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Manipur I, Giordano M, Piccirillo M, Parashuraman S, Maddalena L. Community Detection in Protein-Protein Interaction Networks and Applications. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:217-237. [PMID: 34951849 DOI: 10.1109/tcbb.2021.3138142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The ability to identify and characterize not only the protein-protein interactions but also their internal modular organization through network analysis is fundamental for understanding the mechanisms of biological processes at the molecular level. Indeed, the detection of the network communities can enhance our understanding of the molecular basis of disease pathology, and promote drug discovery and disease treatment in personalized medicine. This work gives an overview of recent computational methods for the detection of protein complexes and functional modules in protein-protein interaction networks, also providing a focus on some of its applications. We propose a systematic reformulation of frequently adopted taxonomies for these methods, also proposing new categories to keep up with the most recent research. We review the literature of the last five years (2017-2021) and provide links to existing data and software resources. Finally, we survey recent works exploiting module identification and analysis, in the context of a variety of disease processes for biomarker identification and therapeutic target detection. Our review provides the interested reader with an up-to-date and self-contained view of the existing research, with links to state-of-the-art literature and resources, as well as hints on open issues and future research directions in complex detection and its applications.
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Dong S, Wu C, Song C, Qi B, Liu L, Xu Y. Identification of Primary and Metastatic Lung Cancer-Related lncRNAs and Potential Targeted Drugs Based on ceRNA Network. Front Oncol 2021; 10:628930. [PMID: 33614509 PMCID: PMC7886985 DOI: 10.3389/fonc.2020.628930] [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: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Lung cancer metastasis is the leading cause of poor prognosis and death for patients. Long noncoding RNAs (lncRNAs) have been validated the close correlation with lung cancer metastasis, but few comprehensive analyses have reported the specific association between lncRNA and cancer metastasis, especially via both competing endogenous RNA (ceRNA) regulatory relationships and functional regulatory networks. Here, we constructed primary and metastatic ceRNA networks, identified 12 and 3 candidate lncRNAs for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) respectively and excavated some drugs that might have potential therapeutic effects on lung cancer progression. In summary, this study systematically analyzed the competitive relationships and regulatory mechanism of the repeatedly dysregulated lncRNAs in lung cancer carcinogenesis and metastasis, and provided a new idea for screening potential therapeutic drugs for lung cancer.
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Affiliation(s)
- Siyao Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Cheng Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chengyan Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Baocui Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Lu HH, Lin SY, Weng RR, Juan YH, Chen YW, Hou HH, Hung ZC, Oswita GA, Huang YJ, Guu SY, Khoo KH, Shih JY, Yu CJ, Tsai HC. Fucosyltransferase 4 shapes oncogenic glycoproteome to drive metastasis of lung adenocarcinoma. EBioMedicine 2020; 57:102846. [PMID: 32629386 PMCID: PMC7339020 DOI: 10.1016/j.ebiom.2020.102846] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aberrant fucosylation plays a critical role in lung cancer progression. Nevertheless, the key fucosyltransferase with prognostic significance in lung cancer patients, the enzyme's intracellular targets, and complex molecular mechanisms underlying lung cancer metastasis remain incompletely understood. METHODS We performed a large-scale transcriptome-clinical correlation to identify major fucosyltransferases with significant prognostic values. Invasion, migration, cell adhesion assays were performed using lung cancer cells subject to genetic manipulation of FUT4 levels. Genome-wide RNA-seq and immunoprecipitation-mass spectrometry were used to characterize major cellular processes driven by FUT4, as well as profiling its intracellular protein targets. We also performed lung homing and metastasis assays in mouse xenograft models to determine in vivo phenotypes of high FUT4-expressing cancer cells. FINDINGS We show that FUT4 is associated with poor overall survival in lung adenocarcinoma patients. High FUT4 expression promotes lung cancer invasion, migration, epithelial-to-mesenchymal transition, and cell adhesion. FUT4-mediated aberrant fucosylation markedly activates multiple cellular processes, including membrane trafficking, cell cycle, and major oncogenic signaling pathways. The effects are independent of receptor tyrosine kinase mutations. Notably, genetic depletion of FUT4 or targeting FUT4-driven pathways diminishes lung colonization and distant metastases of lung cancer cells in mouse xenograft models. INTERPRETATION We propose that FUT4 can be a prognostic predictor and therapeutic target in lung cancer metastasis. Our data provide a scientific basis for a potential therapeutic strategy using targeted therapy in a subset of patients with high FUT4-expressing tumors with no targetable mutations.
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Affiliation(s)
- Hsuan-Hsuan Lu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan
| | - Shu-Yung Lin
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Rueyhung Roc Weng
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan
| | - Yi-Hsiu Juan
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan
| | - Yen-Wei Chen
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No. 1, Jen Ai Rd, Section 1, Zhongzheng District, Taipei 10051, Taiwan
| | - Hsin-Han Hou
- Graduate Institute of Oral Biology, College of Medicine National Taiwan University, Taipei 10051, Taiwan
| | - Zheng-Ci Hung
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan
| | - Giovanni Audrey Oswita
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No. 1, Jen Ai Rd, Section 1, Zhongzheng District, Taipei 10051, Taiwan
| | - Yi-Jhen Huang
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No. 1, Jen Ai Rd, Section 1, Zhongzheng District, Taipei 10051, Taiwan
| | - Shih-Yun Guu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jin-Yuan Shih
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan; Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
| | - Hsing-Chen Tsai
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Zhongshan S Rd, Zhongzheng District, Taipei 10002, Taiwan; Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No. 1, Jen Ai Rd, Section 1, Zhongzheng District, Taipei 10051, Taiwan.
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