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Lüleci HB, Jones A, Çakır T. Multi-omics analyses highlight molecular differences between clinical and neuropathological diagnoses in Alzheimer's disease. Eur J Neurosci 2024. [PMID: 39072881 DOI: 10.1111/ejn.16482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024]
Abstract
Both clinical diagnosis and neuropathological diagnosis are commonly used in literature to categorize individuals as Alzheimer's disease (AD) or non-AD in omics analyses. Whether these diagnostic strategies result in distinct profiles of molecular abnormalities is poorly understood. Here, we analysed one of the most commonly used AD omics datasets in the literature from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort and compared the two diagnosis strategies using brain transcriptome and metabolome by grouping individuals as non-AD and AD according to clinical or neuropathological diagnosis separately. Differentially expressed genes, associated pathways related with AD hallmarks and AD-related genes showed that the categorization based on neuropathological diagnosis more accurately reflects the disease state at the molecular level than the categorization based on clinical diagnosis. We further identified consensus biomarker candidates between the two diagnosis strategies such as 5-hydroxylysine, sphingomyelin and 1-myristoyl-2-palmitoyl-GPC as metabolite biomarkers and sphingolipid metabolism as a pathway biomarker, which could be robust AD biomarkers since they are independent of diagnosis strategies. We also used consensus AD and consensus non-AD individuals between the two diagnostic strategies to train a machine-learning based model, which we used to classify the individuals who were cognitively normal but diagnosed as AD based on neuropathological diagnosis (asymptomatic AD individuals). The majority of these individuals were classified as consensus AD patients for both omics data types. Our study provides a detailed characterization of both diagnostic strategies in terms of the association of the corresponding multi-omics profiles with AD.
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Affiliation(s)
| | - Attila Jones
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
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Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW. A multi-ethnic proteomic profiling analysis in Alzheimer's disease identifies the disparities in dysregulation of proteins and pathogenesis. PeerJ 2024; 12:e17643. [PMID: 39035156 PMCID: PMC11260413 DOI: 10.7717/peerj.17643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/06/2024] [Indexed: 07/23/2024] Open
Abstract
Background Alzheimer's disease (AD) is the most common type of dementia that affects the elderly population. Lately, blood-based proteomics have been intensively sought in the discovery of AD biomarkers studies due to the capability to link external environmental factors with the development of AD. Demographic differences have been shown to affect the expression of the proteins in different populations which play a vital role in the degeneration of cognitive function. Method In this study, a proteomic study focused on Malaysian Chinese and Malay prospects was conducted. Differentially expressed proteins (DEPs) in AD patients and normal controls for Chinese and Malays were identified. Functional enrichment analysis was conducted to further interpret the biological functions and pathways of the DEPs. In addition, a survey investigating behavioural practices among Chinese and Malay participants was conducted to support the results from the proteomic analysis. Result The variation of dysregulated proteins identified in Chinese and Malay samples suggested the disparities of pathways involved in this pathological condition for each respective ethnicity. Functional enrichment analysis supported this assumption in understanding the protein-protein interactions of the identified protein signatures and indicate that differentially expressed proteins identified from the Chinese group were significantly enriched with the functional terms related to Aβ/tau protein-related processes, oxidative stress and inflammation whereas neuroinflammation was associated with the Malay group. Besides that, a significant difference in sweet drinks/food intake habits between these two groups implies a relationship between sugar levels and the dysregulation of protein APOA4 in the Malay group. Additional meta-analysis further supported the dysregulation of proteins TF, AHSG, A1BG, APOA4 and C4A among AD groups. Conclusion These findings serve as a preliminary understanding in the molecular and demographic studies of AD in a multi-ethnic population.
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Affiliation(s)
- Mei Sze Tan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Leng Cheah
- Department of Pathology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Ai-Vyrn Chin
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Siow-Wee Chang
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre of Research in System Biology, Structural, Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, Malaysia
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3
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Sokouti B. The identification of biomarkers for Alzheimer's disease using a systems biology approach based on lncRNA-circRNA-miRNA-mRNA ceRNA networks. Comput Biol Med 2024; 179:108860. [PMID: 38996555 DOI: 10.1016/j.compbiomed.2024.108860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/16/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
In addition to being the most prevalent form of neurodegeneration among the elderly, AD is a devastating multifactorial disease. Currently, treatments address only its symptoms. Several clinical studies have shown that the disease begins to manifest decades before the first symptoms appear, indicating that studying early changes is crucial to improving early diagnosis and discovering novel treatments. Our study used bioinformatics and systems biology to identify biomarkers in AD that could be used for diagnosis and prognosis. The procedure was performed on data from the GEO database, and GO and KEGG enrichment analysis were performed. Then, we set up a network of interactions between proteins. Several miRNA prediction tools including miRDB, miRWalk, and TargetScan were used. The ceRNA network led to the identification of eight mRNAs, four circRNAs, seven miRNAs, and seven lncRNAs. Multiple mechanisms, including the cell cycle and DNA replication, have been linked to the promotion of AD development by the ceRNA network. By using the ceRNA network, it should be possible to extract prospective biomarkers and therapeutic targets for the treatment of AD. It is possible that the processes involved in DNA cell cycle and the replication of DNA contribute to the development of Alzheimer's disease.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Mishra S, Stany B, Das A, Kanagavel D, Vijayan M. A Comprehensive Review of Membrane Transporters and MicroRNA Regulation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04135-2. [PMID: 38558361 DOI: 10.1007/s12035-024-04135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) is a distressing neurodegenerative condition characterized by the accumulation of amyloid-beta (Aβ) plaques and tau tangles within the brain. The interconnectedness between membrane transporters (SLCs) and microRNAs (miRNAs) in AD pathogenesis has gained increasing attention. This review explores the localization, substrates, and functions of SLC transporters in the brain, emphasizing the roles of transporters for glutamate, glucose, nucleosides, and other essential compounds. The examination delves into the significance of SLCs in AD, their potential for drug development, and the intricate realm of miRNAs, encompassing their transcription, processing, functions, and regulation. MiRNAs have emerged as significant players in AD, including those associated with mitochondria and synapses. Furthermore, this review discusses the intriguing nexus of miRNAs targeting SLC transporters and their potential as therapeutic targets in AD. Finally, the review underscores the interaction between SLC transporters and miRNA regulation within the context of Alzheimer's disease, underscoring the need for further research in this area. This comprehensive review aims to shed light on the complex mechanisms underlying the causation of AD and provides insights into potential therapeutic approaches.
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Affiliation(s)
- Shatakshi Mishra
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - B Stany
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Anushka Das
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Deepankumar Kanagavel
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India.
| | - Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA.
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Chen H, Wu L, Zhang Y, Ding W, Xiaofan Y. Steroid inhibited Serpina3n expression which was positively correlated with the degrees of spinal cord injury. Heliyon 2024; 10:e26649. [PMID: 38449654 PMCID: PMC10915347 DOI: 10.1016/j.heliyon.2024.e26649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Aims The aim of our project was to identify proteins associated with the extent of spinal cord injury (SCI) and subsequent long-term neurological recovery. Methods Through proteomic analysis, we identified proteins that are differentially expressed specifically in the acute phase of injury. We analyzed the concentrations of differentially expressed proteins in serum and the injured spinal cord segment by ELISA. Results Serpina3n protein expression in the injured spinal cord segment was increased 101-fold at 12 h after severe SCI and 89-fold at 12 h after mild SCI, as determined by LC‒MS/MS. In the mild and severe SCI groups, serum Serpina3n levels began to increase at 12 h and peaked at 24 h. At 12 h, 24 h and 3 d after injury, serum Serpina3n protein levels were significantly correlated with the severity of injury (12 h: r = 0.6034, P = 0.008; 24 h: r = 0.7542, P = 0.0003; 3 d: r = 0.862, P < 0.001). Serum Serpina3n levels at 2 h, 24 h and 3 d post injury were significantly correlated with long-term neurological recovery at 28 d after SCI (2 h: r = -0.5781, P = 0.012; 24 h: r = -0.5912, P = 0.0098; 3 d: r = -0.7792, P < 0.0001). Methylprednisolone treatment would decrease the serum Serpina3n levels in mice with mild and severe SCI compared with those in placebo-group mice at 12 h and 24 h after SCI. The serum Serpina3n concentration in the severe SCI group was significantly reduced on the third day after steroid treatment. Conclusion Taken together, these data suggest that serpina3n may be a circulating biomarker of acute SCI and may be closely associated with injury severity and long-term motor function recovery.
