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Jin C, Tan K, Yao Z, Lin BH, Zhang DP, Chen WK, Mao SM, Zhang W, Chen L, Lin Z, Weng SJ, Bai BL, Zheng WH, Zheng G, Wu ZY, Yang L. A Novel Anti-Osteoporosis Mechanism of VK2: Interfering with Ferroptosis via AMPK/SIRT1 Pathway in Type 2 Diabetic Osteoporosis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2745-2761. [PMID: 36719855 DOI: 10.1021/acs.jafc.2c05632] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Type 2 diabetic osteoporosis (T2DOP) is a chronic bone metabolic disease. Compared with traditional menopausal osteoporosis, the long-term high glucose (HG) microenvironment increases patients' risk of fracture and osteonecrosis. We were accumulating evidence that implicated ferroptosis as a pivotal mechanism of glucolipotoxicity-mediated death of osteocytes and osteoblast, a novel form of programmed cell death resulting from uncontrolled lipid peroxidation depending on iron. Vitamin K2 (VK2), a fat-soluble vitamin, is clinically applied to prevent osteoporosis and improve coagulation. This study aimed to clarify the role and mechanism of VK2 in HG-mediated ferroptosis. We established the mouse T2DOP model by intraperitoneal injection of streptozotocin solution and a high-fat and high-sugar diet. We also cultured bone marrow mesenchymal stem cells (BMSCs) in HG to simulate the diabetic environment in vitro. Based on our data, VK2 inhibited HG-mediated bone loss and ferroptosis, the latter manifested by decreased levels of mitochondrial reactive oxygen species, lipid peroxidation, and malondialdehyde and increased glutathione in vitro. In addition, VK2 treatment was capable of restoring bone mass and strengthening the expression of SIRT1, GPX4, and osteogenic markers in the distal femurs. As for further mechanism exploration, we found that VK2 could activate AMPK/SIRT1 signaling, and knockdown of SIRT1 by siRNA prevented the VK2-mediated positive effect in HG-cultured BMSCs. Summarily, VK2 could ameliorate T2DOP through the activation of the AMPK/SIRT1 signaling pathway to inhibit ferroptosis.
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Affiliation(s)
- Chen Jin
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Kai Tan
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Zhe Yao
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
- Department of Burn and Wound Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Bing-Hao Lin
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Du-Piao Zhang
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Wei-Kai Chen
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Shu-Ming Mao
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Wei Zhang
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Liang Chen
- Orthopaedic Oncology Services, Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhen Lin
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - She-Ji Weng
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Bing-Li Bai
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Wen-Hao Zheng
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Gang Zheng
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Zong-Yi Wu
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
| | - Lei Yang
- Department of Orthopedic, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou 325000, China
- School of Medicine, Shanghai University, Shanghai 200444, China
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Progress on Prevention and Treatment of Cerebral Small Vascular Disease Using Integrative Medicine. Chin J Integr Med 2023; 29:186-191. [PMID: 36527536 DOI: 10.1007/s11655-022-3622-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 12/23/2022]
Abstract
Cerebral small vessel disease (CSVD) is a senile brain lesion caused by the abnormal structure and function of arterioles, venules and capillaries in the aging brain. The etiology of CSVD is complex, and disease is often asymptomatic in its early stages. However, as CSVD develops, brain disorders may occur, such as stroke, cognitive dysfunction, dyskinesia and mood disorders, and heart, kidney, eye and systemic disorders. As the population continues to age, the burden of CSVD is increasing. Moreover, there is an urgent need for better screening methods and diagnostic markers for CSVD, in addition to preventive and asymptomatic- and mild-stage treatments. Integrative medicine (IM), which combines the holistic concepts and syndrome differentiations of Chinese medicine with modern medical perspectives, has unique advantages for the prevention and treatment of CSVD. In this review, we summarize the biological markers, ultrasound and imaging features, disease-related genes and risk factors relevant to CSVD diagnosis and screening. Furthermore, we discuss IM-based CSVD prevention and treatment strategies to stimulate further research in this field.
