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Tutar Y. Metabologenomics and network pharmacology to understand the molecular mechanism of cancer research. World J Clin Cases 2024; 12:474-478. [PMID: 38322468 PMCID: PMC10841944 DOI: 10.12998/wjcc.v12.i3.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/07/2023] [Accepted: 12/25/2023] [Indexed: 01/18/2024] Open
Abstract
In this editorial I comment on the article "Network pharmacological and molecular docking study of the effect of Liu-Wei-Bu-Qi capsule on lung cancer" published in the recent issue of the World Journal of Clinical Cases 2023 November 6; 11 (31): 7593-7609. Almost all living forms are able to manufacture particular chemicals-metabolites that enable them to differentiate themselves from one another and to overcome the unique obstacles they encounter in their natural habitats. Numerous methods for chemical warfare, communication, nutrition acquisition, and stress prevention are made possible by these specialized metabolites. Metabolomics is a popular technique for collecting direct measurements of metabolic activity from many biological systems. However, confusing metabolite identification is a typical issue, and biochemical interpretation is frequently constrained by imprecise and erroneous genome-based estimates of enzyme activity. Metabolite annotation and gene integration uses a biochemical reaction network to obtain a metabolite-gene association so called metabologenomics. This network uses an approach that emphasizes metabolite-gene consensus via biochemical processes. Combining metabolomics and genomics data is beneficial. Furthermore, computer networking proposes that using metabolomics data may improve annotations in sequenced species and provide testable hypotheses for specific biochemical processes.
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Affiliation(s)
- Yusuf Tutar
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Division of Biochemistry, University of Health Sciences, Istanbul 34668, Turkey
- Health Sciences Faculty, Recep Tayyip Erdogan University, Rize 53350, Turkey
- Molecular Oncology Division, Health Sciences Institutes, University of Health Sciences, Istanbul 34668, Turkey
- Molecular Medicine Division, Health Sciences Institutes, University of Health Sciences, Istanbul 34668, Turkey
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Wang X, Hou L, Cui M, Liu J, Wang M, Xie J. The traditional Chinese medicine and non-small cell lung cancer: from a gut microbiome perspective. Front Cell Infect Microbiol 2023; 13:1151557. [PMID: 37180438 PMCID: PMC10167031 DOI: 10.3389/fcimb.2023.1151557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/29/2023] [Indexed: 05/16/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the most serious diseases affecting human health today, and current research is focusing on gut flora. There is a correlation between intestinal flora imbalance and lung cancer, but the specific mechanism is not clear. Based on the "lung and large intestine being interior-exteriorly related" and the "lung-intestinal axis" theory. Here, based on the theoretical comparisons of Chinese and western medicine, we summarized the regulation of intestinal flora in NSCLC by active ingredients of traditional Chinese medicine and Chinese herbal compounds and their intervention effects, which is conducive to providing new strategies and ideas for clinical prevention and treatment of NSCLC.
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Affiliation(s)
- Xuelin Wang
- School of Food Science and Engineering (School of Biological and Pharmaceutical Sciences), Shaanxi University of Science & Technology, Xi an, China
| | - Liming Hou
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi an, China
| | - Meng Cui
- School of Food Science and Engineering (School of Biological and Pharmaceutical Sciences), Shaanxi University of Science & Technology, Xi an, China
| | - Junnan Liu
- School of Food Science and Engineering (School of Biological and Pharmaceutical Sciences), Shaanxi University of Science & Technology, Xi an, China
| | - Mengzhou Wang
- School of Food Science and Engineering (School of Biological and Pharmaceutical Sciences), Shaanxi University of Science & Technology, Xi an, China
| | - Jianwu Xie
- School of Food Science and Engineering (School of Biological and Pharmaceutical Sciences), Shaanxi University of Science & Technology, Xi an, China
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Li K, Liu H, Lin Y, Gu L, Xiang X, Zhu X. Discovery of therapeutic targets of quercetin for endometrial carcinoma patients infected with COVID-19 through network pharmacology. Front Oncol 2023; 13:1151434. [PMID: 36969077 PMCID: PMC10031047 DOI: 10.3389/fonc.2023.1151434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