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Affiliation(s)
- Haihong Chen
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Liang Wu
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yue Zhang
- Rehabilitation Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Wang Ding
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yin Xiaofan
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
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Zhang Z, Liu X, Zhang S, Song Z, Lu K, Yang W. A review and analysis of key biomarkers in Alzheimer's disease. Front Neurosci 2024; 18:1358998. [PMID: 38445255 PMCID: PMC10912539 DOI: 10.3389/fnins.2024.1358998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects over 50 million elderly individuals worldwide. Although the pathogenesis of AD is not fully understood, based on current research, researchers are able to identify potential biomarker genes and proteins that may serve as effective targets against AD. This article aims to present a comprehensive overview of recent advances in AD biomarker identification, with highlights on the use of various algorithms, the exploration of relevant biological processes, and the investigation of shared biomarkers with co-occurring diseases. Additionally, this article includes a statistical analysis of key genes reported in the research literature, and identifies the intersection with AD-related gene sets from databases such as AlzGen, GeneCard, and DisGeNet. For these gene sets, besides enrichment analysis, protein-protein interaction (PPI) networks utilized to identify central genes among the overlapping genes. Enrichment analysis, protein interaction network analysis, and tissue-specific connectedness analysis based on GTEx database performed on multiple groups of overlapping genes. Our work has laid the foundation for a better understanding of the molecular mechanisms of AD and more accurate identification of key AD markers.
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Affiliation(s)
- Zhihao Zhang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Xiangtao Liu
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Suixia Zhang
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Zhixin Song
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Ke Lu
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
| | - Wenzhong Yang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
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Wang J, Liao N, Du X, Chen Q, Wei B. A semi-supervised approach for the integration of multi-omics data based on transformer multi-head self-attention mechanism and graph convolutional networks. BMC Genomics 2024; 25:86. [PMID: 38254021 PMCID: PMC10802018 DOI: 10.1186/s12864-024-09985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Comprehensive analysis of multi-omics data is crucial for accurately formulating effective treatment plans for complex diseases. Supervised ensemble methods have gained popularity in recent years for multi-omics data analysis. However, existing research based on supervised learning algorithms often fails to fully harness the information from unlabeled nodes and overlooks the latent features within and among different omics, as well as the various associations among features. Here, we present a novel multi-omics integrative method MOSEGCN, based on the Transformer multi-head self-attention mechanism and Graph Convolutional Networks(GCN), with the aim of enhancing the accuracy of complex disease classification. MOSEGCN first employs the Transformer multi-head self-attention mechanism and Similarity Network Fusion (SNF) to separately learn the inherent correlations of latent features within and among different omics, constructing a comprehensive view of diseases. Subsequently, it feeds the learned crucial information into a self-ensembling Graph Convolutional Network (SEGCN) built upon semi-supervised learning methods for training and testing, facilitating a better analysis and utilization of information from multi-omics data to achieve precise classification of disease subtypes. RESULTS The experimental results show that MOSEGCN outperforms several state-of-the-art multi-omics integrative analysis approaches on three types of omics data: mRNA expression data, microRNA expression data, and DNA methylation data, with accuracy rates of 83.0% for Alzheimer's disease and 86.7% for breast cancer subtyping. Furthermore, MOSEGCN exhibits strong generalizability on the GBM dataset, enabling the identification of important biomarkers for related diseases. CONCLUSION MOSEGCN explores the significant relationship information among different omics and within each omics' latent features, effectively leveraging labeled and unlabeled information to further enhance the accuracy of complex disease classification. It also provides a promising approach for identifying reliable biomarkers, paving the way for personalized medicine.
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Affiliation(s)
- Jiahui Wang
- School of Computer and Information Security, Guilin University of Electronic Technology, No. 1 Jinji Road, Guilin City, 541004, Guangxi Zhuang Autonomous Region, China
| | - Nanqing Liao
- School of Medical, Guangxi University, No. 100 East University Road, Nanning, 530004, Guangxi, China
| | - Xiaofei Du
- School of Computer and Information Security, Guilin University of Electronic Technology, No. 1 Jinji Road, Guilin City, 541004, Guangxi Zhuang Autonomous Region, China
| | - Qingfeng Chen
- School of Computer, Electronics and Information, Guangxi University, No. 100 East University Road, Nanning, 530004, Guangxi, China.
| | - Bizhong Wei
- School of Computer and Information Security, Guilin University of Electronic Technology, No. 1 Jinji Road, Guilin City, 541004, Guangxi Zhuang Autonomous Region, China.
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Meem TM, Khan U, Mredul MBR, Awal MA, Rahman MH, Khan MS. A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease. Bioinform Biol Insights 2023; 17:11779322231210098. [PMID: 38033382 PMCID: PMC10683407 DOI: 10.1177/11779322231210098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/07/2023] [Indexed: 12/02/2023] Open
Abstract
Huntington disease (HD) is a degenerative brain disease caused by the expansion of CAG (cytosine-adenine-guanine) repeats, which is inherited as a dominant trait and progressively worsens over time possessing threat. Although HD is monogenetic, the specific pathophysiology and biomarkers are yet unknown specifically, also, complex to diagnose at an early stage, and identification is restricted in accuracy and precision. This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them (DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs interactions (FOXC1, GATA2, etc), TF-microRNA (miRNA) interactions (hsa-miR-340, hsa-miR-34a, etc), protein-drug interactions, and disorders associated with DEGs were predicted. Furthermore, we used gene set enrichment analysis (GSEA) to emphasize relevant gene ontology terms (eg, TF activity, sequence-specific DNA binding) linked to DEGs in HD. Disease interactions revealed the diseases that are linked to HD, and the prospective small drug molecules like cytarabine and arsenite was predicted against HD. This study reveals molecular biomarkers at the RNA and protein levels that may be beneficial to improve the understanding of molecular mechanisms, early diagnosis, as well as prospective pharmacologic targets for designing beneficial HD treatment.
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Affiliation(s)
- Tahera Mahnaz Meem
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Umama Khan
- Biotechnology & Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Bazlur Rahman Mredul
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Md Abdul Awal
- Electronics and Communication Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Salauddin Khan
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
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Anirudhan A, Mahema S, Ahmad SF, Emran TB, Ahmed SSSJ, Paramasivam P. Screening of Crucial Cytosolicproteins Interconnecting the Endoplasmic Reticulum and Mitochondria in Parkinson's Disease and the Impact of Anti-Parkinson Drugs in the Preservation of Organelle Connectivity. Brain Sci 2023; 13:1551. [PMID: 38002511 PMCID: PMC10670093 DOI: 10.3390/brainsci13111551] [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: 09/29/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondrial dysfunction is well-established in Parkinson's disease (PD); however, its dysfunctions associating with cell organelle connectivity remain unknown. We aimed to establish the crucial cytosolic protein involved in organelle connectivity between mitochondria and the endopalmic reticulum (ER) through a computational approach by constructing an organelle protein network to extract functional clusters presenting the crucial PD protein connecting organelles. Then, we assessed the influence of anti-parkinsonism drugs (n = 35) on the crucial protein through molecular docking and molecular dynamic simulation and further validated its gene expression in PD participants under, istradefylline (n = 25) and amantadine (n = 25) treatment. Based on our investigation, D-aspartate oxidase (DDO )protein was found to be the critical that connects both mitochondria and the ER. Further, molecular docking showed that istradefylline has a high affinity (-9.073 kcal/mol) against DDO protein, which may disrupt mitochondrial-ER connectivity. While amantadine (-4.53 kcal/mol) shows negligible effects against DDO that contribute to conformational changes in drug binding, Successively, DDO gene expression was downregulated in istradefylline-treated PD participants, which elucidated the likelihood of an istradefylline off-target mechanism. Overall, our findings illuminate the off-target effects of anti-parkinsonism medications on DDO protein, enabling the recommendation of off-target-free PD treatments.
