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Zhang YH, Huang F, Li J, Shen W, Chen L, Feng K, Huang T, Cai YD. Identification of Protein-Protein Interaction Associated Functions Based on Gene Ontology. Protein J 2024; 43:477-486. [PMID: 38436837 DOI: 10.1007/s10930-024-10180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2024] [Indexed: 03/05/2024]
Abstract
Protein-protein interactions (PPIs) involve the physical or functional contact between two or more proteins. Generally, proteins that can interact with each other always have special relationships. Some previous studies have reported that gene ontology (GO) terms are related to the determination of PPIs, suggesting the special patterns on the GO terms of proteins in PPIs. In this study, we explored the special GO term patterns on human PPIs, trying to uncover the underlying functional mechanism of PPIs. The experimental validated human PPIs were retrieved from STRING database, which were termed as positive samples. Additionally, we randomly paired proteins occurring in positive samples, yielding lots of negative samples. A simple calculation was conducted to count the number of positive samples for each GO term pair, where proteins in samples were annotated by GO terms in the pair individually. The similar number for negative samples was also counted and further adjusted due to the great gap between the numbers of positive and negative samples. The difference of the above two numbers and the relative ratio compared with the number on positive samples were calculated. This ratio provided a precise evaluation of the occurrence of GO term pairs for positive samples and negative samples, indicating the latent GO term patterns for PPIs. Our analysis unveiled several nuclear biological processes, including gene transcription, cell proliferation, and nutrient metabolism, as key biological functions. Interactions between major proliferative or metabolic GO terms consistently correspond with significantly reported PPIs in recent literature.
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Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China
| | - JiaBo Li
- School of Computer Engineering and Science, Shanghai University, Shanghai, 200444, People's Republic of China
| | - WenFeng Shen
- School of Computer and Information Engineering, Shanghai Polytechnic University, Shanghai, 201209, People's Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, 510507, People's Republic of China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.
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Xiao H, Zou Y, Wang J, Wan S. A Review for Artificial Intelligence Based Protein Subcellular Localization. Biomolecules 2024; 14:409. [PMID: 38672426 PMCID: PMC11048326 DOI: 10.3390/biom14040409] [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: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcellular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.
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Affiliation(s)
- Hanyu Xiao
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Jieqiong Wang
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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Hu Y, Liu C, Yang J, Zhong M, Qian B, Chen J, Zhang Y, Song J. HMGB1 is involved in viral replication and the inflammatory response in coxsackievirus A16-infected 16HBE cells via proteomic analysis and identification. Virol J 2023; 20:178. [PMID: 37559147 PMCID: PMC10410909 DOI: 10.1186/s12985-023-02150-8] [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: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Coxsackievirus A16 (CV-A16) is still an important pathogen that causes hand, foot and mouth disease (HFMD) in young children and infants worldwide. Previous studies indicated that CV-A16 infection is usually mild or self-limiting, but it was also found that CV-A16 infection can trigger severe neurological complications and even death. However, there are currently no vaccines or antiviral compounds available to either prevent or treat CV-A16 infection. Therefore, investigation of the virus‒host interaction and identification of host proteins that play a crucial regulatory role in the pathogenesis of CV-A16 infection may provide a novel strategy to develop antiviral drugs. Here, to increase our understanding of the interaction of CV-A16 with the host cell, we analyzed changes in the proteome of 16HBE cells in response to CV-A16 using tandem mass tag (TMT) in combination with LC‒MS/MS. There were 6615 proteins quantified, and 172 proteins showed a significant alteration during CV-A16 infection. These differentially regulated proteins were involved in fundamental biological processes and signaling pathways, including metabolic processes, cytokine‒cytokine receptor interactions, B-cell receptor signaling pathways, and neuroactive ligand‒receptor interactions. Further bioinformatics analysis revealed the characteristics of the protein domains and subcellular localization of these differentially expressed proteins. Then, to validate the proteomics data, 3 randomly selected proteins exhibited consistent changes in protein expression with the TMT results using Western blotting and immunofluorescence methods. Finally, among these differentially regulated proteins, we primarily focused on HMGB1 based on its potential effects on viral replication and virus infection-induced inflammatory responses. It was demonstrated that overexpression of HMGB1 could decrease viral replication and upregulate the release of inflammatory cytokines, but deletion of HMGB1 increased viral replication and downregulated the release of inflammatory cytokines. In conclusion, the results from this study have helped further elucidate the potential molecular pathogenesis of CV-A16 based on numerous protein changes and the functions of HMGB1 Found to be involved in the processes of viral replication and inflammatory response, which may facilitate the development of new antiviral therapies as well as innovative diagnostic methods.
