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Oviya IR, Sankar D, Manoharan S, Prabahar A, Raja K. Comorbidity-Guided Text Mining and Omics Pipeline to Identify Candidate Genes and Drugs for Alzheimer's Disease. Genes (Basel) 2024; 15:614. [PMID: 38790243 PMCID: PMC11121575 DOI: 10.3390/genes15050614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Alzheimer's disease (AD), a multifactorial neurodegenerative disorder, is prevalent among the elderly population. It is a complex trait with mutations in multiple genes. Although the US Food and Drug Administration (FDA) has approved a few drugs for AD treatment, a definitive cure remains elusive. Research efforts persist in seeking improved treatment options for AD. Here, a hybrid pipeline is proposed to apply text mining to identify comorbid diseases for AD and an omics approach to identify the common genes between AD and five comorbid diseases-dementia, type 2 diabetes, hypertension, Parkinson's disease, and Down syndrome. We further identified the pathways and drugs for common genes. The rationale behind this approach is rooted in the fact that elderly individuals often receive multiple medications for various comorbid diseases, and an insight into the genes that are common to comorbid diseases may enhance treatment strategies. We identified seven common genes-PSEN1, PSEN2, MAPT, APP, APOE, NOTCH, and HFE-for AD and five comorbid diseases. We investigated the drugs interacting with these common genes using LINCS gene-drug perturbation. Our analysis unveiled several promising candidates, including MG-132 and Masitinib, which exhibit potential efficacy for both AD and its comorbid diseases. The pipeline can be extended to other diseases.
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Affiliation(s)
- Iyappan Ramalakshmi Oviya
- Department of Computer Science and Engineering, Amrita School of Computing, Amrita Vishwa Vidyapeetham, Chennai 641112, India;
| | - Divya Sankar
- Department of Sciences, Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Chennai 601103, India;
| | - Sharanya Manoharan
- Department of Bioinformatics, Stella Maris College, Chennai 600086, India;
| | - Archana Prabahar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences (BGES), Cleveland State University, Cleveland, OH 44115, USA;
| | - Kalpana Raja
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
- Section for Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, CT 06510, USA
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Chen CY, Lin YS, Lee WJ, Liao YC, Kuo YS, Yang AC, Fuh JL. Endophenotypic effects of the SORL1 variant rs2298813 on regional brain volume in patients with late-onset Alzheimer’s disease. Front Aging Neurosci 2022; 14:885090. [PMID: 35992588 PMCID: PMC9389408 DOI: 10.3389/fnagi.2022.885090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction: Two common variants of sortilin-related receptor 1 gene (SORL1), rs2298813 and rs1784933, have been associated with late-onset Alzheimer’s disease (AD) in the Han Chinese population in Taiwan. However, neuroimaging correlates of these two SORL1 variants remain unknown. We aimed to determine whether the two SORL1 polymorphisms were associated with any volumetric differences in brain regions in late-onset AD patients. Methods: We recruited 200 patients with late-onset AD from Taipei Veterans General Hospital. All patients received a structural magnetic resonance (MR) imaging brain scan and completed a battery of neurocognitive tests at enrollment. We followed up to assess changes in Mini-Mental State Examination (MMSE) scores in 155 patients (77.5%) at an interval of 2 years. Volumetric measures and cortical thickness of various brain regions were performed using FreeSurfer. Regression analysis controlled for apolipoprotein E status. Multiple comparisons were corrected for using the false discovery rate. Results: The homozygous major allele of rs2298813 was associated with larger volumes in the right putamen (p = 0.0442) and right pallidum (p = 0.0346). There was no link between the rs1784933 genotypes with any regional volume or thickness of the brain. In the rs2298813 homozygous major allele carriers, the right putaminal volume was associated with verbal fluency (p = 0.008), and both the right putaminal and pallidal volumes were predictive of clinical progression at follow-up (p = 0.020). In the minor allele carriers, neither of the nuclei was related to cognitive test performance or clinical progression. Conclusion: The major and minor alleles of rs2298813 had differential effects on the right lentiform nucleus volume and distinctively modulated the association between the regional volume and cognitive function in patients with AD.
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Affiliation(s)
- Chun-Yu Chen
- Department of Medicine, Taipei Veterans General Hospital Yuli Branch, Hualien, Taiwan
- Division of General Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yung-Shuan Lin
- Division of General Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Ju Lee
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Neurological Institute, Taichung Veterans General Hospital, Taichung, Taiwan
- Dementia Center and Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Chu Liao
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of Peripheral Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Shan Kuo
- Division of General Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Albert C. Yang
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jong-Ling Fuh
- Division of General Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- *Correspondence: Jong-Ling Fuh
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