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Affiliation(s)
- Athira Anirudhan
- Central Research Laboratory, Believers Church Medical College Hospital, Kuttapuzha, Thiruvalla 689101, Kerala, India
| | - S. Mahema
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Prabu Paramasivam
- Madras Diabetes Research Foundation and Dr. Mohan’s Diabetes Specialities Centre, WHO Collaborating Centre for Non-Communicable Diseases Prevention and Control & IDF Centre of Education, Gopalapuram, Chennai 602105, Tamil Nadu, India
- Department of Neurology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Widjaya MA, Liu CH, Lee SD, Cheng WC. Transcriptomics Meta-Analysis Reveals Phagosome and Innate Immune System Dysfunction as Potential Mechanisms in the Cortex of Alzheimer's Disease Mouse Strains. J Mol Neurosci 2023; 73:773-786. [PMID: 37733230 DOI: 10.1007/s12031-023-02152-9] [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: 07/05/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023]
Abstract
Immune-related pathways can affect the immune system directly, such as the chemokine signaling pathway, or indirectly, such as the phagosome pathway. Alzheimer's disease (AD) is reportedly associated with several immune-related pathways. However, exploring its underlying mechanism is challenging in animal studies because AD mouse strains differentially express immune-related pathway characteristics. To overcome this problem, we performed a meta-analysis to identify significant and consistent immune-related AD pathways that are expressed in different AD mouse strains. Next-generation RNA sequencing (RNA-seq) and microarray datasets for the cortex of AD mice from different strains such as APP/PSEN1, APP/PS2, 3xTg, TREM, and 5xFAD were collected from the NCBI GEO database. Each dataset's quality control and normalization were already processed from each original study source using various methods depending on the high-throughput analysis platform (FastQC, median of ratios, RMA, between array normalization). Datasets were analyzed using DESeq2 for RNA-seq and GEO2R for microarray to identify differentially expressed (DE) genes. Significantly DE genes were meta-analyzed using Stouffer's method, with significant genes further analyzed for functional enrichment. Ten datasets representing 20 conditions were obtained from the NCBI GEO database, comprising 116 control and 120 AD samples. The DE analysis identified 284 significant DE genes. The meta-analysis identified three significantly enriched immune-related AD pathways: phagosome, the complement and coagulation cascade, and chemokine signaling. Phagosomes-related genes correlated with complement and immune system. Meanwhile, phagosomes and chemokine signaling genes overlapped with B cells receptors pathway genes indicating potential correlation between phagosome, chemokines, and adaptive immune system as well. The transcriptomic meta-analysis showed that AD is associated with immune-related pathways in the brain's cortex through the phagosome, complement and coagulation cascade, and chemokine signaling pathways. Interestingly, phagosome and chemokine signaling pathways had potential correlation with B cells receptors pathway.
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Affiliation(s)
- Michael Anekson Widjaya
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Chia-Hsin Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University and Academia Sinica China Medical University, Taichung, 40403, Taiwan
| | - Shin-Da Lee
- Department of Physical Therapy, PhD program in Healthcare Science, China Medical University, Taichung, 406040, Taiwan.
| | - Wei-Chung Cheng
- Cancer Biology and Precision Therapeutics Center, China Medical University and Academia Sinica China Medical University, Taichung, 40403, Taiwan.
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan.
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Brown JS. Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power. Neurosci Biobehav Rev 2023; 151:105206. [PMID: 37178944 DOI: 10.1016/j.neubiorev.2023.105206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.
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Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023; 186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
Abstract
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
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Affiliation(s)
- Joel Rozowsky
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Kun Xiong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keyang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ana Berthel
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - Fabio Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Maxwell S Sun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Justin Chang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Christopher J F Cameron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sergey Aganezov
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Sora Chee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Gabriel Conte Cortez Martins
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cassidy Danyko
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carrie A Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel Farid
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Idan Gabdank
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vivian Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin C Hitz
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Melanie Kirsche
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bonita R Lam
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Khine Zin Lin
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, CHN
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Mudge
- European Bioinformatics Institute, Cambridge, Cambridgeshire, GB
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioann Popov
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Srividya Ramakrishnan
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joe Raymond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
| | - Alexandra Scavelli
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jacob M Schreiber
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fritz J Sedlazeck
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rachel M Sherman
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Minyi Shi
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Cricket Alicia Sloan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - J Seth Strattan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zhen Tan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Forrest Y Tanaka
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anna Vlasova
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain; Institute of Research in Biomedicine, Barcelona, Spain
| | - Jun Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Werner
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lu Yu
- Institute of Cancer Research, London, UK
| | - Christopher Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | | | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Morgan E Levine
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Alexander Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Jesse Gillis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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13
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Bharthur Sanjay A, Patania A, Yan X, Svaldi D, Duran T, Shah N, Nemes S, Chen E, Apostolova LG. Characterization of gene expression patterns in mild cognitive impairment using a transcriptomics approach and neuroimaging endophenotypes. Alzheimers Dement 2022; 18:2493-2508. [PMID: 35142026 PMCID: PMC10078657 DOI: 10.1002/alz.12587] [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: 04/11/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Identification of novel therapeutics and risk assessment in early stages of Alzheimer's disease (AD) is a crucial aspect of addressing this complex disease. We characterized gene-expression patterns at the mild cognitive impairment (MCI) stage to identify critical mRNA measures and gene clusters associated with AD pathogenesis. METHODS We used a transcriptomics approach, integrating magnetic resonance imaging (MRI) and peripheral blood-based gene expression data using persistent homology (PH) followed by kernel-based clustering. RESULTS We identified three clusters of genes significantly associated with diagnosis of amnestic MCI. The biological processes associated with each cluster were mitochondrial function, NF-kB signaling, and apoptosis. Cluster-level associations with cortical thickness displayed canonical AD-like patterns. Driver genes from clusters were also validated in an external dataset for prediction of amyloidosis and clinical diagnosis. DISCUSSION We found a disease-relevant transcriptomic signature sensitive to prodromal AD and identified a subset of potential therapeutic targets associated with AD pathogenesis.
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Affiliation(s)
| | - Alice Patania
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Xiaoran Yan
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Diana Svaldi
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Tugce Duran
- Department of Internal Medicine, Section of Gerontology & Geriatric MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Niraj Shah
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Sara Nemes
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eric Chen
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Liana G. Apostolova
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
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14
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Upadhya S, Gingerich D, Lutz MW, Chiba-Falek O. Differential Gene Expression and DNA Methylation in the Risk of Depression in LOAD Patients. Biomolecules 2022; 12:1679. [PMID: 36421693 PMCID: PMC9687527 DOI: 10.3390/biom12111679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 06/28/2024] Open
Abstract
Depression is common among late-onset Alzheimer's Disease (LOAD) patients. Only a few studies investigated the genetic variability underlying the comorbidity of depression in LOAD. Moreover, the epigenetic and transcriptomic factors that may contribute to comorbid depression in LOAD have yet to be studied. Using transcriptomic and DNA-methylomic datasets from the ROSMAP cohorts, we investigated differential gene expression and DNA-methylation in LOAD patients with and without comorbid depression. Differential expression analysis did not reveal significant association between differences in gene expression and the risk of depression in LOAD. Upon sex-stratification, we identified 25 differential expressed genes (DEG) in males, of which CHI3L2 showed the strongest upregulation, and only 3 DEGs in females. Additionally, testing differences in DNA-methylation found significant hypomethylation of CpG (cg20442550) on chromosome 17 (log2FC = -0.500, p = 0.004). Sex-stratified differential DNA-methylation analysis did not identify any significant CpG probes. Integrating the transcriptomic and DNA-methylomic datasets did not discover relationships underlying the comorbidity of depression and LOAD. Overall, our study is the first multi-omics genome-wide exploration of the role of gene expression and epigenome alterations in the risk of comorbid depression in LOAD patients. Furthermore, we discovered sex-specific differences in gene expression underlying the risk of depression symptoms in LOAD.
