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Meng D, Wu D, Li X, Miao Z. p39 Affects Myelin Formation in Cerebral Ischemic Injury. Neuromolecular Med 2024; 26:22. [PMID: 38824254 DOI: 10.1007/s12017-024-08792-3] [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: 04/22/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
Stroke is a significant public health issue, and research has consistently focused on studying the mechanisms of injury and identifying new targets. As a CDK5 activator, p39 plays a crucial role in various diseases. In this article, we will explore the role and mechanism of p39 in cerebral ischemic injury. We measured the level of p39 using western blot and QPCR at various time points following cerebral ischemia-reperfusion (I/R) injury. The results indicated a significant reduction in the level of p39. TTC staining and behavioral results indicate that the knockout of p39 (p39KO) provides neuroprotection in the short-term. Interestingly, the behavioral dysfunction in p39KO mice was exacerbated after the repair phase of I/R. Further study revealed that this deterioration may be due to demyelination induced by elevated p35 levels. In summary, our study offers profound insights into the significance of p39 in both the acute and repair stages of ischemic injury recovery and a theoretical foundation for future therapeutic drug exploration.
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Affiliation(s)
- Danyang Meng
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Department of Neurology, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Di Wu
- Department of Neurology, Nanjing Jinling Hospital, Nanjing, China
| | - Xiaojing Li
- Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, China.
| | - Zhigang Miao
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Neuroscience of Soochow University, 199 Ren-Ai Road, Suzhou City, 215123, China.
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2
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Ferlazzo GM, Gambetta AM, Amato S, Cannizzaro N, Angiolillo S, Arboit M, Diamante L, Carbognin E, Romani P, La Torre F, Galimberti E, Pflug F, Luoni M, Giannelli S, Pepe G, Capocci L, Di Pardo A, Vanzani P, Zennaro L, Broccoli V, Leeb M, Moro E, Maglione V, Martello G. Genome-wide screening in pluripotent cells identifies Mtf1 as a suppressor of mutant huntingtin toxicity. Nat Commun 2023; 14:3962. [PMID: 37407555 DOI: 10.1038/s41467-023-39552-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by CAG-repeat expansions in the huntingtin (HTT) gene. The resulting mutant HTT (mHTT) protein induces toxicity and cell death via multiple mechanisms and no effective therapy is available. Here, we employ a genome-wide screening in pluripotent mouse embryonic stem cells (ESCs) to identify suppressors of mHTT toxicity. Among the identified suppressors, linked to HD-associated processes, we focus on Metal response element binding transcription factor 1 (Mtf1). Forced expression of Mtf1 counteracts cell death and oxidative stress caused by mHTT in mouse ESCs and in human neuronal precursor cells. In zebrafish, Mtf1 reduces malformations and apoptosis induced by mHTT. In R6/2 mice, Mtf1 ablates motor defects and reduces mHTT aggregates and oxidative stress. Our screening strategy enables a quick in vitro identification of promising suppressor genes and their validation in vivo, and it can be applied to other monogenic diseases.
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Affiliation(s)
- Giorgia Maria Ferlazzo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Aptuit (Verona) S.r.l., an Evotec Company, Campus Levi-Montalcini, 37135, Verona, Italy
| | - Anna Maria Gambetta
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Sonia Amato
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
- Department of Neuroscience, University of Padova, Via Belzoni, 160, 35131, Padua, Italy
| | - Noemi Cannizzaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Silvia Angiolillo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Linda Diamante
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Carbognin
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Patrizia Romani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Federico La Torre
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Florian Pflug
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Serena Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | | | | | | | - Paola Vanzani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Lucio Zennaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20854, Vedrano al Lambro, Italy
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Enrico Moro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | | | - Graziano Martello
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy.
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3
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Abstract
Neuroepigenetics, a new branch of epigenetics, plays an important role in the regulation of gene expression. Neuroepigenetics is associated with holistic neuronal function and helps in formation and maintenance of memory and learning processes. This includes neurodevelopment and neurodegenerative defects in which histone modification enzymes appear to play a crucial role. These modifications, carried out by acetyltransferases and deacetylases, regulate biologic and cellular processes such as apoptosis and autophagy, inflammatory response, mitochondrial dysfunction, cell-cycle progression and oxidative stress. Alterations in acetylation status of histone as well as non-histone substrates lead to transcriptional deregulation. Histone deacetylase decreases acetylation status and causes transcriptional repression of regulatory genes involved in neural plasticity, synaptogenesis, synaptic and neural plasticity, cognition and memory, and neural differentiation. Transcriptional deactivation in the brain results in development of neurodevelopmental and neurodegenerative disorders. Mounting evidence implicates histone deacetylase inhibitors as potential therapeutic targets to combat neurologic disorders. Recent studies have targeted naturally-occurring biomolecules and micro-RNAs to improve cognitive defects and memory. Multi-target drug ligands targeting HDAC have been developed and used in cell-culture and animal-models of neurologic disorders to ameliorate synaptic and cognitive dysfunction. Herein, we focus on the implications of histone deacetylase enzymes in neuropathology, their regulation of brain function and plausible involvement in the pathogenesis of neurologic defects.
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4
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Galli S, Stancheva SH, Dufor T, Gibb AJ, Salinas PC. Striatal Synapse Degeneration and Dysfunction Are Reversed by Reactivation of Wnt Signaling. Front Synaptic Neurosci 2021; 13:670467. [PMID: 34149390 PMCID: PMC8209303 DOI: 10.3389/fnsyn.2021.670467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Synapse degeneration in the striatum has been associated with the early stages of Parkinson’s and Huntington’s diseases (PD and HD). However, the molecular mechanisms that trigger synaptic dysfunction and loss are not fully understood. Increasing evidence suggests that deficiency in Wnt signaling triggers synapse degeneration in the adult brain and that this pathway is affected in neurodegenerative diseases. Here, we demonstrate that endogenous Wnt signaling is essential for the integrity of a subset of inhibitory synapses on striatal medium spiny neurons (MSNs). We found that inducible expression of the specific Wnt antagonist Dickkopf-1 (Dkk1) in the adult striatum leads to the loss of inhibitory synapses on MSNs and affects the synaptic transmission of D2-MSNs. We also discovered that re-activation of the Wnt pathway by turning off Dkk1 expression after substantial loss of synapses resulted in the complete recovery of GABAergic and dopamine synapse number. Our results also show that re-activation of the Wnt pathway leads to a recovery of amphetamine response and motor function. Our studies identify the Wnt signaling pathway as a potential therapeutic target for restoring neuronal circuits after synapse degeneration.
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Affiliation(s)
- Soledad Galli
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Stefka H Stancheva
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Tom Dufor
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Alasdair J Gibb
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Patricia C Salinas
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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5
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Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington's Disease. Cancers (Basel) 2020; 12:cancers12040963. [PMID: 32295075 PMCID: PMC7226183 DOI: 10.3390/cancers12040963] [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: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence points to a link between circadian clock dysfunction and the molecular events that drive tumorigenesis. Here, we investigated the connection between the circadian clock and the hallmarks of cancer in an in vitro model of colorectal cancer (CRC). We used a cross-platform data normalization method to concatenate and compare available microarray and RNA-sequencing time series data of CRC cell lines derived from the same patient at different disease stages. Our data analysis suggests differential regulation of molecular pathways between the CRC cells and identifies several of the circadian and likely clock-controlled genes (CCGs) as cancer hallmarks and circadian drug targets. Notably, we found links of the CCGs to Huntington’s disease (HD) in the metastasis-derived cells. We then investigated the impact of perturbations of our candidate genes in a cohort of 439 patients with colon adenocarcinoma retrieved from the Cancer Genome Atlas (TCGA). The analysis revealed a correlation of the differential expression levels of the candidate genes with the survival of patients. Thus, our study provides a bioinformatics workflow that allows for a comprehensive analysis of circadian properties at different stages of colorectal cancer, and identifies a new association between cancer and HD.
