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Lin L, Long Y, Liu J, Deng D, Yuan Y, Liu L, Tan B, Qi H. FRP-XGBoost: Identification of ferroptosis-related proteins based on multi-view features. Int J Biol Macromol 2024; 262:130180. [PMID: 38360239 DOI: 10.1016/j.ijbiomac.2024.130180] [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: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Ferroptosis represents a novel form of programmed cell death. Pan-cancer bioinformatics analysis indicates that identifying and modulating ferroptosis offer innovative approaches for preventing and treating diverse tumor pathologies. However, the precise detection of ferroptosis-related proteins via conventional wet-laboratory techniques remains a formidable challenge, largely due to the constraints of existing methodologies. These traditional approaches are not only labor-intensive but also financially burdensome. Consequently, there is an imperative need for the development of more sophisticated and efficient computational tools to facilitate the detection of these proteins. In this paper, we presented a XGBoost and multi-view features-based machine learning prediction method for predicting ferroptosis-related proteins, which was referred to as FRP-XGBoost. In this study, we explored four types of protein feature extraction methods and evaluated their effectiveness in predicting ferroptosis-related proteins using six of the most commonly used traditional classifiers. To enhance the representational power of the hybrid features, we employed a two-step feature selection technique to identify the optimal subset of features. Subsequently, we constructed a prediction model using the XGBoost algorithm. The FRP-XGBoost achieved an accuracy of 96.74 % in 10-fold cross-validation and a further accuracy of 91.52 % in an independent test. The implementation source code of FRP-XGBoost is available at https://github.com/linli5417/FRP-XGBoost.
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Affiliation(s)
- Li Lin
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China
| | - Yao Long
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development, Chinese Ministry of Education, Chongqing Medical University, 400016, China; Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jinkai Liu
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development, Chinese Ministry of Education, Chongqing Medical University, 400016, China; Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Dongliang Deng
- Department of Oncology, Chongqing Traditional Chinese Medicine Hospital, Chongqing 400021, China
| | - Yu Yuan
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China
| | - Lubin Liu
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China
| | - Bin Tan
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development, Chinese Ministry of Education, Chongqing Medical University, 400016, China; Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongbo Qi
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China; Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development, Chinese Ministry of Education, Chongqing Medical University, 400016, China.
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Kimira Y, Osawa K, Osawa Y, Mano H. Preventive Effects of Collagen-Derived Dipeptide Prolyl-Hydroxyproline against Dexamethasone-Induced Muscle Atrophy in Mouse C2C12 Skeletal Myotubes. Biomolecules 2023; 13:1617. [PMID: 38002299 PMCID: PMC10669392 DOI: 10.3390/biom13111617] [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: 08/17/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Glucocorticoids, commonly used to manage inflammatory diseases, can induce muscle atrophy by accelerating the breakdown of muscle proteins. This research delves into the influence of Prolyl-hydroxyproline (Pro-Hyp), a collagen-derived peptide, on muscle atrophy induced with dexamethasone (DEX), a synthetic glucocorticoid, in mouse C2C12 skeletal myotubes. Exposure to DEX (10 μM) for 6 days resulted in a decrease in myotube diameter, along with elevated mRNA and protein levels of two muscle-atrophy-related ubiquitin ligases, muscle atrophy F-box (MAFbx, also known as atrogin-1) and muscle ring finger 1 (MuRF-1). Remarkably, treatment with 0.1 mM of Pro-Hyp mitigated the reduction in myotube thickness caused by DEX, while promoting the phosphorylation of Akt, mammalian target of rapamycin (mTOR), and forkhead box O3a (Foxo3a). This led to the inhibition of the upregulation of the ubiquitin ligases atrogin-1 and MuRF-1. These findings indicate the potential significance of Pro-Hyp as a promising therapeutic target for countering DEX-induced muscle atrophy.