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Affiliation(s)
| | | | | | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
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15
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Ai N, Yang Z, Yuan H, Ouyang D, Miao R, Ji Y, Liang Y. A distributed sparse logistic regression with $$L_{1/2}$$ regularization for microarray biomarker discovery in cancer classification. Soft comput 2022. [DOI: 10.1007/s00500-022-07551-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Alzheimer's disease large-scale gene expression portrait identifies exercise as the top theoretical treatment. Sci Rep 2022; 12:17189. [PMID: 36229643 PMCID: PMC9561721 DOI: 10.1038/s41598-022-22179-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/11/2022] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that affects multiple brain regions and is difficult to treat. In this study we used 22 AD large-scale gene expression datasets to identify a consistent underlying portrait of AD gene expression across multiple brain regions. Then we used the portrait as a platform for identifying treatments that could reverse AD dysregulated expression patterns. Enrichment of dysregulated AD genes included multiple processes, ranging from cell adhesion to CNS development. The three most dysregulated genes in the AD portrait were the inositol trisphosphate kinase, ITPKB (upregulated), the astrocyte specific intermediate filament protein, GFAP (upregulated), and the rho GTPase, RHOQ (upregulated). 41 of the top AD dysregulated genes were also identified in a recent human AD GWAS study, including PNOC, C4B, and BCL11A. 42 transcription factors were identified that were both dysregulated in AD and that in turn affect expression of other AD dysregulated genes. Male and female AD portraits were highly congruent. Out of over 250 treatments, three datasets for exercise or activity were identified as the top three theoretical treatments for AD via reversal of large-scale gene expression patterns. Exercise reversed expression patterns of hundreds of AD genes across multiple categories, including cytoskeleton, blood vessel development, mitochondrion, and interferon-stimulated related genes. Exercise also ranked as the best treatment across a majority of individual region-specific AD datasets and meta-analysis AD datasets. Fluoxetine also scored well and a theoretical combination of fluoxetine and exercise reversed 549 AD genes. Other positive treatments included curcumin. Comparisons of the AD portrait to a recent depression portrait revealed a high congruence of downregulated genes in both. Together, the AD portrait provides a new platform for understanding AD and identifying potential treatments for AD.
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17
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Neums L, Koestler DC, Xia Q, Hu J, Patel S, Bell-Glenn S, Pei D, Zhang B, Boyd S, Chalise P, Thompson JA. Assessing equivalent and inverse change in genes between diverse experiments. FRONTIERS IN BIOINFORMATICS 2022; 2:893032. [PMID: 36304274 PMCID: PMC9580844 DOI: 10.3389/fbinf.2022.893032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/22/2022] [Indexed: 05/26/2024] Open
Abstract
Background: It is important to identify when two exposures impact a molecular marker (e.g., a gene's expression) in similar ways, for example, to learn that a new drug has a similar effect to an existing drug. Currently, statistically robust approaches for making comparisons of equivalence of effect sizes obtained from two independently run treatment vs. control comparisons have not been developed. Results: Here, we propose two approaches for evaluating the question of equivalence between effect sizes of two independent studies: a bootstrap test of the Equivalent Change Index (ECI), which we previously developed, and performing Two One-Sided t-Tests (TOST) on the difference in log-fold changes directly. The ECI of a gene is computed by taking the ratio of the effect size estimates obtained from the two different studies, weighted by the maximum of the two p-values and giving it a sign indicating if the effects are in the same or opposite directions, whereas TOST is a test of whether the difference in log-fold changes lies outside a region of equivalence. We used a series of simulation studies to compare the two tests on the basis of sensitivity, specificity, balanced accuracy, and F1-score. We found that TOST is not efficient for identifying equivalently changed gene expression values (F1-score = 0) because it is too conservative, while the ECI bootstrap test shows good performance (F1-score = 0.95). Furthermore, applying the ECI bootstrap test and TOST to publicly available microarray expression data from pancreatic cancer showed that, while TOST was not able to identify any equivalently or inversely changed genes, the ECI bootstrap test identified genes associated with pancreatic cancer. Additionally, when investigating publicly available RNAseq data of smoking vs. vaping, no equivalently changed genes were identified by TOST, but ECI bootstrap test identified genes associated with smoking. Conclusion: A bootstrap test of the ECI is a promising new statistical approach for determining if two diverse studies show similarity in the differential expression of genes and can help to identify genes which are similarly influenced by a specific treatment or exposure. The R package for the ECI bootstrap test is available at https://github.com/Hecate08/ECIbootstrap.
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Affiliation(s)
- Lisa Neums
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Qing Xia
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Jinxiang Hu
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Shachi Patel
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Dong Pei
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Bo Zhang
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Samuel Boyd
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Prabhakar Chalise
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Jeffrey A. Thompson
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
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18
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Keel BN, Lindholm-Perry AK. Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq. Front Genet 2022; 13:983043. [PMID: 36199583 PMCID: PMC9527320 DOI: 10.3389/fgene.2022.983043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates. Meta-analysis procedures can be used to integrate and jointly analyze data from multiple independent studies. Meta-analyses increase the sample size, which in turn increase both statistical power and robustness of the results. In this work, we discuss cutting edge approaches to combining results from multiple independent RNA-Seq studies to improve livestock transcriptomics research. We review currently published RNA-Seq meta-analyses in livestock, describe many of the key issues specific to RNA-Seq meta-analysis in livestock species, and discuss future perspectives.
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19
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Hwang W, Han N. Identification of potential pan-coronavirus therapies using a computational drug repurposing platform. Methods 2022; 203:214-225. [PMID: 34767922 PMCID: PMC8577587 DOI: 10.1016/j.ymeth.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 01/17/2023] Open
Abstract
In the past 20 years, there have been several infectious disease outbreaks in humans for which the causative agent has been a zoonotic coronavirus. Novel infectious disease outbreaks, as illustrated by the current coronavirus disease 2019 (COVID-19) pandemic, demand a rapid response in terms of identifying effective treatments for seriously ill patients. The repurposing of approved drugs from other therapeutic areas is one of the most practical routes through which to approach this. Here, we present a systematic network-based drug repurposing methodology, which interrogates virus-human, human protein-protein and drug-protein interactome data. We identified 196 approved drugs that are appropriate for repurposing against COVID-19 and 102 approved drugs against a related coronavirus, severe acute respiratory syndrome (SARS-CoV). We constructed a protein-protein interaction (PPI) network based on disease signatures from COVID-19 and SARS multi-omics datasets. Analysis of this PPI network uncovered key pathways. Of the 196 drugs predicted to target COVID-19 related pathways, 44 (hypergeometric p-value: 1.98e-04) are already in COVID-19 clinical trials, demonstrating the validity of our approach. Using an artificial neural network, we provide information on the mechanism of action and therapeutic value for each of the identified drugs, to facilitate their rapid repurposing into clinical trials.
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Affiliation(s)
- Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK,Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK,Corresponding author
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20
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Noronha O, Mesarosovo L, Anink JJ, Iyer A, Aronica E, Mills JD. Differentially Expressed miRNAs in Age-Related Neurodegenerative Diseases: A Meta-Analysis. Genes (Basel) 2022; 13:genes13061034. [PMID: 35741796 PMCID: PMC9222420 DOI: 10.3390/genes13061034] [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: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/05/2023] Open
Abstract
To date, no neurodegenerative diseases (NDDs) have cures, and the underlying mechanism of their pathogenesis is undetermined. As miRNAs extensively regulate all biological processes and are crucial regulators of healthy brain function, miRNAs differentially expressed in NDDs may provide insight into the factors that contribute to the emergence of protein inclusions and the propagation of deleterious cellular environments. A meta-analysis of miRNAs dysregulated in Alzheimer’s disease, Parkinson’s disease, multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration, dementia with Lewy bodies and frontotemporal lobar degeneration (TDP43 variant) was performed to determine if diseases within a proteinopathy have distinct or shared mechanisms of action leading to neuronal death, and if proteinopathies can be classified on the basis of their miRNA profiles. Our results identified both miRNAs distinct to the anatomy, disease type and pathology, and miRNAs consistently dysregulated within single proteinopathies and across neurodegeneration in general. Our results also highlight the necessity to minimize the variability between studies. These findings showcase the need for more transcriptomic research on infrequently occurring NDDs, and the need for the standardization of research techniques and platforms utilized across labs and diseases.