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Zhang R, Liu C, Ji Y, Teng L, Guo Y. Neuregulin-1β Plays a Neuroprotective Role by Inhibiting the Cdk5 Signaling Pathway after Cerebral Ischemia-Reperfusion Injury in Rats. J Mol Neurosci 2018; 66:261-272. [PMID: 30206770 DOI: 10.1007/s12031-018-1166-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/28/2018] [Indexed: 01/24/2023]
Abstract
This study investigated the effects of neuregulin-1β (NRG1β) after middle cerebral artery occlusion/reperfusion (MCAO/R) in rats to evaluate whether they occur via the cyclin-dependent kinase (Cdk)5 signaling pathway. One hundred adult male Wistar rats were randomly divided into sham, MCAO/R, treatment (NRG1β), inhibitor (roscovitine; Ros), and inhibitor + treatment (Ros + NRG1β) groups. The MCAO/R model was established using the intraluminal thread method. The neurobehavioral function was evaluated by the modified neurological severity score (mNSS). The cerebral infarction volume (CIV) was measured by triphenyl tetrazolium chloride (TTC) staining. Morphological changes were observed by hematoxylin-eosin (HE) staining. The apoptotic cell index (ACI) was detected by the terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assay. Immunohistochemistry and Western blotting were performed to detect the expression of calpain 1, p35/p25 (regulatory binding partners of Cdk5), Cdk5, and p-Tau in neurons. The neuronal morphology in the MCAO/R, NRG1β, Ros + NRG1β, and Ros groups differed compared to the sham group; the mNSS, CIV, ACI, and the expression of calpain 1, p35/p25, Cdk5, and p-Tau were significantly increased in all four groups (P < 0.05). In the NRG1β, Ros and Ros + NRG1β groups, the neuronal morphology was significantly improved compared to the MCAO/R group, as were the mNSS, CIV, and ACI. The levels of calpain 1, p35/p25, and p-Tau were decreased compared with the MCAO/R group (P < 0.05), while the Cdk5 expression was not significantly different (P > 0.05). NRG1β may exert neuroprotective effects by inhibiting the expression of calpain 1, p35/p25, and p-Tau after cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Rui Zhang
- Department of ICU, Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Cui Liu
- Department Traumic Surgery, Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yaqing Ji
- Institute of Integrative Medicine, Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Lei Teng
- Department of Biology, Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yunliang Guo
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao University, Shandong Provincial Collaborative Innovation Center for Neurodegenerative Disorders, Qingdao, 266003, China.
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Ziemka-Nalecz M, Jaworska J, Sypecka J, Zalewska T. Histone Deacetylase Inhibitors: A Therapeutic Key in Neurological Disorders? J Neuropathol Exp Neurol 2018; 77:855-870. [DOI: 10.1093/jnen/nly073] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Malgorzata Ziemka-Nalecz
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Jaworska
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Sypecka
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Teresa Zalewska
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
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8
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Kalathur RKR, Pedro Pinto J, Sahoo B, Chaurasia G, Futschik ME. HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. Sci Rep 2017; 7:5216. [PMID: 28701700 PMCID: PMC5507972 DOI: 10.1038/s41598-017-05224-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/25/2017] [Indexed: 12/20/2022] Open
Abstract
Huntington’s disease (HD) is a progressive and fatal neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin gene. Although HD is monogenic, its molecular manifestation appears highly complex and involves multiple cellular processes. The recent application of high throughput platforms such as microarrays and mass-spectrometry has indicated multiple pathogenic routes. The massive data generated by these techniques together with the complexity of the pathogenesis, however, pose considerable challenges to researchers. Network-based methods can provide valuable tools to consolidate newly generated data with existing knowledge, and to decipher the interwoven molecular mechanisms underlying HD. To facilitate research on HD in a network-oriented manner, we have developed HDNetDB, a database that integrates molecular interactions with many HD-relevant datasets. It allows users to obtain, visualize and prioritize molecular interaction networks using HD-relevant gene expression, phenotypic and other types of data obtained from human samples or model organisms. We illustrated several HDNetDB functionalities through a case study and identified proteins that constitute potential cross-talk between HD and the unfolded protein response (UPR). HDNetDB is publicly accessible at http://hdnetdb.sysbiolab.eu.
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Affiliation(s)
- Ravi Kiran Reddy Kalathur
- SysBioLab, Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal. .,Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - José Pedro Pinto
- SysBioLab, Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal
| | | | - Gautam Chaurasia
- Institute for Theoretical Biology, Charité, Humboldt-University, Berlin, Germany
| | - Matthias E Futschik
- SysBioLab, Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal. .,Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, Portugal. .,School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, Devon, United Kingdom.
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9
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Cambon K, Zimmer V, Martineau S, Gaillard MC, Jarrige M, Bugi A, Miniarikova J, Rey M, Hassig R, Dufour N, Auregan G, Hantraye P, Perrier AL, Déglon N. Preclinical Evaluation of a Lentiviral Vector for Huntingtin Silencing. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 5:259-276. [PMID: 28603746 PMCID: PMC5453866 DOI: 10.1016/j.omtm.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/07/2017] [Indexed: 01/12/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder resulting from a polyglutamine expansion in the huntingtin (HTT) protein. There is currently no cure for this disease, but recent studies suggest that RNAi to downregulate the expression of both normal and mutant HTT is a promising therapeutic approach. We previously developed a small hairpin RNA (shRNA), vectorized in an HIV-1-derived lentiviral vector (LV), that reduced pathology in an HD rodent model. Here, we modified this vector for preclinical development by using a tat-independent third-generation LV (pCCL) backbone and removing the original reporter genes. We demonstrate that this novel vector efficiently downregulated HTT expression in vitro in striatal neurons derived from induced pluripotent stem cells (iPSCs) of HD patients. It reduced two major pathological HD hallmarks while triggering a minimal inflammatory response, up to 6 weeks after injection, when administered by stereotaxic surgery in the striatum of an in vivo rodent HD model. Further assessment of this shRNA vector in vitro showed proper processing by the endogenous silencing machinery, and we analyzed gene expression changes to identify potential off-targets. These preclinical data suggest that this new shRNA vector fulfills primary biosafety and efficiency requirements for further development in the clinic as a cure for HD.
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Affiliation(s)
- Karine Cambon
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Virginie Zimmer
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Sylvain Martineau
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Margot Jarrige
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Aurore Bugi
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Jana Miniarikova
- Department of Research & Development, uniQure, 1105 Amsterdam, the Netherlands
| | - Maria Rey
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Raymonde Hassig
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Noelle Dufour
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Gwenaelle Auregan
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Anselme L. Perrier
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Nicole Déglon
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Corresponding author: Nicole Déglon, Lausanne University Hospital (CHUV), Laboratory of Cellular and Molecular Neurotherapies (LNCM), Pavillon 3, Avenue de Beaumont, 1011 Lausanne, Switzerland.
