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Lei J, Aimaier G, Aisha Z, Zhang Y, Ma J. eEF1A1 regulates the expression and alternative splicing of genes associated with Parkinson's disease in U251 cells. Genes Genomics 2024; 46:817-829. [PMID: 38776049 DOI: 10.1007/s13258-024-01516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/12/2023] [Indexed: 06/27/2024]
Abstract
BACKGROUND Eukaryotic elongation factor 1A1 (eEF1A1) is an RNA-binding protein that is associated with PARK2 activity in cells, suggesting a possible role in Parkinson's disease (PD). OBJECTIVE To clear whether eEF1A1 plays a role in PD through transcriptional or posttranscriptional regulation. METHODS The GSE68719 dataset was downloaded from the GEO database, and the RNA-seq data of all brain tissue autopsies were obtained from 29 PD patients and 44 neurologically normal control subjects. To inhibit eEF1A1 from being expressed in U251 cells, siRNA was transfected into those cells, and RNA-seq high-throughput sequencing was used to determine the differentially expressed genes (DEGs) and differentially alternative splicing events (ASEs) resulting from eEF1A1 knockdown. RESULTS eEF1A1 was significantly overexpressed in PD brain tissue in the BA9 area. GO and KEGG enrichment analyses revealed that eEF1A1 knockdown significantly upregulated the expression of the genes CXCL10, NGF, PTX3, IL6, ST6GALNAC3, NUPR1, TNFRSF21, and CXCL2 and upregulated the alternative splicing of the genes ACOT7, DDX10, SHMT2, MYEF2, and NDUFAF5. These genes were enriched in pathways related to PD pathogenesis, such as apoptosis, inflammatory response, and mitochondrial dysfunction. CONCLUSION The results suggesting that eEF1A1 involved in the development of PD by regulating the differential expression and alternative splicing of genes, providing a theoretical basis for subsequent research.
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Affiliation(s)
- Jing Lei
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan South Road, Xinshi District, Urumqi, Xinjiang, 830054, P.R. China
| | - Guliqiemu Aimaier
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan South Road, Xinshi District, Urumqi, Xinjiang, 830054, P.R. China
| | - Zaolaguli Aisha
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan South Road, Xinshi District, Urumqi, Xinjiang, 830054, P.R. China
| | - Yan Zhang
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan South Road, Xinshi District, Urumqi, Xinjiang, 830054, P.R. China
| | - Jianhua Ma
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan South Road, Xinshi District, Urumqi, Xinjiang, 830054, P.R. China.
- Xinjiang Medical University, Urumqi, Xinjiang, 830054, China.
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Sun L, Qiu Y, Ching WK, Zhao P, Zou Q. PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression. PLoS Comput Biol 2023; 19:e1010939. [PMID: 36930678 PMCID: PMC10057809 DOI: 10.1371/journal.pcbi.1010939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/29/2023] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
During breast cancer metastasis, the developmental process epithelial-mesenchymal (EM) transition is abnormally activated. Transcriptional regulatory networks controlling EM transition are well-studied; however, alternative RNA splicing also plays a critical regulatory role during this process. Alternative splicing was proved to control the EM transition process, and RNA-binding proteins were determined to regulate alternative splicing. A comprehensive understanding of alternative splicing and the RNA-binding proteins that regulate it during EM transition and their dynamic impact on breast cancer remains largely unknown. To accurately study the dynamic regulatory relationships, time-series data of the EM transition process are essential. However, only cross-sectional data of epithelial and mesenchymal specimens are available. Therefore, we developed a pseudotemporal causality-based Bayesian (PCB) approach to infer the dynamic regulatory relationships between alternative splicing events and RNA-binding proteins. Our study sheds light on facilitating the regulatory network-based approach to identify key RNA-binding proteins or target alternative splicing events for the diagnosis or treatment of cancers. The data and code for PCB are available at: http://hkumath.hku.hk/~wkc/PCB(data+code).zip.