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Affiliation(s)
- Ocana Noronha
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Saitama 351-0106, Japan
| | - Lucia Mesarosovo
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - Jasper J. Anink
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - Anand Iyer
- Department of Internal Medicine, Erasmus Medicine Center, 3015 GD Rotterdam, The Netherlands;
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - James D. Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
- Department of Clinical and Experimental Epilepsy, University College London, London WC1E 6BT, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, Gerrards Cross SL9 0RJ, UK
- Correspondence:
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21
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Identification of Novel Noninvasive Diagnostics Biomarkers in the Parkinson’s Diseases and Improving the Disease Classification Using Support Vector Machine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5009892. [PMID: 35342758 PMCID: PMC8941533 DOI: 10.1155/2022/5009892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022]
Abstract
Background Parkinson's disease (PD) is a neurological disorder that is marked by the deficit of neurons in the midbrain that changes motor and cognitive function. In the substantia nigra, the selective demise of dopamine-producing neurons was the main cause of this disease. The purpose of this research was to discover genes involved in PD development. Methods In this study, the microarray dataset (GSE22491) provided by GEO was used for further analysis. The Limma package under R software was used to examine and assess gene expression and identify DEGs. The DAVID online tool was used to accomplish GO enrichment analysis and KEGG pathway for DEGs. Furthermore, the PPI network of these DEGs was depicted using the STRING database and analyzed through the Cytoscape to identify hub genes. Support vector machine (SVM) classifier was subsequently employed to predict the accuracy of genes. Result PPI network consisted of 264 nodes as well as 502 edges was generated using the DEGs recognized from the Limma package under the R software. Moreover, three genes were identified as hubs: GNB5, GNG11, and ELANE. By using 3-gene combination, SVM found that prediction accuracy of 88% can be achieved. Conclusion According to the findings of the study, the 3 hub genes GNB5, GNG11, and ELANE may be used as PD detection biomarkers. Moreover, the results obtained from SVM with high accuracy can be considered as PD biomarkers in further investigations.
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22
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Cervantes-Gracia K, Chahwan R, Husi H. Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis Approach. Front Genet 2022; 13:828786. [PMID: 35186042 PMCID: PMC8855827 DOI: 10.3389/fgene.2022.828786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
The wealth of high-throughput data has opened up new opportunities to analyze and describe biological processes at higher resolution, ultimately leading to a significant acceleration of scientific output using high-throughput data from the different omics layers and the generation of databases to store and report raw datasets. The great variability among the techniques and the heterogeneous methodologies used to produce this data have placed meta-analysis methods as one of the approaches of choice to correlate the resultant large-scale datasets from different research groups. Through multi-study meta-analyses, it is possible to generate results with greater statistical power compared to individual analyses. Gene signatures, biomarkers and pathways that provide new insights of a phenotype of interest have been identified by the analysis of large-scale datasets in several fields of science. However, despite all the efforts, a standardized regulation to report large-scale data and to identify the molecular targets and signaling networks is still lacking. Integrative analyses have also been introduced as complementation and augmentation for meta-analysis methodologies to generate novel hypotheses. Currently, there is no universal method established and the different methods available follow different purposes. Herein we describe a new unifying, scalable and straightforward methodology to meta-analyze different omics outputs, but also to integrate the significant outcomes into novel pathways describing biological processes of interest. The significance of using proper molecular identifiers is highlighted as well as the potential to further correlate molecules from different regulatory levels. To show the methodology’s potential, a set of transcriptomic datasets are meta-analyzed as an example.
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Affiliation(s)
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- *Correspondence: Richard Chahwan, ; Holger Husi,
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Sciences, Centre for Health Science, University of the Highlands and Islands, Inverness, United Kingdom
- *Correspondence: Richard Chahwan, ; Holger Husi,
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23
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Genetically regulated expression in late-onset Alzheimer's disease implicates risk genes within known and novel loci. Transl Psychiatry 2021; 11:618. [PMID: 34873149 PMCID: PMC8648734 DOI: 10.1038/s41398-021-01677-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022] Open
Abstract
Late-onset Alzheimer disease (LOAD) is highly polygenic, with a heritability estimated between 40 and 80%, yet risk variants identified in genome-wide studies explain only ~8% of phenotypic variance. Due to its increased power and interpretability, genetically regulated expression (GReX) analysis is an emerging approach to investigate the genetic mechanisms of complex diseases. Here, we conducted GReX analysis within and across 51 tissues on 39 LOAD GWAS data sets comprising 58,713 cases and controls from the Alzheimer's Disease Genetics Consortium (ADGC) and the International Genomics of Alzheimer's Project (IGAP). Meta-analysis across studies identified 216 unique significant genes, including 72 with no previously reported LOAD GWAS associations. Cross-brain-tissue and cross-GTEx models revealed eight additional genes significantly associated with LOAD. Conditional analysis of previously reported loci using established LOAD-risk variants identified eight genes reaching genome-wide significance independent of known signals. Moreover, the proportion of SNP-based heritability is highly enriched in genes identified by GReX analysis. In summary, GReX-based meta-analysis in LOAD identifies 216 genes (including 72 novel genes), illuminating the role of gene regulatory models in LOAD.