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10
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Bezulska A, Naczk M, Adach Z, Arlet J, Celichowski J. Sense of extension force and angle of the knee joint are correlated between two generations of men. J Sports Sci 2017; 36:565-570. [PMID: 28471325 DOI: 10.1080/02640414.2017.1324204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Numerous motor abilities depend on the activity of proprioceptors, which has been suggested to be genetically determined. To test this hypothesis, the control of torque generated by knee extensors and knee position was studied in 30 father-son pairs both before and immediately after running. After stabilisation of the participant in a sitting position, the knee joint of his dominant leg was flexed to 90°, and the maximal voluntary torque (MVT) of the dominant knee extensors under static conditions was measured. The participant then tried five times to produce 50% of the MVT. Next, the participant extended the knee to 45° five times without visual control. Significant correlations between the reproducibility of successive trials for groups of fathers and their sons were found. The correlation coefficients for the repeatability of the knee extension torque were 0.69 (confidence interval [CI] = 0.45-0.84; P < 0.01) and 0.75 (CI = 0.54-0.87; P < 0.01) before and after the fatiguing exercise, respectively, whereas the coefficient for the reproducibility of positioning the knee was 0.49 (CI = 0.16-0.72; P < 0.01) after the fatiguing exercise. Our results indicate a significant influence of hereditary factors on the control of limb torque and position.
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Affiliation(s)
- Anna Bezulska
- a Department of Physiological Sciences , University School of Physical Education in Poznan, Faculty of Physical Culture in Gorzow Wielkopolski , Poland
| | - M Naczk
- a Department of Physiological Sciences , University School of Physical Education in Poznan, Faculty of Physical Culture in Gorzow Wielkopolski , Poland
| | - Z Adach
- a Department of Physiological Sciences , University School of Physical Education in Poznan, Faculty of Physical Culture in Gorzow Wielkopolski , Poland
| | - J Arlet
- a Department of Physiological Sciences , University School of Physical Education in Poznan, Faculty of Physical Culture in Gorzow Wielkopolski , Poland
| | - J Celichowski
- b Department of Neurobiology , University School of Physical Education , Poznan , Poland
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11
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Baronchelli S, La Spada A, Ntai A, Barbieri A, Conforti P, Jotti GS, Redaelli S, Bentivegna A, De Blasio P, Biunno I. Epigenetic and transcriptional modulation of WDR5, a chromatin remodeling protein, in Huntington's disease human induced pluripotent stem cell (hiPSC) model. Mol Cell Neurosci 2017; 82:46-57. [PMID: 28476540 DOI: 10.1016/j.mcn.2017.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
DNA methylation (DNAm) changes are of increasing relevance to neurodegenerative disorders, including Huntington's disease (HD). We performed genome-wide screening of possible DNAm changes occurring during striatal differentiation in human induced pluripotent stem cells derived from a HD patient (HD-hiPSCs) as cellular model. We identified 240 differentially methylated regions (DMRs) at promoters in fully differentiated HD-hiPSCs. Subsequently, we focused on the methylation differences in a subcluster of genes related to Jumonji Domain Containing 3 (JMJD3), a demethylase that epigenetically regulates neuronal differentiation and activates neuronal progenitor associated genes, which are indispensable for neuronal fate acquisition. Noticeably among these genes, WD repeat-containing protein 5 (WDR5) promoter was found hypermethylated in HD-hiPSCs, resulting in a significant down-modulation in its expression and of the encoded protein. A similar WDR5 expression decrease was seen in a small series of HD-hiPSC lines characterized by different CAG length. The decrease in WDR5 expression was particularly evident in HD-hiPSCs compared to hESCs and control-hiPSCs from healthy subjects. WDR5 is a core component of the MLL/SET1 chromatin remodeling complexes essential for H3K4me3, previously reported to play an important role in stem cells self-renewal and differentiation. These results suggest the existence of epigenetic mechanisms in HD and the identification of genes, which are able to modulate HD phenotype, is important both for biomarker discovery and therapeutic interventions.
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Affiliation(s)
- Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Aikaterini Ntai
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Andrea Barbieri
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Paola Conforti
- Department of Biosciences, University of Milan and Istituto Nazionale di Genetica Molecolare Padiglione Invernizzi, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Gloria Saccani Jotti
- Department of Biological Science, Biotechnology and Translational - S.Bi.Bi.T., University of Parma, Via Gramsci 14, 43121 Parma, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy
| | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy; NeuroMI, Milan Center of Neuroscience, via Pergolesi 33, 20900 Monza, Italy
| | - Pasquale De Blasio
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy; IRCCS Multimedica, via Fantoli 16/15, 20138 Milano, Italy.
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12
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Wang JKT, Langfelder P, Horvath S, Palazzolo MJ. Exosomes and Homeostatic Synaptic Plasticity Are Linked to Each other and to Huntington's, Parkinson's, and Other Neurodegenerative Diseases by Database-Enabled Analyses of Comprehensively Curated Datasets. Front Neurosci 2017; 11:149. [PMID: 28611571 PMCID: PMC5374209 DOI: 10.3389/fnins.2017.00149] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/09/2017] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a progressive and autosomal dominant neurodegeneration caused by CAG expansion in the huntingtin gene (HTT), but the pathophysiological mechanism of mutant HTT (mHTT) remains unclear. To study HD using systems biological methodologies on all published data, we undertook the first comprehensive curation of two key PubMed HD datasets: perturbation genes that impact mHTT-driven endpoints and therefore are putatively linked causally to pathogenic mechanisms, and the protein interactome of HTT that reflects its biology. We perused PubMed articles containing co-citation of gene IDs and MeSH terms of interest to generate mechanistic gene sets for iterative enrichment analyses and rank ordering. The HD Perturbation database of 1,218 genes highly overlaps the HTT Interactome of 1,619 genes, suggesting links between normal HTT biology and mHTT pathology. These two HD datasets are enriched for protein networks of key genes underlying two mechanisms not previously implicated in HD nor in each other: exosome synaptic functions and homeostatic synaptic plasticity. Moreover, proteins, possibly including HTT, and miRNA detected in exosomes from a wide variety of sources also highly overlap the HD datasets, suggesting both mechanistic and biomarker links. Finally, the HTT Interactome highly intersects protein networks of pathogenic genes underlying Parkinson's, Alzheimer's and eight non-HD polyglutamine diseases, ALS, and spinal muscular atrophy. These protein networks in turn highly overlap the exosome and homeostatic synaptic plasticity gene sets. Thus, we hypothesize that HTT and other neurodegeneration pathogenic genes form a large interlocking protein network involved in exosome and homeostatic synaptic functions, particularly where the two mechanisms intersect. Mutant pathogenic proteins cause dysfunctions at distinct points in this network, each altering the two mechanisms in specific fashion that contributes to distinct disease pathologies, depending on the gene mutation and the cellular and biological context. This protein network is rich with drug targets, and exosomes may provide disease biomarkers, thus enabling drug discovery. All the curated datasets are made available for other investigators. Elucidating the roles of pathogenic neurodegeneration genes in exosome and homeostatic synaptic functions may provide a unifying framework for the age-dependent, progressive and tissue selective nature of multiple neurodegenerative diseases.