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Affiliation(s)
- Liangjie Sun
- Department of Mathematics, The University of Hong Kong, Hong Kong, China
| | - Yushan Qiu
- College of Mathematics and Statistics, Shenzhen University, Shenzhen, China
- * E-mail:
| | - Wai-Ki Ching
- Department of Mathematics, The University of Hong Kong, Hong Kong, China
| | - Pu Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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Cheng X, Yan C, Jiang H, Qiu Y. scHOIS: Determining Cell Heterogeneity Through Hierarchical Clustering Based on Optimal Imputation Strategy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1431-1444. [PMID: 37815942 DOI: 10.1109/tcbb.2022.3203592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Advances in single-cell RNA sequencing (scRNA-seq) technology provide an unbiased and high-throughput analysis of each cell at single-cell resolution, and further facilitate the development of cellular heterogeneity analysis. Despite the promise of scRNA-seq, the data generated by this method are sparse and noisy because of the presence of dropout events, which can greatly impact downstream analyses such as differential gene expression, cell type annotation, and linage trajectory reconstruction. The development of effective and robust computational methods to address both dropout and clustering are thus urgently needed. In this study, we propose a flexible, accurate two-stage algorithm for single cell heterogeneity analysis via hierarchical clustering based on an optimal imputation strategy, called scHOIS. At the first stage, masked non-negative matrix factorization is applied to approximate the original observed scRNA-seq data, with optimal rank determined by variance analysis. At the second stage, hierarchical clustering is applied to group the imputed cells using Pearson correlation to measure similarity, with the optimal number of clusters determined by integrating three classical indexes. We performed extensive experiments on real-world datasets, which showed that scHOIS effectively and robustly distinguished cellular differences and that the clustering performance of this algorithm was superior to that of other state-of-the-art methods.
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Zhang Y, Hu Y, Li H, Liu X. Drug-protein interaction prediction via variational autoencoders and attention mechanisms. Front Genet 2022; 13:1032779. [PMID: 36313473 PMCID: PMC9614151 DOI: 10.3389/fgene.2022.1032779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 09/29/2023] Open
Abstract
During the process of drug discovery, exploring drug-protein interactions (DPIs) is a key step. With the rapid development of biological data, computer-aided methods are much faster than biological experiments. Deep learning methods have become popular and are mainly used to extract the characteristics of drugs and proteins for further DPIs prediction. Since the prediction of DPIs through machine learning cannot fully extract effective features, in our work, we propose a deep learning framework that uses variational autoencoders and attention mechanisms; it utilizes convolutional neural networks (CNNs) to obtain local features and attention mechanisms to obtain important information about drugs and proteins, which is very important for predicting DPIs. Compared with some machine learning methods on the C.elegans and human datasets, our approach provides a better effect. On the BindingDB dataset, its accuracy (ACC) and area under the curve (AUC) reach 0.862 and 0.913, respectively. To verify the robustness of the model, multiclass classification tasks are performed on Davis and KIBA datasets, and the ACC values reach 0.850 and 0.841, respectively, thus further demonstrating the effectiveness of the model.
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Affiliation(s)
- Yue Zhang
- School of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, China
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Yang Y, Tian S, Qiu Y, Zhao P, Zou Q. MDICC: novel method for multi-omics data integration and cancer subtype identification. Brief Bioinform 2022; 23:6569541. [PMID: 35437603 DOI: 10.1093/bib/bbac132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/11/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022] Open
Abstract
Each type of cancer usually has several subtypes with distinct clinical implications, and therefore the discovery of cancer subtypes is an important and urgent task in disease diagnosis and therapy. Using single-omics data to predict cancer subtypes is difficult because genomes are dysregulated and complicated by multiple molecular mechanisms, and therefore linking cancer genomes to cancer phenotypes is not an easy task. Using multi-omics data to effectively predict cancer subtypes is an area of much interest; however, integrating multi-omics data is challenging. Here, we propose a novel method of multi-omics data integration for clustering to identify cancer subtypes (MDICC) that integrates new affinity matrix and network fusion methods. Our experimental results show the effectiveness and generalization of the proposed MDICC model in identifying cancer subtypes, and its performance was better than those of currently available state-of-the-art clustering methods. Furthermore, the survival analysis demonstrates that MDICC delivered comparable or even better results than many typical integrative methods.
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Affiliation(s)
- Ying Yang
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Sha Tian
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Yushan Qiu
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Pu Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610056, China
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Vahabi N, Michailidis G. Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review. Front Genet 2022; 13:854752. [PMID: 35391796 PMCID: PMC8981526 DOI: 10.3389/fgene.2022.854752] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Through the developments of Omics technologies and dissemination of large-scale datasets, such as those from The Cancer Genome Atlas, Alzheimer’s Disease Neuroimaging Initiative, and Genotype-Tissue Expression, it is becoming increasingly possible to study complex biological processes and disease mechanisms more holistically. However, to obtain a comprehensive view of these complex systems, it is crucial to integrate data across various Omics modalities, and also leverage external knowledge available in biological databases. This review aims to provide an overview of multi-Omics data integration methods with different statistical approaches, focusing on unsupervised learning tasks, including disease onset prediction, biomarker discovery, disease subtyping, module discovery, and network/pathway analysis. We also briefly review feature selection methods, multi-Omics data sets, and resources/tools that constitute critical components for carrying out the integration.