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24
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Ruffo P, Strafella C, Cascella R, Caputo V, Conforti FL, Andò S, Giardina E. Deregulation of ncRNA in Neurodegenerative Disease: Focus on circRNA, lncRNA and miRNA in Amyotrophic Lateral Sclerosis. Front Genet 2021; 12:784996. [PMID: 34925464 PMCID: PMC8674781 DOI: 10.3389/fgene.2021.784996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 01/17/2023] Open
Abstract
Parallel and massive sequencing of total RNA samples derived from different samples are possible thanks to the use of NGS (Next Generation Sequencing) technologies. This allowed characterizing the transcriptomic profile of both cell and tissue populations, increasing the knowledge of the molecular pathological processes of complex diseases, such as neurodegenerative diseases (NDs). Among the NDs, Amyotrophic Lateral Sclerosis (ALS) is caused by the progressive loss of motor neurons (MNs), and, to date, the diagnosis is often made by exclusion because there is no specific symptomatologic picture. For this reason, it is important to search for biomarkers that are clinically useful for carrying out a fast and accurate diagnosis of ALS. Thanks to various studies, it has been possible to propose several molecular mechanisms associated with the disease, some of which include the action of non-coding RNA, including circRNAs, miRNAs, and lncRNAs which will be discussed in the present review. The evidence analyzed in this review highlights the importance of conducting studies to better characterize the different ncRNAs in the disease to use them as possible diagnostic, prognostic, and/or predictive biomarkers of ALS and other NDs.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Centro Sanitario, University of Calabria, Arcavacata di Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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25
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Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW. A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach. Comput Biol Med 2021; 139:104947. [PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
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Affiliation(s)
- Mei Sze Tan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Leng Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siow-Wee Chang
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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Kim J, Kim D, Sohn KA. HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball. Bioinformatics 2021; 37:2971-2980. [PMID: 33760022 DOI: 10.1093/bioinformatics/btab193] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Knowledge manipulation of Gene Ontology (GO) and Gene Ontology Annotation (GOA) can be done primarily by using vector representation of GO terms and genes. Previous studies have represented GO terms and genes or gene products in Euclidean space to measure their semantic similarity using an embedding method such as the Word2Vec-based method to represent entities as numeric vectors. However, this method has the limitation that embedding large graph-structured data in the Euclidean space cannot prevent a loss of information of latent hierarchies, thus precluding the semantics of GO and GOA from being captured optimally. On the other hand, hyperbolic spaces such as the Poincaré balls are more suitable for modeling hierarchies, as they have a geometric property in which the distance increases exponentially as it nears the boundary because of negative curvature. RESULTS In this article, we propose hierarchical representations of GO and genes (HiG2Vec) by applying Poincaré embedding specialized in the representation of hierarchy through a two-step procedure: GO embedding and gene embedding. Through experiments, we show that our model represents the hierarchical structure better than other approaches and predicts the interaction of genes or gene products similar to or better than previous studies. The results indicate that HiG2Vec is superior to other methods in capturing the GO and gene semantics and in data utilization as well. It can be robustly applied to manipulate various biological knowledge. AVAILABILITYAND IMPLEMENTATION https://github.com/JaesikKim/HiG2Vec. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jaesik Kim
- Department of Computer Engineering, Ajou University, Suwon 16499, South Korea.,Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyung-Ah Sohn
- Department of Computer Engineering, Ajou University, Suwon 16499, South Korea.,Department of Artificial Intelligence, Ajou University, Suwon 16499, South Korea
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27
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Wu X, Peng C, Nelson PT, Cheng Q. Random forest-integrated analysis in AD and LATE brain transcriptome-wide data to identify disease-specific gene expression. PLoS One 2021; 16:e0256648. [PMID: 34492068 PMCID: PMC8423259 DOI: 10.1371/journal.pone.0256648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that affects thinking, memory, and behavior. Limbic-predominant age-related TDP-43 encephalopathy (LATE) is a recently identified common neurodegenerative disease that mimics the clinical symptoms of AD. The development of drugs to prevent or treat these neurodegenerative diseases has been slow, partly because the genes associated with these diseases are incompletely understood. A notable hindrance from data analysis perspective is that, usually, the clinical samples for patients and controls are highly imbalanced, thus rendering it challenging to apply most existing machine learning algorithms to directly analyze such datasets. Meeting this data analysis challenge is critical, as more specific disease-associated gene identification may enable new insights into underlying disease-driving mechanisms and help find biomarkers and, in turn, improve prospects for effective treatment strategies. In order to detect disease-associated genes based on imbalanced transcriptome-wide data, we proposed an integrated multiple random forests (IMRF) algorithm. IMRF is effective in differentiating putative genes associated with subjects having LATE and/or AD from controls based on transcriptome-wide data, thereby enabling effective discrimination between these samples. Various forms of validations, such as cross-domain verification of our method over other datasets, improved and competitive classification performance by using identified genes, effectiveness of testing data with a classifier that is completely independent from decision trees and random forests, and relationships with prior AD and LATE studies on the genes linked to neurodegeneration, all testify to the effectiveness of IMRF in identifying genes with altered expression in LATE and/or AD. We conclude that IMRF, as an effective feature selection algorithm for imbalanced data, is promising to facilitate the development of new gene biomarkers as well as targets for effective strategies of disease prevention and treatment.
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Affiliation(s)
- Xinxing Wu
- University of Kentucky, Lexington, Kentucky, United States of America
| | - Chong Peng
- Qingdao University, Qingdao, Shandong, China
| | - Peter T. Nelson
- University of Kentucky, Lexington, Kentucky, United States of America
| | - Qiang Cheng
- University of Kentucky, Lexington, Kentucky, United States of America
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28
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Rojas ML, Cruz Del Puerto MM, Flores-Martín J, Racca AC, Kourdova LT, Miranda AL, Panzetta-Dutari GM, Genti-Raimondi S. Role of the lipid transport protein StarD7 in mitochondrial dynamics. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:159029. [PMID: 34416390 DOI: 10.1016/j.bbalip.2021.159029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/16/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Mitochondria are dynamic organelles crucial for cell function and survival implicated in oxidative energy production whose central functions are tightly controlled by lipids. StarD7 is a lipid transport protein involved in the phosphatidylcholine (PC) delivery to mitochondria. Previous studies have shown that StarD7 knockdown induces alterations in mitochondria and endoplasmic reticulum (ER) with a reduction in PC content, however whether StarD7 modulates mitochondrial dynamics remains unexplored. Here, we generated HTR-8/SVneo stable cells expressing the precursor StarD7.I and the mature processed StarD7.II isoforms. We demonstrated that StarD7.I overexpression altered mitochondrial morphology increasing its fragmentation, whereas no changes were observed in StarD7.II-overexpressing cells compared to the control (Ct) stable cells. StarD7.I (D7.I) stable cells were able to transport higher fluorescent PC analog to mitochondria than Ct cells, yield mitochondrial fusions, maintained the membrane potential, and produced lower levels of reactive oxygen species (ROS). Additionally, the expression of Dynamin Related Protein 1 (Drp1) and Mitofusin (Mfn2) proteins were increased, whereas the amount of Mitofusin 1 (Mfn1) decreased. Moreover, transfections with plasmids encoding Drp1-K38A, Drp1-S637D or Drp1-S637A mutants indicated that mitochondrial fragmentation in D7.I cells occurs in a fission-dependent manner via Drp1. In contrast, StarD7 silencing decreased Mfn1 and Mfn2 fusion proteins without modification of Drp1 protein level. These cells increased ROS levels and presented donut-shape mitochondria, indicative of metabolic stress. Altogether our findings provide novel evidence indicating that alterations in StarD7.I expression produce significant changes in mitochondrial morphology and dynamics.
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Affiliation(s)
- María L Rojas
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Mariano M Cruz Del Puerto
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Jésica Flores-Martín
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Ana C Racca
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Lucille T Kourdova
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Andrea L Miranda
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Graciela M Panzetta-Dutari
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Susana Genti-Raimondi
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Ciudad Universitaria, X5000HUA Córdoba, Argentina.
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29
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Ni X, Wang Z, Gao D, Yuan H, Sun L, Zhu X, Zhou Q, Yang Z. A description of the relationship in healthy longevity and aging-related disease: from gene to protein. Immun Ageing 2021; 18:30. [PMID: 34172062 PMCID: PMC8229348 DOI: 10.1186/s12979-021-00241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022]
Abstract
Human longevity is a complex phenotype influenced by both genetic and environmental factors. It is also known to be associated with various types of age-related diseases, such as Alzheimer's disease (AD) and cardiovascular disease (CVD). The central dogma of molecular biology demonstrates the conversion of DNA to RNA to the encoded protein. These proteins interact to form complex cell signaling pathways, which perform various biological functions. With prolonged exposure to the environment, the in vivo homeostasis adapts to the changes, and finally, humans adopt the phenotype of longevity or aging-related diseases. In this review, we focus on two different states: longevity and aging-related diseases, including CVD and AD, to discuss the relationship between genetic characteristics, including gene variation, the level of gene expression, regulation of gene expression, the level of protein expression, both genetic and environmental influences and homeostasis based on these phenotypes shown in organisms.
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Affiliation(s)
- Xiaolin Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China
| | - Zhaoping Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Danni Gao
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Qi Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China.
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China.
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Han N, Hwang W, Tzelepis K, Schmerer P, Yankova E, MacMahon M, Lei W, M Katritsis N, Liu A, Felgenhauer U, Schuldt A, Harris R, Chapman K, McCaughan F, Weber F, Kouzarides T. Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. SCIENCE ADVANCES 2021; 7:eabh3032. [PMID: 34193418 PMCID: PMC8245040 DOI: 10.1126/sciadv.abh3032] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/14/2021] [Indexed: 05/02/2023]
Abstract
The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates the rapid development of new therapies against coronavirus disease 2019 (COVID-19) infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2-induced protein network, based on disease signatures defined by COVID-19 multiomics datasets, and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials, testifying to the validity of the approach. Using artificial neural network analysis, we classified these 200 drugs into nine distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (126) and immune response (74). Two drugs (proguanil and sulfasalazine) implicated in viral replication were shown to inhibit replication in cell assays. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials.