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Affiliation(s)
| | - Peter Langfelder
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
| | - Michael J Palazzolo
- Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
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13
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Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, Vitaterna MH, Turek FW, Kasarskis A. Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease. PLoS Genet 2016; 12:e1006137. [PMID: 27390852 PMCID: PMC4938493 DOI: 10.1371/journal.pgen.1006137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/31/2016] [Indexed: 12/22/2022] Open
Abstract
Recent systems-based analyses have demonstrated that sleep and stress traits emerge from shared genetic and transcriptional networks, and clinical work has elucidated the emergence of sleep dysfunction and stress susceptibility as early symptoms of Huntington's disease. Understanding the biological bases of these early non-motor symptoms may reveal therapeutic targets that prevent disease onset or slow disease progression, but the molecular mechanisms underlying this complex clinical presentation remain largely unknown. In the present work, we specifically examine the relationship between these psychiatric traits and Huntington's disease (HD) by identifying striatal transcriptional networks shared by HD, stress, and sleep phenotypes. First, we utilize a systems-based approach to examine a large publicly available human transcriptomic dataset for HD (GSE3790 from GEO) in a novel way. We use weighted gene coexpression network analysis and differential connectivity analyses to identify transcriptional networks dysregulated in HD, and we use an unbiased ranking scheme that leverages both gene- and network-level information to identify a novel astrocyte-specific network as most relevant to HD caudate. We validate this result in an independent HD cohort. Next, we computationally predict FOXO3 as a regulator of this network, and use multiple publicly available in vitro and in vivo experimental datasets to validate that this astrocyte HD network is downstream of a signaling pathway important in adult neurogenesis (TGFβ-FOXO3). We also map this HD-relevant caudate subnetwork to striatal transcriptional networks in a large (n = 100) chronically stressed (B6xA/J)F2 mouse population that has been extensively phenotyped (328 stress- and sleep-related measurements), and we show that this striatal astrocyte network is correlated to sleep and stress traits, many of which are known to be altered in HD cohorts. We identify causal regulators of this network through Bayesian network analysis, and we highlight their relevance to motor, mood, and sleep traits through multiple in silico approaches, including an examination of their protein binding partners. Finally, we show that these causal regulators may be therapeutically viable for HD because their downstream network was partially modulated by deep brain stimulation of the subthalamic nucleus, a medical intervention thought to confer some therapeutic benefit to HD patients. In conclusion, we show that an astrocyte transcriptional network is primarily associated to HD in the caudate and provide evidence for its relationship to molecular mechanisms of neural stem cell homeostasis. Furthermore, we present a unified systems-based framework for identifying gene networks that are associated with complex non-motor traits that manifest in the earliest phases of HD. By analyzing and integrating multiple independent datasets, we identify a point of molecular convergence between sleep, stress, and HD that reflects their phenotypic comorbidity and reveals a molecular pathway involved in HD progression.
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Affiliation(s)
- Joseph R. Scarpa
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Peng Jiang
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Bojan Losic
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ben Readhead
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Vance D. Gao
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Joel T. Dudley
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Martha H. Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Fred W. Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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14
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Nekrasov ED, Vigont VA, Klyushnikov SA, Lebedeva OS, Vassina EM, Bogomazova AN, Chestkov IV, Semashko TA, Kiseleva E, Suldina LA, Bobrovsky PA, Zimina OA, Ryazantseva MA, Skopin AY, Illarioshkin SN, Kaznacheyeva EV, Lagarkova MA, Kiselev SL. Manifestation of Huntington's disease pathology in human induced pluripotent stem cell-derived neurons. Mol Neurodegener 2016; 11:27. [PMID: 27080129 PMCID: PMC4832474 DOI: 10.1186/s13024-016-0092-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 04/08/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Huntington's disease (HD) is an incurable hereditary neurodegenerative disorder, which manifests itself as a loss of GABAergic medium spiny (GABA MS) neurons in the striatum and caused by an expansion of the CAG repeat in exon 1 of the huntingtin gene. There is no cure for HD, existing pharmaceutical can only relieve its symptoms. RESULTS Here, induced pluripotent stem cells were established from patients with low CAG repeat expansion in the huntingtin gene, and were then efficiently differentiated into GABA MS-like neurons (GMSLNs) under defined culture conditions. The generated HD GMSLNs recapitulated disease pathology in vitro, as evidenced by mutant huntingtin protein aggregation, increased number of lysosomes/autophagosomes, nuclear indentations, and enhanced neuronal death during cell aging. Moreover, store-operated channel (SOC) currents were detected in the differentiated neurons, and enhanced calcium entry was reproducibly demonstrated in all HD GMSLNs genotypes. Additionally, the quinazoline derivative, EVP4593, reduced the number of lysosomes/autophagosomes and SOC currents in HD GMSLNs and exerted neuroprotective effects during cell aging. CONCLUSIONS Our data is the first to demonstrate the direct link of nuclear morphology and SOC calcium deregulation to mutant huntingtin protein expression in iPSCs-derived neurons with disease-mimetic hallmarks, providing a valuable tool for identification of candidate anti-HD drugs. Our experiments demonstrated that EVP4593 may be a promising anti-HD drug.
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Affiliation(s)
- Evgeny D. Nekrasov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333 Russia
| | - Vladimir A. Vigont
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | | | - Olga S. Lebedeva
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow, 119435 Russia
| | - Ekaterina M. Vassina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333 Russia
| | | | - Ilya V. Chestkov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333 Russia
| | - Tatiana A. Semashko
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow, 119435 Russia
| | - Elena Kiseleva
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
| | - Lyubov A. Suldina
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
| | - Pavel A. Bobrovsky
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow, 119435 Russia
| | - Olga A. Zimina
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Maria A. Ryazantseva
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Anton Yu. Skopin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | | | | | - Maria A. Lagarkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333 Russia
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow, 119435 Russia
| | - Sergey L. Kiselev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333 Russia
- Kazan State University, Kazan, 420008 Russia
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15
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Jia H, Wang Y, Morris CD, Jacques V, Gottesfeld JM, Rusche JR, Thomas EA. The Effects of Pharmacological Inhibition of Histone Deacetylase 3 (HDAC3) in Huntington's Disease Mice. PLoS One 2016; 11:e0152498. [PMID: 27031333 PMCID: PMC4816519 DOI: 10.1371/journal.pone.0152498] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/15/2016] [Indexed: 12/23/2022] Open
Abstract
An important epigenetic modification in Huntington’s disease (HD) research is histone acetylation, which is regulated by histone acetyltransferase and histone deacetylase (HDAC) enzymes. HDAC inhibitors have proven effective in HD model systems, and recent work is now focused on functional dissection of the individual HDAC enzymes in these effects. Histone deacetylase 3 (HDAC3), a member of the class I subfamily of HDACs, has previously been implicated in neuronal toxicity and huntingtin-induced cell death. Hence, we tested the effects of RGFP966 ((E)-N-(2-amino-4-fluorophenyl)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamide), a benzamide-type HDAC inhibitor that selectively targets HDAC3, in the N171-82Q transgenic mouse model of HD. We found that RGFP966 at doses of 10 and 25 mg/kg improves motor deficits on rotarod and in open field exploration, accompanied by neuroprotective effects on striatal volume. In light of previous studies implicating HDAC3 in immune function, we measured gene expression changes for 84 immune-related genes elicited by RGFP966 using quantitative PCR arrays. RGFP966 treatment did not cause widespread changes in cytokine/chemokine gene expression patterns, but did significantly alter the striatal expression of macrophage migration inhibitory factor (Mif), a hormone immune modulator associated with glial cell activation, in N171-82Q transgenic mice, but not WT mice. Accordingly, RGFP966-treated mice showed decreased glial fibrillary acidic protein (GFAP) immunoreactivity, a marker of astrocyte activation, in the striatum of N171-82Q transgenic mice compared to vehicle-treated mice. These findings suggest that the beneficial actions of HDAC3 inhibition could be related, in part, with lowered Mif levels and its associated downstream effects.