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Affiliation(s)
- Yoshifumi Kimira
- Department of Clinical Dietetics and Human Nutrition, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado-shi 350-0295, Japan
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Leem KH, Kim S, Lim J, Park HJ, Shin YC, Lee JS. Hydrolyzed Collagen Tripeptide Promotes Longitudinal Bone Growth in Childhood Rats via Increases in Insulin-Like Growth Factor-1 and Bone Morphogenetic Proteins. J Med Food 2023; 26:809-819. [PMID: 37862561 DOI: 10.1089/jmf.2023.k.0024] [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] [Indexed: 10/22/2023] Open
Abstract
Previous studies have reported that collagen tripeptide (CTP) derived from collagen hydrolysate has various beneficial effects on health by protecting against skin aging and improving bone formation and cartilage regeneration. Collagen-Tripep20TM (CTP20), which is a low-molecular-weight CTP derived from fish skin, contains a bioactive CTP, Gly-Pro-Hyp >3.2% with a tripeptide content >20%. Herein, we investigated the osteogenic effects and mechanisms of CTP20 (<500 Da) on MG-63 osteoblast-like cells and SW1353 chondrocytes. And we measured promoting ratio of the longitudinal bone growth in childhood rats. First, CTP20 at 100 μg/mL elevated the proliferation (15.0% and 28.2%), alkaline phosphatase activity (29.3% and 32.0%), collagen synthesis (1.25- and 1.14-fold), and calcium deposition (1.18- and 1.15-fold) in MG-63 cells and SW1353, respectively. In addition, we found that CTP20 could promote the longitudinal growth and height of the growth plate of the tibia in childhood rats. CTP20 enhanced the protein expression of insulin-like growth factor-1 (IGF-1) in MG-63 and SW1353 cells, and in the growth plate of childhood rats, along with Janus Kinase 2, and signal transducer and activator of transcription 5 activation in MG-63 and SW1353 cells. CTP20 also elevated the expression levels of bone morphogenetic proteins (BMPs) in MG-63 and SW1353 cells and in the growth plates of childhood rats. These results indicate that CTP20 may promote the endochondral ossification and longitudinal bone growth, through enhancing of IGF-1 and BMPs. (Clinical Trial Registration number: smecae 19-09-01).
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Affiliation(s)
- Kang Hyun Leem
- College of Korean Medicine, Semyung University, Jecheon, Korea
| | - Sanga Kim
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Junsik Lim
- College of Korean Medicine, Semyung University, Jecheon, Korea
| | - Hae Jeong Park
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, Korea
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Wang H. The Potential of Collagen Treatment for Comorbid Diseases. Polymers (Basel) 2023; 15:3999. [PMID: 37836047 PMCID: PMC10574914 DOI: 10.3390/polym15193999] [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: 08/30/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Collagen, the most abundant protein in our bodies, plays a crucial role in maintaining the structural integrity of various tissues and organs. Beyond its involvement in skin elasticity and joint health, emerging research suggests that collagen may significantly impact the treatment of complex diseases, particularly those associated with tissue damage and inflammation. The versatile functions of collagen, including skin regeneration, improving joint health, and increasing bone strength, make it potentially useful in treating different diseases. To the best of my knowledge, the strategy of using collagen to treat comorbid diseases has not been widely studied. This paper aims to explore the potential of collagen in treating comorbid diseases, including rheumatoid arthritis, osteoarthritis, osteoporosis, psoriatic arthritis, sarcopenia, gastroesophageal reflux, periodontitis, skin aging, and diabetes mellitus. Collagen-based therapies have shown promise in managing comorbidities due to their versatile properties. The multifaceted nature of collagen positions it as a promising candidate for treating complex diseases and addressing comorbid conditions. Its roles in wound healing, musculoskeletal disorders, cardiovascular health, and gastrointestinal conditions highlight the diverse therapeutic applications of collagen in the context of comorbidity management.