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Affiliation(s)
- Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
| | - Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | | | - Patrick Schmerer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Eliza Yankova
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Anika Liu
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Data and Computational Sciences, GSK, London, UK
| | - Ulrike Felgenhauer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Alison Schuldt
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Rebecca Harris
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Frank McCaughan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Tony Kouzarides
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
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Anirudhan A, Angulo-Bejarano PI, Paramasivam P, Manokaran K, Kamath SM, Murugesan R, Sharma A, Ahmed SSSJ. RPL6: A Key Molecule Regulating Zinc- and Magnesium-Bound Metalloproteins of Parkinson's Disease. Front Neurosci 2021; 15:631892. [PMID: 33790735 PMCID: PMC8006920 DOI: 10.3389/fnins.2021.631892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease with no definite molecular markers for diagnosis. Metal exposure may alter cellular proteins that contribute to PD. Exploring the cross-talk between metal and its binding proteins in PD could reveal a new strategy for PD diagnosis. We performed a meta-analysis from different PD tissue microarray datasets to identify differentially expressed genes (DEGs) common to the blood and brain. Among common DEGs, we extracted 280 metalloprotein-encoding genes to construct protein networks describing the regulation of metalloproteins in the PD blood and brain. From the metalloprotein network, we identified three important functional hubs. Further analysis shows 60S ribosomal protein L6 (RPL6), a novel intermediary molecule connecting the three hubs of the metalloproteins network. Quantitative real-time PCR analysis showed that RPL6 was downregulated in PD peripheral blood mononuclear cell (PBMC) samples. Simultaneously, trace element analysis revealed altered serum zinc and magnesium concentrations in PD samples. The Pearson's correlation analysis shows that serum zinc and magnesium regulate the RPL6 gene expression in PBMC. Thus, metal-regulating RPL6 acts as an intermediary molecule connecting the three hubs that are functionally associated with PD. Overall our study explores the understanding of metal-mediated pathogenesis in PD, which provides a serum metal environment regulating the cellular gene expression that may light toward metal and gene expression-based biomarkers for PD diagnosis.
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Affiliation(s)
- Athira Anirudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
| | | | - Prabu Paramasivam
- Department of Neurology, School of Medicine, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, United States
| | - Kalaivani Manokaran
- Department of Medical Laboratory Technology, Manipal College of Health Professions, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - S Manjunath Kamath
- Department of Pharmacology, Saveetha Dental College (SDC), Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Ram Murugesan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Ashutosh Sharma
- School of Engineering and Sciences, Centre of Bioengineering, Tecnologico de Monterrey, Queretaro, Mexico
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
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32
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Singh S, Nguyen HC, Ehsan M, Michels DCR, Singh P, Qadura M, Singh KK. Pravastatin-induced changes in expression of long non-coding and coding RNAs in endothelial cells. Physiol Rep 2021; 9:e14661. [PMID: 33369888 PMCID: PMC7769171 DOI: 10.14814/phy2.14661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Atherosclerosis is the main cause of the cardiovascular disease (CVD). Elevated blood cholesterol and inflammation of the endothelium are two major mechanisms contributing to the establishment of atherosclerotic plaques. Statins, such as pravastatin, are blood-cholesterol lowering drugs commonly prescribed for patients with or at risk for CVDs. In addition to lowering blood cholesterols, statins have recently been shown to improve endothelial function in both hyper- and normocholesterolemic patients with atherosclerosis. To understand the molecular mechanisms underlying the endothelial function improvement by statins, we assessed the RNA profile of pravastatin-treated endothelial cells, particularly their mRNAs and long non-coding RNAs (lncRNAs). METHODS Human umbilical vein endothelial cells (HUVECs) treated with pravastatin (10 µM) for 24 hr were profiled for lncRNAs and mRNAs using the Arraystar Human lncRNA Expression Microarray V3.0. RESULTS Of the 30,584 different lncRNAs screened, 95 were significantly upregulated, while 86 were downregulated in HUVECs responding to pravastatin. LINC00281 and BC045663 were the most upregulated (~8-fold) and downregulated (~3.5-fold) lncRNAs, respectively. Of the 26,106 different mRNAs screened in the pravastatin-treated HUVEC samples, 190 were significantly upregulated, while 90 were downregulated. Assigning the differentially expressed genes by bioinformatics into functional groups revealed their molecular signaling involvement in the following physiological processes: osteoclast differentiation, Rap1 signaling pathway, hematopoiesis, immunity, and neurotrophin signaling pathway. CONCLUSIONS This is the first lncRNA and mRNA expression profiling of pravastatin-mediated changes in human endothelial cells. Our results reveal potential novel targets and mechanisms for pravastatin-mediated vascular protection in atherosclerosis.
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Affiliation(s)
- Shweta Singh
- Department of Chemical and Biochemical EngineeringSchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
| | - Hien C. Nguyen
- Department of Medical BiophysicsSchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
- Department of Anatomy and Cell BiologySchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
| | - Mehroz Ehsan
- Department of Medical BiophysicsSchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
- Schulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
| | - David C. R. Michels
- Department of Medical BiophysicsSchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
| | - Priyanka Singh
- Schulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
| | - Mohammad Qadura
- Vascular SurgeryKeenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoONCanada
- Institute of Medical ScienceUniversity of TorontoTorontoONCanada
| | - Krishna K. Singh
- Department of Medical BiophysicsSchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
- Department of Anatomy and Cell BiologySchulich School of Medicine and DentistryUniversity of Western OntarioLondonONCanada
- Institute of Medical ScienceUniversity of TorontoTorontoONCanada
- Pharmacology and ToxicologyUniversity of TorontoTorontoONCanada
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33
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Regional Differences in Neuroinflammation-Associated Gene Expression in the Brain of Sporadic Creutzfeldt-Jakob Disease Patients. Int J Mol Sci 2020; 22:ijms22010140. [PMID: 33375642 PMCID: PMC7795938 DOI: 10.3390/ijms22010140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/15/2023] Open
Abstract
Neuroinflammation is an essential part of neurodegeneration. Yet, the current understanding of neuroinflammation-associated molecular events in distinct brain regions of prion disease patients is insufficient to lay the ground for effective treatment strategies targeting this complex neuropathological process. To address this problem, we analyzed the expression of 800 neuroinflammation-associated genes to create a profile of biological processes taking place in the frontal cortex and cerebellum of patients who suffered from sporadic Creutzfeldt-Jakob disease. The analysis was performed using NanoString nCounter technology with human neuroinflammation panel+. The observed gene expression patterns were regionally and sub-regionally distinct, suggesting a variable neuroinflammatory response. Interestingly, the observed differences could not be explained by the molecular subtypes of sporadic Creutzfeldt-Jakob disease. Furthermore, analyses of canonical pathways and upstream regulators based on differentially expressed genes indicated an overlap between biological processes taking place in different brain regions. This suggests that even smaller-scale spatial data reflecting subtle changes in brain cells' functional heterogeneity and their immediate pathologic microenvironments are needed to explain the observed differential gene expression in a greater detail.
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34
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Ali AM, Kunugi H. Royal Jelly as an Intelligent Anti-Aging Agent-A Focus on Cognitive Aging and Alzheimer's Disease: A Review. Antioxidants (Basel) 2020; 9:E937. [PMID: 33003559 PMCID: PMC7601550 DOI: 10.3390/antiox9100937] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
The astronomical increase of the world's aged population is associated with the increased prevalence of neurodegenerative diseases, heightened disability, and extremely high costs of care. Alzheimer's Disease (AD) is a widespread, age-related, multifactorial neurodegenerative disease that has enormous social and financial drawbacks worldwide. The unsatisfactory outcomes of available AD pharmacotherapy necessitate the search for alternative natural resources that can target various the underlying mechanisms of AD pathology and reduce disease occurrence and/or progression. Royal jelly (RJ) is the main food of bee queens; it contributes to their fertility, long lifespan, and memory performance. It represents a potent nutraceutical with various pharmacological properties, and has been used in a number of preclinical studies to target AD and age-related cognitive deterioration. To understand the mechanisms through which RJ affects cognitive performance both in natural aging and AD, we reviewed the literature, elaborating on the metabolic, molecular, and cellular mechanisms that mediate its anti-AD effects. Preclinical findings revealed that RJ acts as a multidomain cognitive enhancer that can restore cognitive performance in aged and AD models. It promotes brain cell survival and function by targeting multiple adversities in the neuronal microenvironment such as inflammation, oxidative stress, mitochondrial alterations, impaired proteostasis, amyloid-β toxicity, Ca excitotoxicity, and bioenergetic challenges. Human trials using RJ in AD are limited in quantity and quality. Here, the limitations of RJ-based treatment strategies are discussed, and directions for future studies examining the effect of RJ in cognitively impaired subjects are noted.