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Affiliation(s)
- Haiqun Jia
- Department of Cellular and Molecular Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- California Institute for Biomedical Research, La Jolla, California, United States of America
| | - Ying Wang
- Department of Cellular and Molecular Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- California Institute for Biomedical Research, La Jolla, California, United States of America
| | - Charles D. Morris
- Department of Cellular and Molecular Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
| | - Vincent Jacques
- Repligen Corporation, Waltham, Massachusetts, United States of America
| | - Joel M. Gottesfeld
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James R. Rusche
- Repligen Corporation, Waltham, Massachusetts, United States of America
| | - Elizabeth A. Thomas
- Department of Cellular and Molecular Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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16
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Chandrasekaran S, Bonchev D. Network analysis of human post-mortem microarrays reveals novel genes, microRNAs, and mechanistic scenarios of potential importance in fighting huntington's disease. Comput Struct Biotechnol J 2016; 14:117-130. [PMID: 27924190 PMCID: PMC5128196 DOI: 10.1016/j.csbj.2016.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 01/18/2023] Open
Abstract
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes. Several protein-protein interaction networks, as well as microRNA-mRNA networks were constructed for these gene sets with the Elsevier Pathway Studio software and its associated ResNet database. We applied a gene prioritizing procedure based on vital network topological measures, such as high node connectivity and centrality. Adding to these criteria the guilt-by-association rule and exploring their innate biomolecular functions, we propose 19 novel genes from the analyzed microarrays, from which CEBPA, CDK1, CX3CL1, EGR1, E2F1, ERBB2, LRP1, HSP90AA1 and ZNF148 might be of particular interest for experimental validation. A possibility is discussed for dual-level gene regulation by both transcription factors and microRNAs in Huntington's disease mechanism. We propose several possible scenarios for experimental studies initiated via the extra-cellular ligands TGFB1, FGF2 and TNF aiming at restoring the cellular homeostasis in Huntington's disease.
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Affiliation(s)
- Sreedevi Chandrasekaran
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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17
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Stroedicke M, Bounab Y, Strempel N, Klockmeier K, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F, Riechers SP, Russ J, Nicoletti C, Boeddrich A, Wiglenda T, Haenig C, Schnoegl S, Fournier D, Graham RK, Hayden MR, Sigrist S, Bates GP, Priller J, Andrade-Navarro MA, Futschik ME, Wanker EE. Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Res 2016; 25:701-13. [PMID: 25908449 PMCID: PMC4417118 DOI: 10.1101/gr.182444.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Assemblies of huntingtin (HTT) fragments with expanded polyglutamine (polyQ) tracts are a pathological hallmark of Huntington's disease (HD). The molecular mechanisms by which these structures are formed and cause neuronal dysfunction and toxicity are poorly understood. Here, we utilized available gene expression data sets of selected brain regions of HD patients and controls for systematic interaction network filtering in order to predict disease-relevant, brain region-specific HTT interaction partners. Starting from a large protein-protein interaction (PPI) data set, a step-by-step computational filtering strategy facilitated the generation of a focused PPI network that directly or indirectly connects 13 proteins potentially dysregulated in HD with the disease protein HTT. This network enabled the discovery of the neuron-specific protein CRMP1 that targets aggregation-prone, N-terminal HTT fragments and suppresses their spontaneous self-assembly into proteotoxic structures in various models of HD. Experimental validation indicates that our network filtering procedure provides a simple but powerful strategy to identify disease-relevant proteins that influence misfolding and aggregation of polyQ disease proteins.
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Affiliation(s)
| | - Yacine Bounab
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Nadine Strempel
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Sargon Yigit
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ralf P Friedrich
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Gautam Chaurasia
- Institute of Theoretical Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Shuang Li
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Franziska Hesse
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Jenny Russ
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Cecilia Nicoletti
- Department of Neuropsychiatry, Charité-Universitaetsmedizin Berlin, 10117 Berlin, Germany
| | - Annett Boeddrich
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Wiglenda
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Christian Haenig
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Sigrid Schnoegl
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - David Fournier
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Rona K Graham
- Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Michael R Hayden
- Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Stephan Sigrist
- Institute of Biology/Genetics, Free University Berlin, 14195 Berlin, Germany
| | - Gillian P Bates
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom
| | - Josef Priller
- Department of Neuropsychiatry, Charité-Universitaetsmedizin Berlin, 10117 Berlin, Germany
| | | | - Matthias E Futschik
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany; Centre for Molecular and Structural Biomedicine, Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal
| | - Erich E Wanker
- Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
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18
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Functional characterization of CDK5 and CDK5R1 mutations identified in patients with non-syndromic intellectual disability. J Hum Genet 2015; 61:283-93. [PMID: 26657932 DOI: 10.1038/jhg.2015.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/27/2015] [Accepted: 11/06/2015] [Indexed: 12/13/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) and cyclin-dependent kinase 5, regulatory subunit 1 (CDK5R1), encoding CDK5 activator p35, have a fundamental role in central nervous system (CNS) development and function, and are involved in the pathogenesis of several neurodegenerative disorders, thus constituting strong candidate genes for the onset of intellectual disability (ID). We carried out a mutation screening of CDK5 and CDK5R1 coding regions and CDK5R1 3'-UTR on a cohort of 360 patients with non-syndromic ID (NS-ID) using denaturing high performance liquid chromatography (DHPLC) and direct sequencing. We found one novel silent mutation in CDK5 and one novel silent mutation in CDK5R1 coding regions, three novel intronic variations in CDK5, not causing any splicing defect, and four novel heterozygous variations in CDK5R1 3'-UTR. None of these variations was present in 450 healthy controls and single-nucleotide polymorphism (SNP) databases. The functional study of CDK5R1 p.A108V mutation evidenced an impaired p35 cleavage by the calcium-dependent protease calpain. Moreover, luciferase constructs containing the CDK5R1 3'-UTR mutations showed altered gene expression levels. Eight known polymorphisms were also identified displaying different frequencies in NS-ID patients compared with the controls. In particular, the minor allele of CDK5R1 3'-UTR rs735555 polymorphism was associated with increased risk for NS-ID. In conclusion, our data suggest that mutations and polymorphisms in CDK5 and CDK5R1 genes may contribute to the onset of the NS-ID phenotype.
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19
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Sharma S, Taliyan R. Transcriptional dysregulation in Huntington's disease: The role of histone deacetylases. Pharmacol Res 2015; 100:157-69. [PMID: 26254871 DOI: 10.1016/j.phrs.2015.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 12/16/2022]
Abstract
Huntington's disease (HD) is a progressive neurological disorder for which there are no disease-modifying treatments. Although, the exact underlying mechanism(s) leading to the neural cell death in HD still remains elusive, the transcriptional dysregulation is a major molecular feature. Recently, the transcriptional activation and repression regulated by chromatin acetylation has been found to be impaired in HD pathology. The acetylation and deacetylation of histone proteins is carried out by opposing actions of histone acetyl-transferases and histone deacetylases (HDACs), respectively. Studies carried out in cell culture, yeast, Drosophila and rodent model(s) have indicated that HDAC inhibitors (HDACIs) might provide useful class of therapeutic agents for HD. Clinical trials have also reported the beneficial effects of HDACIs in patients suffering from HD. Therefore, the development of HDACIs as therapeutics for HD has been vigorously pursued. In this review, we highlight and summarize the putative role of HDACs in HD like pathology and further discuss the potential of HDACIs as new therapeutic avenues for the treatment of HD.
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Affiliation(s)
- Sorabh Sharma
- Neuropharmacology Division, Department of Pharmacy Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Rajeev Taliyan
- Neuropharmacology Division, Department of Pharmacy Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
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20
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Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME. StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Nucleic Acids Res 2015; 43:W72-7. [PMID: 26007653 PMCID: PMC4489266 DOI: 10.1093/nar/gkv529] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/10/2015] [Indexed: 11/25/2022] Open
Abstract
Stem cells present unique regenerative abilities, offering great potential for treatment of prevalent pathologies such as diabetes, neurodegenerative and heart diseases. Various research groups dedicated significant effort to identify sets of genes—so-called stemness signatures—considered essential to define stem cells. However, their usage has been hindered by the lack of comprehensive resources and easy-to-use tools. For this we developed StemChecker, a novel stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, Transcription Factor (TF) binding sites, literature reviews and computational approaches. StemChecker allows researchers to explore the presence of stemness signatures in user-defined gene sets, without carrying-out lengthy literature curation or data processing. To assist in exploring underlying regulatory mechanisms, we collected over 80 target gene sets of TFs associated with pluri- or multipotency. StemChecker presents an intuitive graphical display, as well as detailed statistical results in table format, which helps revealing transcriptionally regulatory programs, indicating the putative involvement of stemness-associated processes in diseases like cancer. Overall, StemChecker substantially expands the available repertoire of online tools, designed to assist the stem cell biology, developmental biology, regenerative medicine and human disease research community. StemChecker is freely accessible at http://stemchecker.sysbiolab.eu.
