502 PMCID: PMC4124811 DOI: 10.3389/fncel.2014.00218] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/17/2014] [Indexed: 12/23/2022] Open
Abstract
Selective neuronal loss is a hallmark of neurodegenerative diseases, including Huntington’s disease (HD). Although mutant huntingtin, the protein responsible for HD, is expressed ubiquitously, a subpopulation of neurons in the striatum is the first to succumb. In this review, we examine evidence that protein quality control pathways, including the ubiquitin proteasome system, autophagy, and chaperones, are significantly altered in striatal neurons. These alterations may increase the susceptibility of striatal neurons to mutant huntingtin-mediated toxicity. This novel view of HD pathogenesis has profound therapeutic implications: protein homeostasis pathways in the striatum may be valuable targets for treating HD and other misfolded protein disorders.
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Affiliation(s)
- Julia Margulis
- Gladstone Institute of Neurological Disease, J. David Gladstone Institutes San Francisco, CA, USA ; Department of Neurology, University of California at San Francisco San Francisco, CA, USA ; Department of Physiology, University of California at San Francisco San Francisco, CA, USA
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, J. David Gladstone Institutes San Francisco, CA, USA ; Department of Neurology, University of California at San Francisco San Francisco, CA, USA ; Department of Physiology, University of California at San Francisco San Francisco, CA, USA ; Taube/Koret Center for Huntington's Disease Research San Francisco, CA, USA
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21
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Boyer-Guittaut M, Poillet L, Liang Q, Bôle-Richard E, Ouyang X, Benavides GA, Chakrama FZ, Fraichard A, Darley-Usmar VM, Despouy G, Jouvenot M, Delage-Mourroux R, Zhang J. The role of GABARAPL1/GEC1 in autophagic flux and mitochondrial quality control in MDA-MB-436 breast cancer cells. Autophagy 2014; 10:986-1003. [PMID: 24879149 PMCID: PMC4091181 DOI: 10.4161/auto.28390] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/18/2014] [Accepted: 02/28/2014] [Indexed: 12/14/2022] Open
Abstract
GABARAPL1/GEC1 is an early estrogen-induced gene which encodes a protein highly conserved from C. elegans to humans. Overexpressed GABARAPL1 interacts with GABAA or kappa opioid receptors, associates with autophagic vesicles, and inhibits breast cancer cell proliferation. However, the function of endogenous GABARAPL1 has not been extensively studied. We hypothesized that GABARAPL1 is required for maintaining normal autophagic flux, and plays an important role in regulating cellular bioenergetics and metabolism. To test this hypothesis, we knocked down GABARAPL1 expression in the breast cancer MDA-MB-436 cell line by shRNA. Decreased expression of GABARAPL1 activated procancer responses of the MDA-MB-436 cells including increased proliferation, colony formation, and invasion. In addition, cells with decreased expression of GABARAPL1 exhibited attenuated autophagic flux and a decreased number of lysosomes. Moreover, decreased GABARAPL1 expression led to cellular bioenergetic changes including increased basal oxygen consumption rate, increased intracellular ATP, increased total glutathione, and an accumulation of damaged mitochondria. Taken together, our results demonstrate that GABARAPL1 plays an important role in cell proliferation, invasion, and autophagic flux, as well as in mitochondrial homeostasis and cellular metabolic programs.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Aldehydes/pharmacology
- Apoptosis Regulatory Proteins/metabolism
- Autophagy/genetics
- Autophagy/physiology
- Beclin-1
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival/drug effects
- DNA Damage
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Energy Metabolism
- Female
- Gene Knockdown Techniques
- Humans
- Lysosomal Membrane Proteins/genetics
- Lysosomal Membrane Proteins/metabolism
- Lysosomes/metabolism
- Lysosomes/pathology
- Membrane Potential, Mitochondrial
- Membrane Proteins/metabolism
- Microtubule-Associated Proteins/antagonists & inhibitors
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Mitophagy/genetics
- Mitophagy/physiology
- Neoplasm Invasiveness
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RNA, Small Interfering/genetics
- Sequestosome-1 Protein
- Tumor Stem Cell Assay
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Affiliation(s)
- Michaël Boyer-Guittaut
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
| | - Laura Poillet
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Qiuli Liang
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
| | - Elodie Bôle-Richard
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Xiaosen Ouyang
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
- Department of Veterans Affairs; Birmingham VA Medical Center; Birmingham, AL USA
| | - Gloria A Benavides
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
| | - Fatima-Zahra Chakrama
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Annick Fraichard
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Victor M Darley-Usmar
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
| | - Gilles Despouy
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Michèle Jouvenot
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Régis Delage-Mourroux
- Université de Franche-Comté; Laboratoire de Biochimie; EA3922 Estrogènes; Expression Génique et Pathologies du Système Nerveux Central; Sciences et Techniques; Besançon, France
| | - Jianhua Zhang
- Department of Pathology; University of Alabama at Birmingham; Birmingham, AL USA
- Center for Free Radical Biology; University of Alabama at Birmingham; Birmingham, AL USA
- Department of Veterans Affairs; Birmingham VA Medical Center; Birmingham, AL USA
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Poultney C, Goldberg A, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnström K, Palotie A, Daly M, Ma’ayan A, Fromer M, Buxbaum J. Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet 2013; 93:607-19. [PMID: 24094742 DOI: 10.1016/j.ajhg.2013.09.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/29/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022] Open
Abstract
Copy number variation (CNV) is an important determinant of human diversity and plays important roles in susceptibility to disease. Most studies of CNV carried out to date have made use of chromosome microarray and have had a lower size limit for detection of about 30 kilobases (kb). With the emergence of whole-exome sequencing studies, we asked whether such data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), making use of the eXome Hidden Markov Model (XHMM) program. By using both transmission information and validation by molecular methods, we confirmed that small CNV encompassing as few as three exons can be reliably called from whole-exome data. We applied this approach to an autism case-control sample (n = 811, mean per-target read depth = 161) and observed a significant increase in the burden of rare (MAF ≤1%) 1-30 kb CNV, 1-30 kb deletions, and 1-10 kb deletions in ASD. CNV in the 1-30 kb range frequently hit just a single gene, and we were therefore able to carry out enrichment and pathway analyses, where we observed enrichment for disruption of genes in cytoskeletal and autophagy pathways in ASD. In summary, our results showed that XHMM provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-30 kb exonic deletions could contribute to risk in up to 7% of individuals with ASD, and implicated a candidate pathway in developmental delay syndromes.
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