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Affiliation(s)
- Amira Mohammed Ali
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatric Nursing and Mental Health, Faculty of Nursing, Alexandria University, Alexandria 21527, Egypt
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan
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35
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Dhirachaikulpanich D, Li X, Porter LF, Paraoan L. Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration. Front Cell Dev Biol 2020; 8:808. [PMID: 32984320 PMCID: PMC7480186 DOI: 10.3389/fcell.2020.00808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
We report for the first time an integrated transcriptomic analysis of RPE/choroid dysfunction in AMD (mixed stages) based on combining data from publicly available microarray (GSE29801) and RNAseq (GSE135092) datasets aimed at increasing the ability and power of detection of differentially expressed genes and AMD-associated pathways. The analysis approach employed an integrating quantitative method designed to eliminate bias among different transcriptomic studies. The analysis highlighted 764 meta-genes (366 downregulated and 398 upregulated) in macular AMD RPE/choroid and 445 meta-genes (244 downregulated and 201 upregulated) in non-macular AMD RPE/choroid. Of these, 731 genes were newly detected as differentially expressed (DE) genes in macular AMD RPE/choroid and 434 genes in non-macular AMD RPE/choroid compared with controls. Over-representation analysis of KEGG pathways associated with these DE genes mapped revealed two most significantly associated biological processes in macular RPE/choroid in AMD, namely the neuroactive ligand-receptor interaction pathway (represented by 30 DE genes) and the extracellular matrix-receptor interaction signaling pathway (represented by 12 DE genes). Furthermore, protein-protein interaction (PPI) network identified two central hub genes involved in the control of cell proliferation/differentiation processes, HDAC1 and CDK1. Overall, the analysis provided novel insights for broadening the exploration of AMD pathogenesis by extending the number of molecular determinants and functional pathways that underpin AMD-associated RPE/choroid dysfunction.
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Affiliation(s)
- Dhanach Dhirachaikulpanich
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom.,Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xin Li
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Louise F Porter
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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36
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Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis. Commun Biol 2020; 3:409. [PMID: 32732995 PMCID: PMC7393105 DOI: 10.1038/s42003-020-01124-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/26/2020] [Indexed: 12/23/2022] Open
Abstract
The imbalance of prenatal micronutrients may perturb one-carbon (C1) metabolism and increase the risk for neuropsychiatric disorders. Prenatal excessive methionine (MET) produces in mice behavioral phenotypes reminiscent of human schizophrenia. Whether in-utero programming or early life caregiving mediate these effects is, however, unknown. Here, we show that the behavioral deficits of MET are independent of the early life mother-infant interaction. We also show that MET produces in early life profound changes in the brain C1 pathway components as well as glutamate transmission, mitochondrial function, and lipid metabolism. Bioinformatics analysis integrating metabolomics and transcriptomic data reveal dysregulations of glutamate transmission and lipid metabolism, and identify perturbed pathways of methylation and redox reactions. Our transcriptomics Linkage analysis of MET mice and schizophrenia subjects reveals master genes involved in inflammation and myelination. Finally, we identify potential metabolites as early biomarkers for neurodevelopmental defects and suggest therapeutic targets for schizophrenia. Chen, Alhassen et al. show that schizophrenia-like behavioral deficits induced by excessive prenatal methionine administration are due to in-uterus aberrations rather than through early life mother-infant interaction in mice. This study identifies the brain metabolites and transcriptomic signatures, which potentially serve as early biomarkers for schizophrenia-like behaviors.
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37
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Gil L, Niño SA, Chi-Ahumada E, Rodríguez-Leyva I, Guerrero C, Rebolledo AB, Arias JA, Jiménez-Capdeville ME. Perinuclear Lamin A and Nucleoplasmic Lamin B2 Characterize Two Types of Hippocampal Neurons through Alzheimer's Disease Progression. Int J Mol Sci 2020; 21:E1841. [PMID: 32155994 PMCID: PMC7084765 DOI: 10.3390/ijms21051841] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent reports point to a nuclear origin of Alzheimer's disease (AD). Aged postmitotic neurons try to repair their damaged DNA by entering the cell cycle. This aberrant cell cycle re-entry involves chromatin modifications where nuclear Tau and the nuclear lamin are involved. The purpose of this work was to elucidate their participation in the nuclear pathological transformation of neurons at early AD. METHODOLOGY The study was performed in hippocampal paraffin embedded sections of adult, senile, and AD brains at I-VI Braak stages. We analyzed phospho-Tau, lamins A, B1, B2, and C, nucleophosmin (B23) and the epigenetic marker H4K20me3 by immunohistochemistry. RESULTS Two neuronal populations were found across AD stages, one is characterized by a significant increase of Lamin A expression, reinforced perinuclear Lamin B2, elevated expression of H4K20me3 and nuclear Tau loss, while neurons with nucleoplasmic Lamin B2 constitute a second population. CONCLUSIONS The abnormal cell cycle reentry in early AD implies a fundamental neuronal transformation. This implies the reorganization of the nucleo-cytoskeleton through the expression of the highly regulated Lamin A, heterochromatin repression and building of toxic neuronal tangles. This work demonstrates that nuclear Tau and lamin modifications in hippocampal neurons are crucial events in age-related neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Erika Chi-Ahumada
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | | | - Carmen Guerrero
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Belén Rebolledo
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - José A. Arias
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
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38
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Toro-Domínguez D, Villatoro-García JA, Martorell-Marugán J, Román-Montoya Y, Alarcón-Riquelme ME, Carmona-Sáez P. A survey of gene expression meta-analysis: methods and applications. Brief Bioinform 2020; 22:1694-1705. [PMID: 32095826 DOI: 10.1093/bib/bbaa019] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.
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Affiliation(s)
- Daniel Toro-Domínguez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Juan Antonio Villatoro-García
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Jordi Martorell-Marugán
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Yolanda Román-Montoya
- Department of Statistics and Operations Research, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain.,Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute, 171 67, Solna, Sweden
| | - Pedro Carmona-Sáez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
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Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer's Disease Dementia. Int J Mol Sci 2019; 20:ijms20215403. [PMID: 31671574 PMCID: PMC6862214 DOI: 10.3390/ijms20215403] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Dementia is a major public health concern affecting approximately 47 million people worldwide. Mild cognitive impairment (MCI) is one form of dementia that affects an individual’s memory with or without affecting their daily life. Alzheimer’s disease dementia (ADD) is a more severe form of dementia that usually affects elderly individuals. It remains unclear whether MCI is a distinct disorder from or an early stage of ADD. Methods: Gene expression data from blood were analyzed to identify potential biomarkers that may be useful for distinguishing between these two forms of dementia. Results: A meta-analysis revealed 91 genes dysregulated in individuals with MCI and 387 genes dysregulated in ADD. Pathway analysis identified seven pathways shared between MCI and ADD and nine ADD-specific pathways. Fifteen transcription factors were associated with MCI and ADD, whereas seven transcription factors were specific for ADD. Mir-335-5p was specific for ADD, suggesting that it may be useful as a biomarker. Diseases that are associated with MCI and ADD included developmental delays, cognition impairment, and movement disorders. Conclusion: These results provide a better molecular understanding of peripheral changes that occur in MCI and ADD patients and may be useful in the identification of diagnostic and prognostic biomarkers.
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