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Affiliation(s)
- José P Pinto
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Ravi K Kalathur
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Experimental and Clinical Cell Therapy Institute, Spinal Cord and Tissue Regeneration Center Salzburg, Paracelsus Medizinische Privatuniversität, Salzburg, A-5020, Austria
| | - Daniel V Oliveira
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Tânia Barata
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Rui S R Machado
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Susana Machado
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Ivette Pacheco-Leyva
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Isabel Duarte
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, 8005-139, Portugal
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Kalathur RKR, Giner-Lamia J, Machado S, Barata T, Ayasolla KRS, Futschik ME. The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach. F1000Res 2015; 4:103. [PMID: 26949515 PMCID: PMC4758378 DOI: 10.12688/f1000research.6358.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 12/22/2022] Open
Abstract
Huntington ´s disease (HD) is a progressive, neurodegenerative disease with a fatal outcome. Although the disease-causing gene (huntingtin) has been known for over 20 years, the exact mechanisms leading to neuronal cell death are still controversial. One potential mechanism contributing to the massive loss of neurons observed in the brain of HD patients could be the unfolded protein response (UPR) activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, persistent ER stress and an activated UPR can also cause apoptotic cell death. Although different studies have indicated a role for the UPR in HD, the evidence remains inconclusive. Here, we present extensive bioinformatic analyses that revealed UPR activation in different experimental HD models based on transcriptomic data. Accordingly, we have identified 53 genes, including RAB5A, HMGB1, CTNNB1, DNM1, TUBB, TSG101, EEF2, DYNC1H1, SLC12A5, ATG5, AKT1, CASP7 and SYVN1 that provide a potential link between UPR and HD. To further elucidate the potential role of UPR as a disease-relevant process, we examined its connection to apoptosis based on molecular interaction data, and identified a set of 40 genes including ADD1, HSP90B1, IKBKB, IKBKG, RPS3A and LMNB1, which seem to be at the crossroads between these two important cellular processes. Remarkably, we also found strong correlation of UPR gene expression with the length of the polyglutamine tract of Huntingtin, which is a critical determinant of age of disease onset in human HD patients pointing to the UPR as a promising target for therapeutic intervention. The study is complemented by a newly developed web-portal called UPR-HD (http://uprhd.sysbiolab.eu) that enables visualization and interactive analysis of UPR-associated gene expression across various HD models.
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Affiliation(s)
| | - Joaquin Giner-Lamia
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | - Susana Machado
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | - Tania Barata
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | | | - Matthias E Futschik
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal; Centre of Marine Sciences, University of Algarve, Faro, 8005-139, Portugal
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22
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Kalathur RKR, Giner-Lamia J, Machado S, Barata T, Ayasolla KRS, Futschik ME. The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach. F1000Res 2015; 4:103. [PMID: 26949515 PMCID: PMC4758378 DOI: 10.12688/f1000research.6358.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 09/26/2023] Open
Abstract
Huntington ´s disease (HD) is a progressive, neurodegenerative disease with a fatal outcome. Although the disease-causing gene (huntingtin) has been known for over 20 years, the exact mechanisms leading to neuronal cell death are still controversial. One potential mechanism contributing to the massive loss of neurons observed in the brain of HD patients could be the unfolded protein response (UPR) activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, persistent ER stress and an activated UPR can also cause apoptotic cell death. Although different studies have indicated a role for the UPR in HD, the evidence remains inconclusive. Here, we present extensive bioinformatic analyses that revealed UPR activation in different experimental HD models based on transcriptomic data. Accordingly, we have identified 53 genes, including RAB5A, HMGB1, CTNNB1, DNM1, TUBB, TSG101, EEF2, DYNC1H1, SLC12A5, ATG5, AKT1, CASP7 and SYVN1 that provide a potential link between UPR and HD. To further elucidate the potential role of UPR as a disease-relevant process, we examined its connection to apoptosis based on molecular interaction data, and identified a set of 40 genes including ADD1, HSP90B1, IKBKB, IKBKG, RPS3A and LMNB1, which seem to be at the crossroads between these two important cellular processes. Remarkably, we also found strong correlation of UPR gene expression with the length of the polyglutamine tract of Huntingtin, which is a critical determinant of age of disease onset in human HD patients pointing to the UPR as a promising target for therapeutic intervention. The study is complemented by a newly developed web-portal called UPR-HD (http://uprhd.sysbiolab.eu) that enables visualization and interactive analysis of UPR-associated gene expression across various HD models.
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Affiliation(s)
| | - Joaquin Giner-Lamia
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | - Susana Machado
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | - Tania Barata
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
| | | | - Matthias E. Futschik
- Centre for Biomedical Research, University of Algarve, Faro, 8005-139, Portugal
- Centre of Marine Sciences, University of Algarve, Faro, 8005-139, Portugal
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23
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Laprairie RB, Bagher AM, Precious SV, Denovan-Wright EM. Components of the endocannabinoid and dopamine systems are dysregulated in Huntington's disease: analysis of publicly available microarray datasets. Pharmacol Res Perspect 2015; 3:e00104. [PMID: 25692022 PMCID: PMC4317235 DOI: 10.1002/prp2.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/20/2014] [Accepted: 09/28/2014] [Indexed: 01/20/2023] Open
Abstract
The endocannabinoid system (ECS) and the dopaminergic system (DAS) are two major regulators of basal ganglia function. During Huntington's disease (HD) pathogenesis, the expression of genes in both the ECS and DAS is dysregulated. The purpose of this study was to determine the changes that were consistently observed in the ECS and DAS during HD progression in the central nervous system (CNS) and in the periphery in different models of HD and human HD tissue. To do this, we conducted a meta-analysis of differential gene expression in the ECS and DAS using publicly available microarray data. The consolidated data were summarized as observed changes in gene expression (OCGE) using a weighted sum for each gene. In addition, consolidated data were compared to previously published studies that were not available in the gene expression omnibus (GEO) database. The resulting data confirm gene expression changes observed using different approaches and provide novel insights into the consistency between changes observed in human tissue and various models, as well as disease stage- and tissue-specific transcriptional dysregulation in HD. The major implication of the systems-wide data presented here is that therapeutic strategies targeting the ECS or DAS must consider the dynamic changes in gene expression over time and in different body areas, which occur during HD progression and the interconnectedness of the two systems.
