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Yu L, Zhang Y, Xue L, Liu F, Jing R, Luo J. EnsembleDL-ATG: Identifying autophagy proteins by integrating their sequence and evolutionary information using an ensemble deep learning framework. Comput Struct Biotechnol J 2023; 21:4836-4848. [PMID: 37854634 PMCID: PMC10579870 DOI: 10.1016/j.csbj.2023.09.036] [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: 05/09/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
Autophagy is a primary mechanism for maintaining cellular homeostasis. The synergistic actions of autophagy-related (ATG) proteins strictly regulate the whole autophagic process. Therefore, accurate identification of ATGs is a first and critical step to reveal the molecular mechanism underlying the regulation of autophagy. Current computational methods can predict ATGs from primary protein sequences, but owing to the limitations of algorithms, significant room for improvement still exists. In this research, we propose EnsembleDL-ATG, an ensemble deep learning framework that aggregates multiple deep learning models to predict ATGs from protein sequence and evolutionary information. We first evaluated the performance of individual networks for various feature descriptors to identify the most promising models. Then, we explored all possible combinations of independent models to select the most effective ensemble architecture. The final framework was built and maintained by an organization of four different deep learning models. Experimental results show that our proposed method achieves a prediction accuracy of 94.5 % and MCC of 0.890, which are nearly 4 % and 0.08 higher than ATGPred-FL, respectively. Overall, EnsembleDL-ATG is the first ATG machine learning predictor based on ensemble deep learning. The benchmark data and code utilized in this study can be accessed for free at https://github.com/jingry/autoBioSeqpy/tree/2.0/examples/EnsembleDL-ATG.
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Affiliation(s)
- Lezheng Yu
- School of Chemistry and Materials Science, Guizhou Education University, Guiyang 550018, Guizhou, China
- Basic Medical College, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Yonglin Zhang
- Department of Pharmacy, The Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan, China
| | - Li Xue
- School of Public Health, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Fengjuan Liu
- School of Geography and Resources, Guizhou Education University, Guiyang 550018, Guizhou, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Jiesi Luo
- Basic Medical College, Southwest Medical University, Luzhou 646000, Sichuan, China
- Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, Sichuan, China
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Xiong S, Yu S, Wang K, Xiong X, Xia M, Zeng G, Huang Q. Dietary Apigenin Relieves Body Weight and Glycolipid Metabolic Disturbance via Pro-Browning of White Adipose Mediated by Autophagy Inhibition. Mol Nutr Food Res 2023; 67:e2200763. [PMID: 37436078 DOI: 10.1002/mnfr.202200763] [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: 11/03/2022] [Revised: 06/05/2023] [Indexed: 07/13/2023]
Abstract
SCOPE Apigenin (AP) has many pharmacological activities, including anti-inflammation, hyperlipidemia-lowering, and so on. Previous studies show that AP can reduce lipid accumulation in adipocytes in vitro. However, it remains unclear whether and how AP can promote fat-browning. Therefore, mouse obesity model and preadipocyte induction model in vitro are used to investigate the effects of AP on glycolipid metabolism, browning and autophagy as well as the possible mechanisms. METHODS AND RESULTS The obese mice are intragastrically administrated with AP (0.1 mg g-1 d-1 ) for 4 weeks; meanwhile, the differentiating preadipocytes are respectively treated with the indicated concentrations of AP for 48 h. Metabolic phenotype, lipid accumulation, and fat-browning are respectively evaluated by morphological, functional, and specific markers analysis. The results show that AP treatment alleviates the body weight, glycolipid metabolic disorder, and insulin resistance in the obese mice , which is contributed to the pro-browning effects of AP in vivo and in vitro. Moreover, the study finds that the pro-browning effect of AP is accomplished through autophagy inhibition mediated by the activation of PI3K-Akt-mTOR pathway. CONCLUSIONS The findings highlight that autophagy inhibition promotes the browning of white adipocytes and suggest that AP would prevent and treat obesity and the associated metabolic disorders.