PurposeAimed to identify the anti-uterine corpus endometrial carcinoma (UCEC) function and characterize the mechanism of quercetin in the treatment of patients infected with COVID-19 via integrated in silico analysis.MethodsThe Cancer Genome Atlas and Genotype Tissue Expression databases were applied to obtain differentially expressed genes of UCEC and non-tumor tissue. Several in silico methods such as network pharmacology, functional enrichment analysis, Cox regression analyses, somatic mutation analysis, immune infiltration and molecular docking were used to investigate and analysis the biological targets, functions and mechanisms of anti-UCEC/COVID-19 of quercetin. Multiple methods such as CCK8 assay, Transwell assay and western blotting were performed to test proliferation, migration, and protein level of UCEC (HEC-1 and Ishikawa) cells.ResultsFunctional analysis disclosed that quercetin against UCEC/COVID-19 mainly by ‘biological regulation’, ‘response to stimulus’, and ‘regulation of cellular process’. Then, regression analyses indicated that 9 prognostic genes (including ANPEP, OAS1, SCGB1A1, HLA‐A, NPPB, FGB, CCL2, TLR4, and SERPINE1) might play important roles in quercetin for treating UCEC/COVID-19. Molecular docking analysis revealed that the protein products of 9 prognostic genes were the important anti-UCEC/COVID-19 biological targets of quercetin. Meanwhile, the proliferation and migration of UCEC cells were inhibited by quercetin. Moreover, after treatment with quercetin, the protein level of ubiquitination-related gene ISG15 was decreased in UCEC cells in vitro.ConclusionsTaken together, this study provides new treatment option for UCEC patients infected with COVID-19. Quercetin may work by reducing the expression of ISG15 and participating in ubiquitination-related pathways.
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Affiliation(s)
- Kehan Li
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hejing Liu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yibin Lin
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Liang Gu
- Department of Obstetrics and Gynecology, Taizhou Women and Children’s Hospital of Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Xinli Xiang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Obstetrics and Gynecology, Taizhou Women and Children’s Hospital of Wenzhou Medical University, Taizhou, Zhejiang, China
- *Correspondence: Xueqiong Zhu,
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Khan SA, Wu Y, Li ASM, Fu XQ, Yu ZL. Network pharmacology and molecular docking-based prediction of active compounds and mechanisms of action of Cnidii Fructus in treating atopic dermatitis. BMC Complement Med Ther 2022; 22:275. [PMID: 36261841 PMCID: PMC9580115 DOI: 10.1186/s12906-022-03734-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Atopic dermatitis (AD) is a common inflammatory skin disease that compromises the skin's barrier function and capacity to retain moisture. Cnidii Fructus (CF), the dried fruits of Cnidium monnieri, has long been used to treat atopic dermatitis (AD) in China. However, the anti-AD compounds and mechanisms of CF are not fully understood. In this study, we evaluated the active compounds and molecular targets of CF in treating AD. METHODS The Traditional Chinese Medicine Systems Pharmacology database was used to acquire information regarding the compounds that occur in the herb. Targets of these compounds were predicted using the SwissTargetPrediction website tool. AD-related genes were collected from the GeneCards database. Gene ontology (GO) enrichment analysis and KEGG pathway analysis of proteins that are targeted by active compounds of CF and encoded by AD-related genes were performed using Database for Annotation, Visualization, and Integrated Discovery Bioinformatics Resources. A "compound-target" network was constructed and analyzed using Cytoscape Software. Molecular docking was performed using BIOVIA Discovery Studio Visualizer and AutoDock Vina. RESULTS We identified 19 active compounds in CF, 532 potential targets for these compounds, and 1540 genes related to AD. Results of GO enrichment indicated that CF affects biological processes and molecular functions, such as inflammatory response and steroid hormone receptor activity, which may be associated with its anti-AD effects. KEGG pathway analyses showed that PI3K-Akt signaling, calcium signaling, Rap1 signaling, and cAMP signaling pathways are the main pathways involved in the anti-AD effects of CF. Molecular docking analyses revealed that the key active compounds in CF, such as (E)-2,3-bis(2-keto-7-methoxy-chromen-8-yl)acrolein, ar-curcumene, and diosmetin, can bind the main therapeutic targets AKT1, SRC, MAPK3, EGFR, CASP3, and PTGS2. CONCLUSIONS Results of the present study establish a foundation for further investigation of the anti-AD compounds and mechanisms of CF and provide a basis for developing modern anti-AD agents based on compounds that occur in CF.