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Ren Y, Ye D, Ding Y, Wei N. Ginsenoside Rk1 prevents 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced Parkinson's disease via activating silence information regulator 3-mediated Nrf2/HO-1 signaling pathway. Hum Exp Toxicol 2023; 42:9603271231220610. [PMID: 38105596 DOI: 10.1177/09603271231220610] [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: 12/19/2023]
Abstract
Objectives: Ginsenoside Rk1, a novel ginsenoside isolated from red ginseng, has anti-inflammatory and anti-tumor activities. This study was designed to elucidate the role of RK1 in an in vitro 1-methyl-4-phenylpyridinium (MPP+) cell model and an in vivo 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) of Parkinson's disease (PD).Methods: The grasping test, pole-climbing test, and rotarod test were performed to measure the effects of RK1 on MPTP-induced motor disorders. The expression of tyrosine hydroxylase (TH) and IBA-1 were evaluated by western blotting. CCK-8 and flow cytometry assays were utilized to assess cell viability and apoptosis. Reactive oxygen species (ROS), Lactate dehydrogenase (LDH), and superoxide dismutase (SOD) were detected to analyze the effects of RK1 on oxidative stress. The levels of inflammatory cytokines were evaluated by enzyme-linked immunosorbent assay (ELISA).Results: The results showed that RK1 allayed motor deficit elicited by MPTP in a mouse model. RK1 administration augmented tyrosine hydroxylase (TH) expression in the brain striatum and substantia nigra (SN) of MPTP-treated mice. Moreover, RK1 pretreatment promoted viability and suppressed apoptosis in MPP+-induced PC-12 cells. Further, RK1 also attenuated MPP+-stimulated oxidative stress and inflammatory response in PC-12 cells. Besides, RK1 augmented the level of SIRT3, and SIRT3 deletion counteracted RK1-induced repression on MPP+-elicited apoptosis, oxidative stress, and inflammatory response in PC-12 cells via modulating the Nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) pathway.Conclusions: RK1 might exert neuroprotective effects against MPP+/MPTP-induced neurotoxicity via activating SIRT3-mediated Nrf2/HO-1 signaling. RK1 might be a promising candidate against PD.
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Affiliation(s)
- Yi Ren
- Department of Neurology, the First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Dan Ye
- Department of Neurology, the First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yiping Ding
- Department of Neurology, the First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Ning Wei
- Department of Neurology, the First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, China
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Dong W, Chen W, Zou H, Shen Z, Yu D, Chen W, Jiang H, Yan X, Yu Z. Ginsenoside Rb1 Prevents Oxidative Stress-Induced Apoptosis and Mitochondrial Dysfunction in Muscle Stem Cells via NF- κB Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9159101. [PMID: 36466088 PMCID: PMC9715322 DOI: 10.1155/2022/9159101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 07/22/2023]
Abstract
Sarcopenia, featured by the progressive loss of skeletal muscle function and mass, is associated with the impaired function of muscle stem cells (MuSCs) caused by increasing oxidative stress in senescent skeletal muscle tissue during aging. Intact function of MuSCs maintains the regenerative potential as well as the homeostasis of skeletal muscle tissues during aging. Ginsenoside Rb1, a natural compound from ginseng, exhibited the effects of antioxidation and against apoptosis. However, its effects of restoring MuSC function during aging and improving age-related sarcopenia remained unknown. In this study, we investigated the role of Rb1 in improving MuSC function and inhibiting apoptosis by reducing oxidative stress levels. We found that Rb1 inhibited the accumulation of reactive oxygen species (ROS) and protected the cells from oxidative stress to attenuate the H2O2-induced cytotoxicity. Rb1 also blocked oxidative stress-induced apoptosis by inhibiting the activation of caspase-3/9, which antagonized the decrease in mitochondrial content and the increase in mitochondrial abnormalities caused by oxidative stress via promoting the protein expression of genes involved in mitochondrial biogenesis. Mechanistically, it was proven that Rb1 exerted its antioxidant effects and avoided the apoptosis of myoblasts by targeting the core regulator of the nuclear factor-kappa B (NF-κB) signal pathway. Therefore, these findings suggest that Rb1 may have a beneficial role in the prevention and treatment of MuSC exhaustion-related diseases like sarcopenia.