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Affiliation(s)
- Robert B Laprairie
- Department of Pharmacology, Dalhousie UniversityHalifax, NS, Canada, B3H 4R2
| | - Amina M Bagher
- Department of Pharmacology, Dalhousie UniversityHalifax, NS, Canada, B3H 4R2
| | - Sophie V Precious
- Department of Pharmacology, Dalhousie UniversityHalifax, NS, Canada, B3H 4R2
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24
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Mason RP, Breda C, Kooner GS, Mallucci GR, Kyriacou CP, Giorgini F. Modeling Huntington Disease in Yeast and Invertebrates. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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25
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Hill R, Kalathur RKR, Callejas S, Colaço L, Brandão R, Serelde B, Cebriá A, Blanco-Aparicio C, Pastor J, Futschik M, Dopazo A, Link W. A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes. Breast Cancer Res 2014; 16:482. [PMID: 25488803 PMCID: PMC4303209 DOI: 10.1186/s13058-014-0482-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/14/2014] [Indexed: 02/01/2023] Open
Abstract
Introduction The activation of the phosphoinositide 3-kinase (PI3K)/AKT signalling pathway is one the most frequent genetic events in breast cancer, consequently the development of PI3K inhibitors has attracted much attention. Here we evaluate the effect of PI3K inhibition on global gene expression in breast cancer cells. Methods We used a range of methodologies that include in silico compound analysis, in vitro kinase assays, cell invasion assays, proliferation assays, genome-wide transcription studies (Agilent Technologies full genome arrays), gene set enrichment analysis, quantitative real-time PCR, immunoblotting in addition to chromatin immunoprecipitation. Results We defined the physico-chemical and the biological properties of ETP-45658, a novel potent PI3K inhibitor. We demonstrated that ETP-45658 potently inhibited cell proliferation within a broad range of human cancer cells, most potently suppressing the growth of breast cancer cells via inhibiting cell cycle. We show that this response is Forkhead box O (FOXO) protein dependent and p53 independent. Our genome-wide microarray analysis revealed that the cell cycle was the most affected biological process after exposure to ETP-45658 (or our control PI3K inhibitor PI-103), that despite the multiple transcription factors that are regulated by the PI3K/AKT signalling cascade, only the binding sites for FOXO transcription factors were significantly enriched and only a subset of all FOXO-dependent genes were induced. This disparity in gene transcription was not due to differential FOXO promoter recruitment. Conclusions The constitutive activation of PI3Ks and thus the exclusion of FOXO transcription factors from the nucleus is a key feature of breast cancer. Our results presented here highlight that PI3K inhibition activates specific FOXO-dependent genes that mediate cell cycle arrest in breast cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0482-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Hill
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Regenerative Medicine Program, Department of Biomedical Sciences and Medicine, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Ravi Kiran Reddy Kalathur
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Sergio Callejas
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Laura Colaço
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Ricardo Brandão
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Beatriz Serelde
- Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Antonio Cebriá
- Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Carmen Blanco-Aparicio
- Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Joaquín Pastor
- Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Matthias Futschik
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle de Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Wolfgang Link
- IBB-Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine (CBME), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Regenerative Medicine Program, Department of Biomedical Sciences and Medicine, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
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26
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Müller S. In silico analysis of regulatory networks underlines the role of miR-10b-5p and its target BDNF in huntington's disease. Transl Neurodegener 2014; 3:17. [PMID: 25210621 PMCID: PMC4160136 DOI: 10.1186/2047-9158-3-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/13/2014] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play various roles during central nervous system development. MicroRNAs (miRNAs) are a class of ncRNAs that exert their function together with argonaute proteins by post-transcriptional gene silencing of messenger RNAs (mRNAs). Several studies provide evidence for alterations in miRNA expression in patients with neurodegenerative diseases. Among these is huntington's disease (HD), a dominantly inherited fatal disorder characterized by deregulation of neuronal-specific mRNAs as well as miRNAs. Recently, next-generation sequencing (NGS) miRNA profiles from human HD and neurologically normal control brain tissues were reported. Five consistently upregulated miRNAs affect the expression of genes involved in neuronal differentiation, neurite outgrowth, cell death and survival. We re-analyzed the NGS data publicly available in array express and detected nineteen additional differentially expressed miRNAs. Subsequently, we connected these miRNAs to genes implicated in HD development and network analysis pointed to miRNA-mediated downregulation of twenty-two genes with roles in the pathogenesis as well as treatment of the disease. In silico prediction and reporter systems prove that levels of BDNF, a central node in the miRNA-mRNA regulatory network, can be post-transcriptionally controlled by upregulated miR-10b-5p and miR-30a-5p. Reduced BDNF expression is associated with neuronal dysfunction and death in HD. Moreover, the 3'UTR of CREB1 harbors a predicted binding site for these two miRNAs. CREB1 is similarly downregulated in HD and overexpression decreased susceptibility to 3-nitropropionic-induced toxicity in a cell model. In contradiction to these observations, it is presumed that miR-10b-5p upregulation in HD exerts a neuroprotective role in response to the mutation in the huntingtin gene. Therefore, the function of miR-10b-5p and especially its effect on BDNF expression in HD requires further academic research.
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Affiliation(s)
- Sören Müller
- Molecular BioSciences, University of Frankfurt, Marie-Curie-Str.9, 60439 Frankfurt a.M., Germany
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27
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Pinto JP, Reddy Kalathur RK, Machado RSR, Xavier JM, Bragança J, Futschik ME. StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. Nucleic Acids Res 2014; 42:W154-60. [PMID: 24852251 PMCID: PMC4086070 DOI: 10.1093/nar/gku455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Stem cells are characterized by their potential for self-renewal and their
capacity to differentiate into mature cells. These two key features emerge
through the interplay of various factors within complex molecular networks. To
provide researchers with a dedicated tool to investigate these networks, we have
developed StemCellNet, a versatile web server for interactive network analysis
and visualization. It rapidly generates focused networks based on a large
collection of physical and regulatory interactions identified in human and
murine stem cells. The StemCellNet web-interface has various easy-to-use tools
for selection and prioritization of network components, as well as for
integration of expression data provided by the user. As a unique feature, the
networks generated can be screened against a compendium of stemness-associated
genes. StemCellNet can also indicate novel candidate genes by evaluating their
connectivity patterns. Finally, an optional dataset of generic interactions,
which provides large coverage of the human and mouse proteome, extends the
versatility of StemCellNet to other biomedical research areas in which stem
cells play important roles, such as in degenerative diseases or cancer. The
StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.
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Affiliation(s)
- José P Pinto
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal
| | - Ravi Kiran Reddy Kalathur
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal
| | - Rui S R Machado
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal
| | - Joana M Xavier
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal
| | - José Bragança
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Algarve 8005-139, Portugal
| | - Matthias E Futschik
- Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal Centre of Marine Science, University of Algarve, Faro, Algarve 8005-139, Portugal
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28
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Marchina E, Misasi S, Bozzato A, Ferraboli S, Agosti C, Rozzini L, Borsani G, Barlati S, Padovani A. Gene expression profile in fibroblasts of Huntington's disease patients and controls. J Neurol Sci 2013; 337:42-6. [PMID: 24296361 DOI: 10.1016/j.jns.2013.11.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/19/2013] [Accepted: 11/11/2013] [Indexed: 01/08/2023]
Abstract
Huntington's disease is an inherited disorder caused by expanded stretch of consecutive trinucleotides (cytosine-adenosine-guanine, CAG) within the first exon of the huntingtin (HTT) gene on chromosome 4 (p16.3). The mutated huntingtin (mHTT) gains toxic function, probably through mechanisms that involve aberrant interactions in several pathways, causing cytotoxicity. Pathophysiology of disease involves several tissues; indeed it has been shown that there is a broad toxic effect of mHTT in the peripheral tissue of patients with HD, not only in the central nervous system. In this study we compared gene expression profiles (GEP) of HD fibroblasts and matched controls using microarray technology. We used RT-PCR to test the consistency of the microarray data and we found four genes up-regulated in HD patients with respect to control individuals. The genes appear to be involved in different pathways that have been shown to be perturbed even in HD models and patients. Although our study is preliminary and has to be extended to a larger cohort of HD patients and controls, nevertheless it shows that gene expression profiles seem to be altered in the fibroblasts of HD patients. Validation of the differential expressions at the protein level is required to ascertain if this cell type can be considered a suitable model for the identification of HD biomarkers.
