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Akgüller Ö, Balcı MA, Cioca G. A Multi-Modal Graph Neural Network Framework for Parkinson's Disease Therapeutic Discovery. Int J Mol Sci 2025; 26:4453. [PMID: 40362692 PMCID: PMC12072649 DOI: 10.3390/ijms26094453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2025] [Revised: 04/26/2025] [Accepted: 05/02/2025] [Indexed: 05/15/2025] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disorder lacking effective disease-modifying treatments. In this study, we integrated large-scale protein-protein interaction networks with a multi-modal graph neural network (GNN) to identify and prioritize multi-target drug repurposing candidates for PD. Network analysis and advanced clustering methods delineated functional modules, and a novel Functional Centrality Index was employed to pinpoint key nodes within the PD interactome. The GNN model, incorporating molecular descriptors, network topology, and uncertainty quantification, predicted candidate drugs that simultaneously target critical proteins implicated in lysosomal dysfunction, mitochondrial impairment, synaptic disruption, and neuroinflammation. Among the top hits were compounds such as dithiazanine, ceftolozane, DL-α-tocopherol, bromisoval, imidurea, medronic acid, and modufolin. These findings provide mechanistic insights into PD pathology and demonstrate that a polypharmacology approach can reveal repurposing opportunities for existing drugs. Our results highlight the potential of network-based deep learning frameworks to accelerate the discovery of multi-target therapies for PD and other multifactorial neurodegenerative diseases.
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Affiliation(s)
- Ömer Akgüller
- Faculty of Science, Department of Mathematics, Mugla Sitki Kocman University, Mugla 48000, Turkey;
| | - Mehmet Ali Balcı
- Faculty of Science, Department of Mathematics, Mugla Sitki Kocman University, Mugla 48000, Turkey;
| | - Gabriela Cioca
- Faculty of Medicine, Preclinical Department, Lucian Blaga University of Sibiu, 550024 Sibiu, Romania;
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Dou L, Xu Z, Xu J, Zang C, Su C, Pieper AA, Leverenz JB, Wang F, Zhu X, Cummings J, Cheng F. A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson's disease. NPJ Parkinsons Dis 2025; 11:22. [PMID: 39837893 PMCID: PMC11751448 DOI: 10.1038/s41531-025-00870-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 01/06/2025] [Indexed: 01/23/2025] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. However, current treatments only manage symptoms and lack the ability to slow or prevent disease progression. We utilized a systems genetics approach to identify potential risk genes and repurposable drugs for PD. First, we leveraged non-coding genome-wide association studies (GWAS) loci effects on five types of brain-specific quantitative trait loci (xQTLs, including expression, protein, splicing, methylation and histone acetylation) under the protein-protein interactome (PPI) network. We then prioritized 175 PD likely risk genes (pdRGs), such as SNCA, CTSB, LRRK2, DGKQ, and CD44, which are enriched in druggable targets and differentially expressed genes across multiple human brain-specific cell types. Integrating network proximity-based drug repurposing and patient electronic health record (EHR) data observations, we identified Simvastatin as being significantly associated with reduced incidence of PD (hazard ratio (HR) = 0.91 for fall outcome, 95% confidence interval (CI): 0.87-0.94; HR = 0.88 for dementia outcome, 95% CI: 0.86-0.89) after adjusting for 267 covariates. In summary, our network-based systems genetics framework identifies potential risk genes and repurposable drugs for PD and other neurodegenerative diseases if broadly applied.
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Affiliation(s)
- Lijun Dou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Zhenxing Xu
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Jielin Xu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Chengxi Zang
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Chang Su
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Andrew A Pieper
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH, USA
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, 44106, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - James B Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, Kirk Kerkorian School of Medicine, UNLV, Las Vegas, NV, 89154, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA.
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Dou L, Xu Z, Xu J, Su C, Pieper AA, Zhu X, Leverenz JB, Wang F, Cummings J, Cheng F. A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson's disease. RESEARCH SQUARE 2024:rs.3.rs-4869009. [PMID: 39483867 PMCID: PMC11527220 DOI: 10.21203/rs.3.rs-4869009/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. However, current treatments are directed at symptoms and lack ability to slow or prevent disease progression. Large-scale genome-wide association studies (GWAS) have identified numerous genomic loci associated with PD, which may guide the development of disease-modifying treatments. We presented a systems genetics approach to identify potential risk genes and repurposable drugs for PD. First, we leveraged non-coding GWAS loci effects on multiple human brain-specific quantitative trait loci (xQTLs) under the protein-protein interactome (PPI) network. We then prioritized a set of PD likely risk genes (pdRGs) by integrating five types of molecular xQTLs: expression (eQTLs), protein (pQTLs), splicing (sQTLs), methylation (meQTLs), and histone acetylation (haQTLs). We also integrated network proximity-based drug repurposing and patient electronic health record (EHR) data observations to propose potential drug candidates for PD treatments. We identified 175 pdRGs from QTL-regulated GWAS findings, such as SNCA, CTSB, LRRK2, DGKQ, CD38 and CD44. Multi-omics data validation revealed that the identified pdRGs are likely to be druggable targets, differentially expressed in multiple cell types and impact both the parkin ubiquitin-proteasome and alpha-synuclein (a-syn) pathways. Based on the network proximity-based drug repurposing followed by EHR data validation, we identified usage of simvastatin as being significantly associated with reduced incidence of PD (fall outcome: hazard ratio (HR) = 0.91, 95% confidence interval (CI): 0.87-0.94; for dementia outcome: HR = 0.88, 95% CI: 0.86-0.89), after adjusting for 267 covariates. Our network-based systems genetics framework identifies potential risk genes and repurposable drugs for PD and other neurodegenerative diseases if broadly applied.