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Affiliation(s)
- Wenxi Dong
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenhao Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hongbo Zou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surgery, People's Hospital of Deyang City, Deyang, Sichuan, China
| | - Zile Shen
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dingye Yu
- Department of General Surgery, Huadong Hospital, Fudan University, Shanghai, China
| | - Weizhe Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haojie Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xialin Yan
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhen Yu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Gong L, Yin J, Zhang Y, Huang R, Lou Y, Jiang H, Sun L, Jia J, Zeng X. Neuroprotective Mechanisms of Ginsenoside Rb1 in Central Nervous System Diseases. Front Pharmacol 2022; 13:914352. [PMID: 35721176 PMCID: PMC9201244 DOI: 10.3389/fphar.2022.914352] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Panax ginseng and Panax notoginseng, two well-known herbs with enormous medical value in Asian countries, have a long usage history in China for the therapy of some diseases, such as stroke. Ginsenoside Rb1 is one of most important active ingredients in Panax ginseng and Panax notoginseng. In the last two decades, more attention has focused on ginsenoside Rb1 as an antioxidative, anti-apoptotic and anti-inflammatory agent that can protect the nervous system. In the review, we summarize the neuroprotective roles of ginsenoside Rb1 and its potential mechanisms in central nervous system diseases (CNSDs), including neurodegenerative diseases, cerebral ischemia injury, depression and spinal cord injury. In conclusion, ginsenoside Rb1 has a potential neuroprotection due to its inhibition of oxidative stress, apoptosis, neuroinflammation and autophagy in CNSDs and may be a promising candidate agent for clinical therapy of CNSDs in the future.
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Affiliation(s)
- Liang Gong
- Jiaxing University Medical College, Jiaxing, China
| | - Jiayi Yin
- Jiaxing University Medical College, Jiaxing, China
| | - Yu Zhang
- Jiaxing University Medical College, Jiaxing, China
| | - Ren Huang
- Jiaxing University Medical College, Jiaxing, China
| | - Yuxuan Lou
- Jiaxing University Medical College, Jiaxing, China
| | - Haojie Jiang
- Jiaxing University Medical College, Jiaxing, China
| | - Liyan Sun
- Department of Clinical Medicine, Jiaxing University Medical College, Jiaxing, China
| | - Jinjing Jia
- Research Center of Neuroscience, Jiaxing University Medical College, Jiaxing, China
| | - Xiansi Zeng
- Research Center of Neuroscience, Jiaxing University Medical College, Jiaxing, China
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6
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Gong L, Yin J, Zhang Y, Huang R, Lou Y, Jiang H, Sun L, Jia J, Zeng X. Neuroprotective Mechanisms of Ginsenoside Rb1 in Central Nervous System Diseases. Front Pharmacol 2022; 13:914352. [PMID: 35721176 DOI: 10.3389/fphar.2022.914352if:] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2024] Open
Abstract
Panax ginseng and Panax notoginseng, two well-known herbs with enormous medical value in Asian countries, have a long usage history in China for the therapy of some diseases, such as stroke. Ginsenoside Rb1 is one of most important active ingredients in Panax ginseng and Panax notoginseng. In the last two decades, more attention has focused on ginsenoside Rb1 as an antioxidative, anti-apoptotic and anti-inflammatory agent that can protect the nervous system. In the review, we summarize the neuroprotective roles of ginsenoside Rb1 and its potential mechanisms in central nervous system diseases (CNSDs), including neurodegenerative diseases, cerebral ischemia injury, depression and spinal cord injury. In conclusion, ginsenoside Rb1 has a potential neuroprotection due to its inhibition of oxidative stress, apoptosis, neuroinflammation and autophagy in CNSDs and may be a promising candidate agent for clinical therapy of CNSDs in the future.