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Affiliation(s)
- Shakeel Ahmad Khan
- grid.221309.b0000 0004 1764 5980Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Ying Wu
- grid.221309.b0000 0004 1764 5980Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Amy Sze-Man Li
- grid.221309.b0000 0004 1764 5980Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Xiu-Qiong Fu
- grid.221309.b0000 0004 1764 5980Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Zhi-Ling Yu
- grid.221309.b0000 0004 1764 5980Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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Nguyen M, Osipo C. Targeting Breast Cancer Stem Cells Using Naturally Occurring Phytoestrogens. Int J Mol Sci 2022; 23:6813. [PMID: 35743256 DOI: 10.3390/ijms23126813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer therapies have made significant strides in improving survival for patients over the past decades. However, recurrence and drug resistance continue to challenge long-term recurrence-free and overall survival rates. Mounting evidence supports the cancer stem cell model in which the existence of a small population of breast cancer stem cells (BCSCs) within the tumor enables these cells to evade conventional therapies and repopulate the tumor, giving rise to more aggressive, recurrent tumors. Thus, successful breast cancer therapy would need to target these BCSCs, as well the tumor bulk cells. Since the Women’s Health Initiative study reported an increased risk of breast cancer with the use of conventional hormone replacement therapy in postmenopausal women, many have turned their attention to phytoestrogens as a natural alternative. Phytoestrogens are plant compounds that share structural similarities with human estrogens and can bind to the estrogen receptors to alter the endocrine responses. Recent studies have found that phytoestrogens can also target BCSCs and have the potential to complement conventional therapy eradicating BCSCs. This review summarized the latest findings of different phytoestrogens and their effect on BCSCs, along with their mechanisms of action, including selective estrogen receptor binding and inhibition of molecular pathways used by BCSCs. The latest results of phytoestrogens in clinical trials are also discussed to further evaluate the use of phytoestrogen in the treatment and prevention of breast cancer.
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Li C, Wang X, Chen T, Li W, Zhou X, Wang L, Yang Q. Huaier Induces Immunogenic Cell Death Via CircCLASP1/PKR/eIF2α Signaling Pathway in Triple Negative Breast Cancer. Front Cell Dev Biol 2022; 10:913824. [PMID: 35784473 PMCID: PMC9243662 DOI: 10.3389/fcell.2022.913824] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most lethal breast cancer subtype owing to the lack of targeted therapeutic strategies. Immunogenic cell death (ICD), a modality of regulated cancer cell death, offered a novel option for TNBC via augmenting tumor immunogenic microenvironment. However, few ICD-inducing agents are currently available. Here, we showed that Trametes robiniophila Murr (Huaier) triggered ICD in TNBC cells by promoting cell surface calreticulin (CRT) exposure, and increasing release of adenosine triphosphate (ATP) and high-mobility group protein B1 (HMGB1). Co-culturing with Huaier-treated TNBC cells efficiently enhanced the maturation of dendritic cells (DCs), which was further validated via cell-based vaccination assay. In the xenograft mouse model, oral administration of Huaier led to tumor-infiltrating lymphocytes (TILs) accumulation and significantly delayed tumor growth. Besides, depletion of endogenous T cells obviously abrogated the effect. Mechanically, Huaier could elicit endoplasmic reticulum (ER) stress-associated ICD through eIF2α signaling pathway. Further studies revealed that circCLASP1 was involved in the Huaier-induced immunogenicity by binding with PKR in the cytoplasm and thus blocking its degradation. Taken together, we highlighted an essential role of circCLASP1/PKR/eIF2α axis in Huaier-induced ICD. The findings of our study carried significant translational potential that Huaier might serve as a promising option to achieve long-term tumor remission in patients with TNBC.
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Affiliation(s)
- Chen Li
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tong Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenhao Li
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xianyong Zhou
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lishui Wang
- Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Lishui Wang, ; Qifeng Yang,
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Pathology Tissue Bank, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Research Institute of Breast Cancer, Shandong University, Jinan, China
- *Correspondence: Lishui Wang, ; Qifeng Yang,
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