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Affiliation(s)
- Shaofeng Xiong
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Shumin Yu
- Nanchang Joint Programme, Queen Mary University of London, Nanchang, Jiangxi, 330006, P. R. China
- 302 Clinical Medical School, Peking University, Beijing, 100039, P. R. China
| | - Kun Wang
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Xiaowei Xiong
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Min Xia
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Guohua Zeng
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Qiren Huang
- Provincial Key Laboratory of Basic Pharmacology, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
- Department of Pharmacology, School of Pharmacy, Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
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Ivanova T, Mariienko Y, Mehterov N, Kazakova M, Sbirkov Y, Todorova K, Hayrabedyan S, Sarafian V. Autophagy and SARS-CoV-2-Old Players in New Games. Int J Mol Sci 2023; 24:7734. [PMID: 37175443 PMCID: PMC10178552 DOI: 10.3390/ijms24097734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
At present it is well-defined that autophagy is a fundamental process essential for cell life but its pro-viral and anti-viral role has been stated out with the COVID pandemic. However, viruses in turn have evolved diverse adaptive strategies to cope with autophagy driven host defense, either by blocking or hijacking the autophagy machinery for their own benefit. The mechanisms underlying autophagy modulation are presented in the current review which summarizes the accumulated knowledge on the crosstalk between autophagy and viral infections, with a particular emphasizes on SARS-CoV-2. The different types of autophagy related to infections and their molecular mechanisms are focused in the context of inflammation. In particular, SARS-CoV-2 entry, replication and disease pathogenesis are discussed. Models to study autophagy and to formulate novel treatment approaches and pharmacological modulation to fight COVID-19 are debated. The SARS-CoV-2-autophagy interplay is presented, revealing the complex dynamics and the molecular machinery of autophagy. The new molecular targets and strategies to treat COVID-19 effectively are envisaged. In conclusion, our finding underline the importance of development new treatment strategies and pharmacological modulation of autophagy to fight COVID-19.
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Affiliation(s)
- Tsvetomira Ivanova
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Yuliia Mariienko
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Krassimira Todorova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Soren Hayrabedyan
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
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Huang H, Pan R, Wang S, Guan Y, Zhao Y, Liu X. Current and potential roles of RNA modification-mediated autophagy dysregulation in cancer. Arch Biochem Biophys 2023; 736:109542. [PMID: 36758911 DOI: 10.1016/j.abb.2023.109542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Autophagy, a cellular lysosomal degradation and survival pathway, supports nutrient recycling and adaptation to metabolic stress and participates in various stages of tumor development, including tumorigenesis, metastasis, and malignant state maintenance. Among the various factors contributing to the dysregulation of autophagy in cancer, RNA modification can regulate autophagy by directly affecting the expression of core autophagy proteins. We propose that autophagy disorder mediated by RNA modification is an important mechanism for cancer development. Therefore, this review mainly discusses the role of RNA modification-mediated autophagy regulation in tumorigenesis. We summarize the molecular basis of autophagy and the core proteins and complexes at different stages of autophagy, especially those involved in cancer development. Moreover, we describe the crosstalk of RNA modification and autophagy and review the recent advances and potential role of the RNA modification/autophagy axis in the development of multiple cancers. Furthermore, the dual role of the RNA modification/autophagy axis in cancer drug resistance is discussed. A comprehensive understanding and extensive exploration of the molecular crosstalk of RNA modifications with autophagy will provide important insights into tumor pathophysiology and provide more options for cancer therapeutic strategies.
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Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Ruining Pan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhao
- Intensive Care Unit, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
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DI Stefano A, Gnemmi I, Dossena F, Ricciardolo FL, Maniscalco M, Lo Bello F, Balbi B. Pathogenesis of COPD at the cellular and molecular level. Minerva Med 2022; 113:405-423. [PMID: 35138077 DOI: 10.23736/s0026-4806.22.07927-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chronic inflammatory responses in the lung of patients with stable mild-to severe forms of COPD play a central role in the definition, comprehension and monitoring of the disease state. A better understanding of the COPD pathogenesis can't avoid a detailed knowledge of these inflammatory changes altering the functional health of the lung during the disease progression. We here summarize and discuss the role and principal functions of the inflammatory cells populating the large, small airways and lung parenchyma of patients with COPD of increasing severity in comparison with healthy control subjects: T and B lymphocytes, NK and Innate Lymphoid cells, macrophages, and neutrophils. The differential inflammatory distribution in large and small airways of patients is also discussed. Furthermore, relevant cellular mechanisms controlling the homeostasis and the "normal" balance of these inflammatory cells and of structural cells in the lung, such as autophagy, apoptosis, necroptosis and pyroptosis are as well presented and discussed in the context of the COPD severity.
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Affiliation(s)
- Antonino DI Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell'Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, SpA, Società Benefit, IRCCS, Veruno, Novara, Italy -
| | - Isabella Gnemmi
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell'Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, SpA, Società Benefit, IRCCS, Veruno, Novara, Italy
| | - Francesca Dossena
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell'Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, SpA, Società Benefit, IRCCS, Veruno, Novara, Italy
| | - Fabio L Ricciardolo
- Rare Lung Disease Unit and Severe Asthma Centre, Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital Orbassano, University of Turin, Turin, Italy
| | - Mauro Maniscalco
- Divisione di Pneumologia, Istituti Clinici Scientifici Maugeri, SpA, Società Benefit, IRCCS, Telese, Benevento, Italy
| | - Federica Lo Bello
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Bruno Balbi
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell'Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, SpA, Società Benefit, IRCCS, Veruno, Novara, Italy
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Su HC, Casanova JL. Editorial overview: Human inborn errors of immunity to infection. Curr Opin Immunol 2021; 72:iii-v. [PMID: 34742535 DOI: 10.1016/j.coi.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Intramural Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA
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