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Affiliation(s)
- Liang Gong
- Jiaxing University Medical College, Jiaxing, China
| | - Jiayi Yin
- Jiaxing University Medical College, Jiaxing, China
| | - Yu Zhang
- Jiaxing University Medical College, Jiaxing, China
| | - Ren Huang
- Jiaxing University Medical College, Jiaxing, China
| | - Yuxuan Lou
- Jiaxing University Medical College, Jiaxing, China
| | - Haojie Jiang
- Jiaxing University Medical College, Jiaxing, China
| | - Liyan Sun
- Department of Clinical Medicine, Jiaxing University Medical College, Jiaxing, China
| | - Jinjing Jia
- Research Center of Neuroscience, Jiaxing University Medical College, Jiaxing, China
| | - Xiansi Zeng
- Research Center of Neuroscience, Jiaxing University Medical College, Jiaxing, China
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Grismaldo Rodríguez A, Zamudio Rodríguez JA, Mendieta CV, Quijano Gómez S, Sanabria Barrera S, Morales Álvarez L. Effect of Platelet-Derived Growth Factor C on Mitochondrial Oxidative Stress Induced by High d-Glucose in Human Aortic Endothelial Cells. Pharmaceuticals (Basel) 2022; 15:ph15050639. [PMID: 35631465 PMCID: PMC9143891 DOI: 10.3390/ph15050639] [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: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/10/2022] Open
Abstract
Endothelial dysfunction is an early marker for cardiovascular diseases. Hyperglycemia induces endothelial dysfunction, increasing the production of reactive oxygen species. Platelet-derived growth factor C stimulates angiogenesis and revascularization in ischemic tissues of diabetic mice and promotes the migration of progenitors and mature ECs to injury sites; however, the molecular mechanisms of its actions are not described yet. Here, we evaluated the effect of PDGF-C on oxidative stress induced by HG. Human aortic endothelial cells were grown in glucose concentrations ranging from 5 mmol/L to 35 mmol/L for 1 to 24 h. Treatment with 50 ng/mL PDGF-C was done for 1 to 3 h. Cytosolic and mitochondrial ROS were measured by fluorometry, and the expression of antioxidant enzymes was evaluated by Western blot. Nrf2 and Keap1 expression was assessed by real-time PCR. High glucose induced mitochondrial ROS production. PDGF-C diminished the oxidative stress induced by high glucose, increasing SOD2 expression and SOD activity, and modulating the Keap1 expression gene. These results give new evidence about the mitochondrial antioxidant effect that PDGF-C could exert on endothelial cells exposed to high glucose and its considerable role as a therapeutic target in diabetes.
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Affiliation(s)
- Adriana Grismaldo Rodríguez
- Experimental and Computational Biochemistry Group, Faculty of Sciences, Nutrition and Biochemistry Department, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (J.A.Z.R.); (C.V.M.)
- Correspondence: (A.G.R.); (L.M.Á.); Tel.: +57-3114566976 (A.G.R.); +57-3132107272 (L.M.Á.)
| | - Jairo A. Zamudio Rodríguez
- Experimental and Computational Biochemistry Group, Faculty of Sciences, Nutrition and Biochemistry Department, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (J.A.Z.R.); (C.V.M.)
| | - Cindy V. Mendieta
- Experimental and Computational Biochemistry Group, Faculty of Sciences, Nutrition and Biochemistry Department, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (J.A.Z.R.); (C.V.M.)
- Department of Clinical Epidemiology and Biostatistics, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Sandra Quijano Gómez
- Immunology and Cell Biology Group, Faculty of Sciences, Microbiology Department, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
| | - Sandra Sanabria Barrera
- Traslational Biomedical Research Group, Fundación Cardiovascular de Colombia, Floridablanca 680004, Colombia;
| | - Ludis Morales Álvarez
- Experimental and Computational Biochemistry Group, Faculty of Sciences, Nutrition and Biochemistry Department, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (J.A.Z.R.); (C.V.M.)
- Correspondence: (A.G.R.); (L.M.Á.); Tel.: +57-3114566976 (A.G.R.); +57-3132107272 (L.M.Á.)
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Zhang W, Wang SL, Liu Y. Identification of Cancer Driver Modules Based on Graph Clustering from Multiomics Data. J Comput Biol 2021; 28:1007-1020. [PMID: 34529511 DOI: 10.1089/cmb.2021.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A major challenge in cancer genomics is to identify cancer driver genes and modules. Most existing methods to identify cancer driver modules (iCDM) identify groups of genes whose somatic mutational patterns exhibit either mutual exclusivity or high coverage of patient samples, without considering other biological information from multiomics data sets. Here we integrate mutual exclusivity, coverage, and protein-protein interaction information to construct an edge-weighted network, and present a graph clustering approach based on symmetric non-negative matrix factorization to iCDM. iCDM was tested on pan-cancer data and the results were compared with those from several advanced computational methods. Our approach outperformed other methods in recovering known cancer driver modules, and the identified driver modules showed high accuracy in classifying normal and tumor samples.
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Affiliation(s)
- Wei Zhang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China
| | - Shu-Lin Wang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, China
| | - Yue Liu
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, China
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