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Xu L, Zuo SM, Liu M, Wang T, Li Z, Yun YH, Zhang W. Integrated Analysis of Metabolomics Combined with Network Pharmacology and Molecular Docking Reveals the Effects of Processing on Metabolites of Dendrobium officinale. Metabolites 2023; 13:886. [PMID: 37623830 PMCID: PMC10456568 DOI: 10.3390/metabo13080886] [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: 06/19/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Dendrobium officinale (D. officinale) is a precious medicinal species of Dendrobium Orchidaceae, and the product obtained by hot processing is called "Fengdou". At present, the research on the processing quality of D. officinale mainly focuses on the chemical composition indicators such as polysaccharides and flavonoids content. However, the changes in metabolites during D. officinale processing are still unclear. In this study, the process was divided into two stages and three important conditions including fresh stems, semiproducts and "Fengdou" products. To investigate the effect of processing on metabolites of D. officinale in different processing stages, an approach of combining metabolomics with network pharmacology and molecular docking was employed. Through UPLC-MS/MS analysis, a total of 628 metabolites were detected, and 109 of them were identified as differential metabolites (VIP ≥ 1, |log2 (FC)| ≥ 1). Next, the differential metabolites were analyzed using the network pharmacology method, resulting in the selection of 29 differential metabolites as they have a potential pharmacological activity. Combining seven diseases, 14 key metabolites and nine important targets were screened by constructing a metabolite-target-disease network. The results showed that seven metabolites with potential anticoagulant, hypoglycemic and tumor-inhibiting activities increased in relative abundance in the "Fengdou" product. Molecular docking results indicated that seven metabolites may act on five important targets. In general, processing can increase the content of some active metabolites of D. officinale and improve its medicinal quality to a certain extent.
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Affiliation(s)
| | | | | | | | | | - Yong-Huan Yun
- Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.X.)
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Cai L. Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes. AMERICAN JOURNAL OF BOTANY 2023; 110:e16174. [PMID: 37154532 DOI: 10.1002/ajb2.16174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.
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Affiliation(s)
- Liming Cai
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Zhang X, Sun X, Miao Y, Zhang M, Tian L, Yang J, Liu C, Huang L. Ecotype Division and Chemical Diversity of Cynomorium songaricum from Different Geographical Regions. Molecules 2022; 27:molecules27133967. [PMID: 35807215 PMCID: PMC9268089 DOI: 10.3390/molecules27133967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cynomorium songaricum is an important endangered plant with significant medicinal and edible values. However, the lack of resources and quality variation have limited the comprehensive developments and sustainable utilization of C. songaricum. Here, we evaluated the chemical and genetic traits of C. songaricum from the highly suitable habitat regions simulated with species distribution models. The PCA and NJ tree analyses displayed intraspecific variation in C. songaricum, which could be divided into two ecotypes: ecotype I and ecotype II. Furthermore, the LC-MS/MS-based metabolomic was used to identify and analyze the metabolites of two ecotypes. The results indicated that a total of 589 compounds were detected, 236 of which were significantly different between the two ecotypes. Specifically, the relative content and the kind of flavonoids were more abundant in ecotype I, which were closely associated with the medicinal activities. In contrast, amino acids and organic acids were more enriched in ecotype II, which may provide better nutritional quality and unique flavor. In summary, our findings demonstrate the ecotype division and chemical diversity of C. songaricum in China from different geographical regions and provide a reference for the development of germplasm and directed plant breeding of endangered medicinal plants.
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Affiliation(s)
- Xinke Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
| | - Xiao Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
| | - Yujing Miao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
| | - Min Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Baotou 014040, China;
| | - Lixia Tian
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
| | - Jie Yang
- Tongren Tobacco Company Songtao Branch, Tongren 554100, China;
| | - Chang Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
| | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (X.Z.); (X.S.); (Y.M.); (L.T.); (C.L.)
- Correspondence: or ; Tel.: +86-010-5783-3197
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Wang JH, Zeng Z, Sun J, Chen Y, Gao X. A novel small-molecule antagonist enhances the sensitivity of osteosarcoma to cabozantinib in vitro and in vivo by targeting DNMT-1 correlated with disease severity in human patients. Pharmacol Res 2021; 173:105869. [PMID: 34481973 DOI: 10.1016/j.phrs.2021.105869] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/21/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Advanced osteosarcoma (OSA) is highly aggressive and can lead to distant metastasis or recurrence. Here, a novel small-molecule inhibitor/antagonist of DNA methyltransferase 1 (DNMT-1) named DI-1 (inhibitor of DNMT-1) was explored to enhance the antitumor effect of a molecular-targeted agent, cabozantinib, on OSA cell lines. In patients with OSA, expression of DNMT-1 was negatively related with that of microRNA (miR)-34a and associated with a poor prognosis. In OSA cell lines (OSA cell line U2OS and an OSA cell line U2OSR resistance to cabozantinib), DI-1 treatment enhanced miR-34a expression by inhibiting hypermethylation of the promoter region of miR-34a mediated by DNMT-1. DI-1 enhanced the sensitivity of OSA cells (U2OS, 143B and MG63) to cabozantinib and other molecular-targeted agents by enhancing miR-34a expression and repressing activation of the Notch pathway. Mechanistically, DI-1 repressed recruitment of DNMT-1 to the promoter region of miR-34a and, in turn, decreased the methylation rate in the promoter region of miR-34a in OSA cells. These results suggest that repressing DNMT-1 activation by DI-1 enhances miR-34a expression in OSA cells and could be a promising therapeutic strategy for OSA.
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Affiliation(s)
- Ji-Hai Wang
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, Henan Province, China.
| | - Zhen Zeng
- Department of Liver Disease, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China.
| | - Jie Sun
- Department of Liver Disease, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China.
| | - Yan Chen
- Department of Liver Disease, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China.
| | - Xudong Gao
- Department of Liver Disease, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China.
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