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Affiliation(s)
- Eleonora Marchina
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Silvia Misasi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Bozzato
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Ferraboli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Chiara Agosti
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Luca Rozzini
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Barlati
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandro Padovani
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
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29
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de Oliveira GP, Alves CJ, Chadi G. Early gene expression changes in spinal cord from SOD1(G93A) Amyotrophic Lateral Sclerosis animal model. Front Cell Neurosci 2013; 7:216. [PMID: 24302897 PMCID: PMC3831149 DOI: 10.3389/fncel.2013.00216] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/29/2013] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is an adult-onset and fast progression neurodegenerative disease that leads to the loss of motor neurons. Mechanisms of selective motor neuron loss in ALS are unknown. The early events occurring in the spinal cord that may contribute to motor neuron death are not described, neither astrocytes participation in the pre-symptomatic phases of the disease. In order to identify ALS early events, we performed a microarray analysis employing a whole mouse genome platform to evaluate the gene expression pattern of lumbar spinal cords of transgenic SOD1G93A mice and their littermate controls at pre-symptomatic ages of 40 and 80 days. Differentially expressed genes were identified by means of the Bioconductor packages Agi4×44Preprocess and limma. FunNet web based tool was used for analysis of over-represented pathways. Furthermore, immunolabeled astrocytes from 40 and 80 days old mice were submitted to laser microdissection and RNA was extracted for evaluation of a selected gene by qPCR. Statistical analysis has pointed to 492 differentially expressed genes (155 up and 337 down regulated) in 40 days and 1105 (433 up and 672 down) in 80 days old ALS mice. KEGG analysis demonstrated the over-represented pathways tight junction, antigen processing and presentation, oxidative phosphorylation, endocytosis, chemokine signaling pathway, ubiquitin mediated proteolysis and glutamatergic synapse at both pre-symptomatic ages. Ube2i gene expression was evaluated in astrocytes from both transgenic ages, being up regulated in 40 and 80 days astrocytes enriched samples. Our data points to important early molecular events occurring in pre-symptomatic phases of ALS in mouse model. Early SUMOylation process linked to astrocytes might account to non-autonomous cell toxicity in ALS. Further studies on the signaling pathways presented here may provide new insights to better understand the events triggering motor neuron death in this devastating disorder.
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Affiliation(s)
- Gabriela P de Oliveira
- Department of Neurology, Neuroregeneration Center, University of São Paulo School of Medicine São Paulo, Brazil
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30
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Lauterbach EC. Neuroprotective effects of psychotropic drugs in Huntington's disease. Int J Mol Sci 2013; 14:22558-603. [PMID: 24248060 PMCID: PMC3856079 DOI: 10.3390/ijms141122558] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 02/06/2023] Open
Abstract
Psychotropics (antipsychotics, mood stabilizers, antidepressants, anxiolytics, etc.) are commonly prescribed to treat Huntington’s disease (HD). In HD preclinical models, while no psychotropic has convincingly affected huntingtin gene, HD modifying gene, or huntingtin protein expression, psychotropic neuroprotective effects include upregulated huntingtin autophagy (lithium), histone acetylation (lithium, valproate, lamotrigine), miR-222 (lithium-plus-valproate), mitochondrial protection (haloperidol, trifluoperazine, imipramine, desipramine, nortriptyline, maprotiline, trazodone, sertraline, venlafaxine, melatonin), neurogenesis (lithium, valproate, fluoxetine, sertraline), and BDNF (lithium, valproate, sertraline) and downregulated AP-1 DNA binding (lithium), p53 (lithium), huntingtin aggregation (antipsychotics, lithium), and apoptosis (trifluoperazine, loxapine, lithium, desipramine, nortriptyline, maprotiline, cyproheptadine, melatonin). In HD live mouse models, delayed disease onset (nortriptyline, melatonin), striatal preservation (haloperidol, tetrabenazine, lithium, sertraline), memory preservation (imipramine, trazodone, fluoxetine, sertraline, venlafaxine), motor improvement (tetrabenazine, lithium, valproate, imipramine, nortriptyline, trazodone, sertraline, venlafaxine), and extended survival (lithium, valproate, sertraline, melatonin) have been documented. Upregulated CREB binding protein (CBP; valproate, dextromethorphan) and downregulated histone deacetylase (HDAC; valproate) await demonstration in HD models. Most preclinical findings await replication and their limitations are reviewed. The most promising findings involve replicated striatal neuroprotection and phenotypic disease modification in transgenic mice for tetrabenazine and for sertraline. Clinical data consist of an uncontrolled lithium case series (n = 3) suggesting non-progression and a primarily negative double-blind, placebo-controlled clinical trial of lamotrigine.
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Affiliation(s)
- Edward C Lauterbach
- Department of Psychiatry and Behavioral Sciences, Mercer University School of Medicine, 655 First Street, Macon, GA 31201, USA.
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31
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Kocerha J, Liu Y, Willoughby D, Chidamparam K, Benito J, Nelson K, Xu Y, Chi T, Engelhardt H, Moran S, Yang SH, Li SH, Li XJ, Larkin K, Neumann A, Banta H, Yang JJ, Chan AWS. Longitudinal transcriptomic dysregulation in the peripheral blood of transgenic Huntington's disease monkeys. BMC Neurosci 2013; 14:88. [PMID: 23957861 PMCID: PMC3751855 DOI: 10.1186/1471-2202-14-88] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/14/2013] [Indexed: 12/30/2022] Open
Abstract
Background Huntington’s Disease (HD) is a progressive neurodegenerative disorder caused by an expansion in the polyglutamine (polyQ) region of the Huntingtin (HTT) gene. The clinical features of HD are characterized by cognitive, psychological, and motor deficits. Molecular instability, a core component in neurological disease progression, can be comprehensively evaluated through longitudinal transcriptomic profiling. Development of animal models amenable to longitudinal examination enables distinct disease-associated mechanisms to be identified. Results Here we report the first longitudinal study of transgenic monkeys with genomic integration of various lengths of the human HTT gene and a range of polyQ repeats. With this unique group of transgenic HD nonhuman primates (HD monkeys), we profiled over 47,000 transcripts from peripheral blood collected over a 2 year timespan from HD monkeys and age-matched wild-type control monkeys. Conclusions Messenger RNAs with expression patterns which diverged with disease progression in the HD monkeys considerably facilitated our search for transcripts with diagnostic or therapeutic potential in the blood of human HD patients, opening up a new avenue for clinical investigation.
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32
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Ellrichmann G, Reick C, Saft C, Linker RA. The role of the immune system in Huntington's disease. Clin Dev Immunol 2013; 2013:541259. [PMID: 23956761 PMCID: PMC3727178 DOI: 10.1155/2013/541259] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/19/2013] [Indexed: 01/19/2023]
Abstract
Huntington's disease (HD) is characterized by a progressive course of disease until death 15-20 years after the first symptoms occur and is caused by a mutation with expanded CAG repeats in the huntingtin (htt) protein. Mutant htt (mhtt) in the striatum is assumed to be the main reason for neurodegeneration. Knowledge about pathophysiology has rapidly improved discussing influences of excitotoxicity, mitochondrial damage, free radicals, and inflammatory mechanisms. Both innate and adaptive immune systems may play an important role in HD. Activation of microglia with expression of proinflammatory cytokines, impaired migration of macrophages, and deposition of complement factors in the striatum indicate an activation of the innate immune system. As part of the adaptive immune system, dendritic cells (DCs) prime T-cell responses secreting inflammatory mediators. In HD, DCs may contain mhtt which brings the adaptive immune system into the focus of interest. These data underline an increasing interest in the peripheral immune system for pathomechanisms of HD. It is still unclear if neuroinflammation is a reactive process or if there is an active influence on disease progression. Further understanding the influence of inflammation in HD using mouse models may open various avenues for promising therapeutic approaches aiming at slowing disease progression or forestalling onset of disease.
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Affiliation(s)
- Gisa Ellrichmann
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, 44791 Bochum, Germany.
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