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Zhu X, Wang J, Lu Y, Zhao Y, Zhang N, Wu W, Zhang Y, Fu Y. Potential of Food Protein-Derived Bioactive Peptides against Sarcopenia: A Comprehensive Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5419-5437. [PMID: 36988097 DOI: 10.1021/acs.jafc.2c09094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sarcopenia is an age-related progressive muscle disorder characterized by accelerated loss of muscle mass, strength, and function, which are important causes of physiological dysfunctions in the elderly. At present, the main alleviating method includes protein supplements to stimulate synthesis of muscle proteins. Food protein-derived peptides containing abundant branched-chain amino acids have a remarkable effect on the improvement of sarcopenia. Understanding the underlying molecular mechanism and clarifying the structure-activity relationship is essential for the mitigation of sarcopenia. This present review recaps the epidemiology, pathogenesis, diagnosis, and treatment of sarcopenia, which facilitates a comprehensive understanding of sarcopenia. Moreover, the latest research progress on food-derived antisarcopenic peptides is reviewed, including their antisarcopenic activity, molecular mechanism as well as structural characteristics. Food-derived bioactive peptides can indeed alleviate/mitigate sarcopenia. These antisarcopenic peptides play a pivotal role mainly by activating the PI3K/Akt/mTOR and MAPK pathways and inhibiting the ubiquitin-proteasome system and AMPK pathway, thus promoting the synthesis of muscle proteins and inhibiting their degradation. Antisarcopenic peptides alleviate sarcopenia via specific peptides, which may be absorbed into the circulation and exhibit their bioactivity in intact forms. The present review provides a theoretical reference for mitigation and prevention of sarcopenia by food protein-derived bioactive peptides.
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Affiliation(s)
- Xiaoxue Zhu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Yujia Lu
- Department of Epidemiology, Harvard University T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Yuchen Zhao
- Department of Epidemiology, Harvard University T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Na Zhang
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Wei Wu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing 400715, China
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The Synergistic Action of Metformin and Glycyrrhiza uralensis Fischer Extract Alleviates Metabolic Disorders in Mice with Diet-Induced Obesity. Int J Mol Sci 2023; 24:ijms24020936. [PMID: 36674447 PMCID: PMC9862386 DOI: 10.3390/ijms24020936] [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: 11/29/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023] Open
Abstract
Metformin, an antidiabetic drug, and Glycyrrhiza uralensis Fischer (GU), an oriental medicinal herb, have been reported to exert anti-obesity effects. This study investigated the synergistic action of metformin and GU in improving diet-induced obesity. Mice were fed a normal diet, a high-fat diet (HFD), or HFD + 0.015% GU water extract for 8 weeks. The HFD and GU groups were then randomly divided into two groups and fed the following diets for the next 8 weeks: HFD with 50 mg/kg metformin (HFDM) and GU with 50 mg/kg metformin (GUM). GUM prevented hepatic steatosis and adiposity by suppressing expression of mRNAs and enzyme activities related to lipogenesis in the liver and upregulating the expression of adipocyte mRNAs associated with fatty acid oxidation and lipolysis, and as a result, improved dyslipidemia. Moreover, GUM improved glucose homeostasis by inducing glucose uptake in tissues and upregulating mRNA expressions associated with glycolysis in the liver and muscle through AMP-activated protein kinase activation. GUM also improved inflammation by increasing antioxidant activity in the liver and erythrocytes and decreasing inflammatory cytokine productions. Here, we demonstrate that GU and metformin exert synergistic action in the prevention of obesity and its complications.
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Mammalian Target of Rapamycin (mTOR) Signaling at the Crossroad of Muscle Fiber Fate in Sarcopenia. Int J Mol Sci 2022; 23:ijms232213823. [PMID: 36430301 PMCID: PMC9696247 DOI: 10.3390/ijms232213823] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) is a major regulator of skeletal myocyte viability. The signaling pathways triggered by mTOR vary according to the type of endogenous and exogenous factors (e.g., redox balance, nutrient availability, physical activity) as well as organismal age. Here, we provide an overview of mTOR signaling in skeletal muscle, with a special focus on the role played by mTOR in the development of sarcopenia. Intervention strategies targeting mTOR in sarcopenia (e.g., supplementation of plant extracts, hormones, inorganic ions, calorie restriction, and exercise) have also been discussed.
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