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Affiliation(s)
- Lijun Dou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhenxin Xu
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Jielin Xu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Chang Su
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Andrew A. Pieper
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH, USA
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - James B. Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, UNLV, Las Vegas, Nevada 89154, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
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Gerasimova T, Poberezhniy D, Nenasheva V, Stepanenko E, Arsenyeva E, Novosadova L, Grivennikov I, Illarioshkin S, Lagarkova M, Tarantul V, Novosadova E. Inflammatory Intracellular Signaling in Neurons Is Influenced by Glial Soluble Factors in iPSC-Based Cell Model of PARK2-Associated Parkinson's Disease. Int J Mol Sci 2024; 25:9621. [PMID: 39273568 PMCID: PMC11395490 DOI: 10.3390/ijms25179621] [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: 07/22/2024] [Revised: 08/20/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Neuroinflammation is considered to be one of the driving factors in Parkinson's disease (PD). This study was conducted using neuronal and glial cell cultures differentiated from induced pluripotent stem cells (iPSC) of healthy donors (HD) and PD patients with different PARK2 mutations (PD). Based on the results of RNA sequencing, qPCR and ELISA, we revealed transcriptional and post-transcriptional changes in HD and PD neurons cultivated in HD and PD glial-conditioned medium. We demonstrated that if one or both of the components of the system, neurons or glia, is Parkin-deficient, the interaction resulted in the down-regulation of a number of key genes related to inflammatory intracellular pathways and negative regulation of apoptosis in neurons, which might be neuroprotective. In PD neurons, the stress-induced up-regulation of APLNR was significantly stronger compared to HD neurons and was diminished by glial soluble factors, both HD and PD. PD neurons in PD glial conditioned medium increased APLN expression and also up-regulated apelin synthesis and release into intracellular fluid, which represented another compensatory action. Overall, the reported results indicate that neuronal self-defense mechanisms contribute to cell survival, which might be characteristic of PD patients with Parkin-deficiency.
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Affiliation(s)
- Tatiana Gerasimova
- Laboratory of Translative Biomedicine, Lopukhin Federal Research and Clinical Center of Physical–Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Daniil Poberezhniy
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Valentina Nenasheva
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Ekaterina Stepanenko
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Elena Arsenyeva
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Lyudmila Novosadova
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Igor Grivennikov
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | | | - Maria Lagarkova
- Laboratory of Translative Biomedicine, Lopukhin Federal Research and Clinical Center of Physical–Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Vyacheslav Tarantul
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
| | - Ekaterina Novosadova
- Laboratory of Molecular Neurogenetics and Innate Immunity, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (D.P.); (E.S.); (E.A.); (L.N.); (I.G.); (V.T.); (E.N.)
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Lee H, Jeon J, Jung D, Won JI, Kim K, Kim YJ, Yoon J. RelCurator: a text mining-based curation system for extracting gene-phenotype relationships specific to neurodegenerative disorders. Genes Genomics 2023; 45:1025-1036. [PMID: 37300788 DOI: 10.1007/s13258-023-01405-6] [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: 03/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The identification of gene-phenotype relationships is important in medical genetics as it serves as a basis for precision medicine. However, most of the gene-phenotype relationship data are buried in the biomedical literature in textual form. OBJECTIVE We propose RelCurator, a curation system that extracts sentences including both gene and phenotype entities related to specific disease categories from PubMed articles, provides rich additional information such as entity taggings, and predictions of gene-phenotype relationships. METHODS We targeted neurodegenerative disorders and developed a deep learning model using Bidirectional Gated Recurrent Unit (BiGRU) networks and BioWordVec word embeddings for predicting gene-phenotype relationships from biomedical texts. The prediction model is trained with more than 130,000 labeled PubMed sentences including gene and phenotype entities, which are related to or unrelated to neurodegenerative disorders. RESULTS We compared the performance of our deep learning model with those of Bidirectional Encoder Representations from Transformers (BERT), Support Vector Machine (SVM), and simple Recurrent Neural Network (simple RNN) models. Our model performed better with an F1-score of 0.96. Furthermore, the evaluation done using a few curation cases in the real scenario showed the effectiveness of our work. Therefore, we conclude that RelCurator can identify not only new causative genes, but also new genes associated with neurodegenerative disorders' phenotype. CONCLUSION RelCurator is a user-friendly method for accessing deep learning-based supporting information and a concise web interface to assist curators while browsing the PubMed articles. Our curation process represents an important and broadly applicable improvement to the state of the art for the curation of gene-phenotype relationships.
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Affiliation(s)
- Heonwoo Lee
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Junbeom Jeon
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Dawoon Jung
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Jung-Im Won
- Center for Innovation in Engineering Education, Hanyang University, Seoul, Republic of Korea
| | - Kiyong Kim
- Department of Electronic Engineering, Kyonggi University, Suwon, Republic of Korea
| | - Yun Joong Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Neurology, Yongin Severance Hospital, Yonsei University College of Medicine, Yonsei University Health System, Yongin, Gyeonggi-do, 16995, Republic of Korea.
| | - Jeehee Yoon
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea.
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