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Maier A, Hartung M, Abovsky M, Adamowicz K, Bader G, Baier S, Blumenthal D, Chen J, Elkjaer M, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico A, Pillich R, Poschenrieder J, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J. Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Res 2024; 52:W481-W488. [PMID: 38783119 PMCID: PMC11223884 DOI: 10.1093/nar/gkae388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.
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Affiliation(s)
- Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Mark Abovsky
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Sylvie Baier
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - David B Blumenthal
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Jing Chen
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maria L Elkjaer
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Mohamed Helmy
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Canada
- School of Public Health, University of Saskatchewan, Canada
- Department of Computer Science, University of Saskatchewan, Canada
- Department of Computer Science, Lakehead University, Canada
- Department of Computer Science, Idaho State University, USA
- Bioinformatics Institute (BII), A*STAR, Singapore
| | - Markus Hoffmann
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, USA
| | - Igor Jurisica
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Max Kotlyar
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
| | - Olga Lazareva
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Hagai Levi
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Sebastian Lobentanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quirin Manz
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Julian Matschinske
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Miles Mee
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Chiara Pastrello
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158 California, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Julian M Poschenrieder
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nataša Pržulj
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Department of Computer Science, University College London, London WC1E 6BT, UK
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Sepideh Sadegh
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Suryadipto Sarkar
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Gideon Shaked
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Nico Trummer
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ugur Turhan
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Rui-Sheng Wang
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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Ward C, Nasrallah K, Tran D, Sabri E, Vazquez A, Sjulson L, Castillo PE, Batista-Brito R. Developmental Disruption of Mef2c in Medial Ganglionic Eminence-derived cortical inhibitory interneurons impairs cellular and circuit function. Biol Psychiatry 2024:S0006-3223(24)01360-X. [PMID: 38848814 DOI: 10.1016/j.biopsych.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND MEF2C is strongly linked to various neurodevelopmental disorders (NDDs) including autism, intellectual disability, schizophrenia, and attention-deficit/hyperactivity. Mice constitutively lacking one copy of Mef2c, or selectively lacking both copies of Mef2c in cortical excitatory neurons, display a variety of behavioral phenotypes associated with NDDs. The MEF2C protein is a transcription factor necessary for cellular development and synaptic modulation of excitatory neurons. MEF2C is also expressed in a subset of cortical GABAergic inhibitory neurons, but its function in those cell types remains largely unknown. METHODS Using conditional deletions of the Mef2c gene in mice, we investigated the role of MEF2C in Parvalbumin-expressing Interneurons (PV-INs), the largest subpopulation of cortical GABAergic cells, at two developmental timepoints. We performed slice electrophysiology, in vivo recordings, and behavior assays to test how embryonic and late postnatal loss of MEF2C from GABAergic interneurons impacts their survival and maturation, and alters brain function and behavior. RESULTS Loss of MEF2C from PV-INs during embryonic, but not late postnatal, development resulted in reduced PV-IN number and failure of PV-INs to molecularly and synaptically mature. In association with these deficits, early loss of MEF2C in GABAergic interneurons lead to abnormal cortical network activity, hyperactive and stereotypic behavior, and impaired cognitive and social behavior. CONCLUSIONS MEF2C expression is critical for the development of cortical GABAergic interneurons, particularly PV-INs. Embryonic loss of function of MEF2C mediates dysfunction of GABAergic interneurons, leading to altered in vivo patterns of cortical activity and behavioral phenotypes associated with neurodevelopmental disorders.
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Affiliation(s)
- Claire Ward
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Kaoutsar Nasrallah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; Department of Biological Sciences, Fordham University, 441 E. Fordham Road, Bronx, NY 10458
| | - Duy Tran
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Ehsan Sabri
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Arenski Vazquez
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Lucas Sjulson
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Renata Batista-Brito
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461.
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Dai X, Lin A, Zhuang L, Zeng Q, Cai L, Wei Y, Liang H, Gao W, Zhang J, Chen X. Targeting SIK3 to modulate hippocampal synaptic plasticity and cognitive function by regulating the transcription of HDAC4 in a mouse model of Alzheimer's disease. Neuropsychopharmacology 2024; 49:942-952. [PMID: 38057370 PMCID: PMC11039747 DOI: 10.1038/s41386-023-01775-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Cognitive deterioration and memory decline associated with the progression of Alzheimer's disease (AD) primarily results from synaptic failure. However, current understanding of the upstream regulatory mechanisms controlling synaptic plasticity remains limited. Salt-inducible kinase 3 (SIK3) is central to the signal pathway and is involved in neuronal regulation of sleep duration in mice. We speculated that the SIK3 cascade signaling pathway might contribute to the pathogenesis of AD. Thus, the present study employed AD transgenic mouse models, Morris Water Maze, virus-mediated gene transfer, electrophysiology, co-immunoprecipitation, western blotting, quantitative polymerase chain reaction, immunofluorescence, ChIP-qPCR, Golgi-Cox staining and dendritic spine analysis to investigate this connection. Our results revealed that SIK3 mRNA/protein expression was significantly reduced in middle-aged AD transgenic mouse models and AD patients. Conditional deletion of SIK3 gene in dorsal hippocampal neurons of 5×FAD mice further accelerated cognitive deterioration and impaired synaptic plasticity. In hippocampal neuronal cultures, SIK3 formed a complex with HDAC4, directly phosphorylated HDAC4 and regulated its nuclear cytoplasmic shuttle. Overexpression of SIK3 could facilitate the expression of synaptic plasticity-related genes by directly repressing mef2c or involving the recruitment of histone deacetylase to promoter regions of target genes through regulation of p-HDAC4, and vice versa. Moreover, up-regulation of SLP-S, the truncated fragment of SIK3, in dorsal hippocampal neurons, restored the synaptic plasticity and alleviates the cognitive impairment in 5×FAD mice. Collectively, these findings revealed a novel and important role of SIK3-HDAC4 regulation of synaptic plasticity and propose a new target for therapeutic approaches of cognitive deficits associated with AD.
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Affiliation(s)
- Xiaoman Dai
- Department of Neurology and Geriatrics, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China
| | - Anlan Lin
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China
| | - Lvping Zhuang
- Department of Neurology and Geriatrics, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, China
| | - Qingyong Zeng
- Department of Neurology and Geriatrics, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, China
| | - Lili Cai
- Department of Neurology and Geriatrics, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, China
| | - Yuanxiang Wei
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China
| | - Hongjie Liang
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China
| | - Weijie Gao
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China
| | - Jing Zhang
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China.
| | - Xiaochun Chen
- Department of Neurology and Geriatrics, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, China.
- Fujian Key Laboratory of Molecular Neurology, Fujian Key Laboratory of Vascular Aging, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian, 350001, China.
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