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Affiliation(s)
- Yajie Hu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chen Liu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jinghui Yang
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- Department of Pediatrics, The First People's Hospital of Yunnan Province, Kunming, China
| | - Mingmei Zhong
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Baojiang Qian
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Juan Chen
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
| | - Jie Song
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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Yajie H, Shenglan W, Wei Z, Rufang L, Tingting Y, Yunhui Z, Jie S. Global quantitative proteomic analysis profiles of host protein expression in response to Enterovirus A71 infection in bronchial epithelial cells based on tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS uncovers the key role of proteasome in virus replication. Virus Res 2023; 330:199118. [PMID: 37072100 DOI: 10.1016/j.virusres.2023.199118] [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: 11/24/2022] [Revised: 03/30/2023] [Accepted: 04/15/2023] [Indexed: 04/20/2023]
Abstract
Enterovirus A71 (EV-A71) is a neurotropic human pathogen which mainly caused hand, foot and mouth disease (HFMD) mostly in children under 5 years-old. Generally, EV-A71-associated HFMD is a relatively self-limiting febrile disease, but there will still be a small percentage of patients with rapid disease progression and severe neurological complications. To date, the underlying mechanism of EV-A71 inducing pathological injury of central nervous system (CNS) remains largely unclear. It has been investigated and discussed the changes of mRNA, miRNA and circRNA expression profile during infection by EV-A71 in our previous studies. However, these studies were only analyzed at the RNA level, not at the protein level. It's the protein levels that ultimately do the work in the body. Here, to address this, we performed a tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS approach to quantitatively identify cellular proteome changes at 24 h post-infection (hpi) in EV-A71-infected 16HBE cells. In total, 6615 proteins were identified by using TMT coupled with LC-MS/MS in this study. In the EV-A71- and mock-infected groups, 210 differentially expressed proteins were found, including 86 upregulated and 124 downregulated proteins, at 24 hpi. To ensure the validity and reliability of the proteomics data, 3 randomly selected proteins were verified by Western blot and Immunofluorescence analysis, and the results were consistent with the TMT results. Subsequently, functional enrichment analysis indicated that the up-regulated and down-regulated proteins were individually involved in various biological processes and signaling pathways, including metabolic process, AMPK signaling pathway, Neurotrophin signaling pathway, Viral myocarditis, GABAergic synapse, and so on. Moreover, among these enriched functional analysis, the "Proteasome" pathway was up-regulated, which has caught our attention. Inhibition of proteasome was found to obviously suppress the EV-A71 replication. Finally, further in-depth analysis revealed that these differentially expressed proteins contained distinct domains and localized in different subcellular components. Taken together, our data provided a comprehensive view of host cell response to EV-A71 and identified host proteins may lead to better understanding of the pathogenic mechanisms and host responses to EV-A71 infection, and also to the identification of new therapeutic targets for EV-A71 infection.
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Affiliation(s)
- Hu Yajie
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.; Yunnan Provincial Key Laboratory of Clinical Virology
| | - Wang Shenglan
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhao Wei
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Rufang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yang Tingting
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhang Yunhui
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China..
| | - Song Jie
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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Nakai K, Wei L. Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. FRONTIERS IN BIOINFORMATICS 2022; 2:910531. [PMID: 36304291 PMCID: PMC9580943 DOI: 10.3389/fbinf.2022.910531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Prediction of subcellular localization of proteins from their amino acid sequences has a long history in bioinformatics and is still actively developing, incorporating the latest advances in machine learning and proteomics. Notably, deep learning-based methods for natural language processing have made great contributions. Here, we review recent advances in the field as well as its related fields, such as subcellular proteomics and the prediction/recognition of subcellular localization from image data.
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Affiliation(s)
- Kenta Nakai
- Institute of Medical Science, The University of Tokyo, Minato-Ku, Japan
- *Correspondence: Kenta Nakai,
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China
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Wang S, Wu R, Lu J, Jiang Y, Huang T, Cai YD. Protein-protein interaction networks as miners of biological discovery. Proteomics 2022; 22:e2100190. [PMID: 35567424 DOI: 10.1002/pmic.202100190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022]
Abstract
Protein-protein interactions (PPIs) form the basis of a myriad of biological pathways and mechanism, such as the formation of protein-complexes or the components of signaling cascades. Here, we reviewed experimental methods for identifying PPI pairs, including yeast two-hybrid, mass spectrometry, co-localization, and co-immunoprecipitation. Furthermore, a range of computational methods leveraging biochemical properties, evolution history, protein structures and more have enabled identification of additional PPIs. Given the wealth of known PPIs, we reviewed important network methods to construct and analyze networks of PPIs. These methods aid biological discovery through identifying hub genes and dynamic changes in the network, and have been thoroughly applied in various fields of biological research. Lastly, we discussed the challenges and future direction of research utilizing the power of PPI networks. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Steven Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Runxin Wu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jiaqi Lu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Yijia Jiang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tao Huang
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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