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Affiliation(s)
- Nasim Vahabi
- Informatics Institute, University of Florida, Gainesville, FL, United States
| | - George Michailidis
- Informatics Institute, University of Florida, Gainesville, FL, United States
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Yao Z, Zhu G, Too J, Duan M, Wang Z. Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches. Front Genet 2022; 12:793629. [PMID: 35350819 PMCID: PMC8957794 DOI: 10.3389/fgene.2021.793629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022] Open
Abstract
OMIC datasets have high dimensions, and the connection among OMIC features is very complicated. It is difficult to establish linkages among these features and certain biological traits of significance. The proposed ensemble swarm intelligence-based approaches can identify key biomarkers and reduce feature dimension efficiently. It is an end-to-end method that only relies on the rules of the algorithm itself, without presets such as the number of filtering features. Additionally, this method achieves good classification accuracy without excessive consumption of computing resources.
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Affiliation(s)
- Zhaomin Yao
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Gancheng Zhu
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Jingwei Too
- Faculty of Electrical Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, Melaka, Malaysia
| | - Meiyu Duan
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Zhiguo Wang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
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Yang X, Kuang L, Chen Z, Wang L. Multi-Similarities Bilinear Matrix Factorization-Based Method for Predicting Human Microbe-Disease Associations. Front Genet 2021; 12:754425. [PMID: 34721543 PMCID: PMC8551558 DOI: 10.3389/fgene.2021.754425] [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: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Accumulating studies have shown that microbes are closely related to human diseases. In this paper, a novel method called MSBMFHMDA was designed to predict potential microbe-disease associations by adopting multi-similarities bilinear matrix factorization. In MSBMFHMDA, a microbe multiple similarities matrix was constructed first based on the Gaussian interaction profile kernel similarity and cosine similarity for microbes. Then, we use the Gaussian interaction profile kernel similarity, cosine similarity, and symptom similarity for diseases to compose the disease multiple similarities matrix. Finally, we integrate these two similarity matrices and the microbe-disease association matrix into our model to predict potential associations. The results indicate that our method can achieve reliable AUCs of 0.9186 and 0.9043 ± 0.0048 in the framework of leave-one-out cross validation (LOOCV) and fivefold cross validation, respectively. What is more, experimental results indicated that there are 10, 10, and 8 out of the top 10 related microbes for asthma, inflammatory bowel disease, and type 2 diabetes mellitus, respectively, which were confirmed by experiments and literatures. Therefore, our model has favorable performance in predicting potential microbe-disease associations.
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Affiliation(s)
- Xiaoyu Yang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China.,College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Linai Kuang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
| | - Zhiping Chen
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Lei Wang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China.,College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
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9
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Guo K, Feng Y, Zheng X, Sun L, Wasan HS, Ruan S, Shen M. Resveratrol and Its Analogs: Potent Agents to Reverse Epithelial-to-Mesenchymal Transition in Tumors. Front Oncol 2021; 11:644134. [PMID: 33937049 PMCID: PMC8085503 DOI: 10.3389/fonc.2021.644134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT), a complicated program through which polarized epithelial cells acquire motile mesothelial traits, is regulated by tumor microenvironment. EMT is involved in tumor progression, invasion and metastasis via reconstructing the cytoskeleton and degrading the tumor basement membrane. Accumulating evidence shows that resveratrol, as a non-flavonoid polyphenol, can reverse EMT and inhibit invasion and migration of human tumors via diverse mechanisms and signaling pathways. In the present review, we will summarize the detailed mechanisms and pathways by which resveratrol and its analogs (e.g. Triacetyl resveratrol, 3,5,4'-Trimethoxystilbene) might regulate the EMT process in cancer cells to better understand their potential as novel anti-tumor agents. Resveratrol can also reverse chemoresistance via EMT inhibition and improvement of the antiproliferative effects of conventional treatments. Therefore, resveratrol and its analogs have the potential to become novel adjunctive agents to inhibit cancer metastasis, which might be partly related to their blocking of the EMT process.
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Affiliation(s)
- Kaibo Guo
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqian Feng
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xueer Zheng
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Leitao Sun
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Harpreet S. Wasan
- Department of Cancer Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Shanming Ruan
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Minhe Shen
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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