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Jiang Y, Zhong S, Tan H, Fu Y, Lai J, Liu L, Weng J, Chen H, He S. Study on the mechanism of action of Saposhnikovia divaricata and its key phytochemical on rheumatoid arthritis based on network pharmacology and bioinformatics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 322:117586. [PMID: 38104871 DOI: 10.1016/j.jep.2023.117586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Saposhnikovia divaricata (Turcz.) Schischk (SD; called "fangfeng" in China) has been widely used in the clinical treatment of rheumatoid arthritis (RA) and has shown well therapeutic effects, but the specific mechanisms of action of its bioactive phytochemicals remain unclear. AIM OF THE STUDY This study aimed to investigate the molecular biological mechanism of SD in treating RA through a pharmacology-based strategy. The SD-specific core ingredient Prangenidin was screened for further in-depth study. MATERIALS AND METHODS The bioactive phytochemicals of SD and potential targets for the treatment of RA were screened by network pharmacology, and phytochemicals-related parameters such as pharmacology, and toxicology were evaluated. The protein interaction network was established to screen the core targets, and the correlation between the core targets and RA was further validated by bioinformatics strategy. Finally, molecular docking of core components and corresponding targets was performed. The in vitro experiments were performed to elucidate the regulation of Prangenidin on MH7A cells and on the PI3K/AKT pathway, and the in vivo therapeutic effect of Prangenidin was validated in collagen-induced arthritis (CIA) mice. RESULTS A total of 18 bioactive phytochemicals and 66 potential target genes intersecting with the screened RA disease target genes were identified from SD. Finally, core ingredients such as wogonin, beta-sitosterol, 5-O-Methylvisamminol, and prangenidin and core targets such as PTGS2, RELA, and AKT1 were obtained. The underlying mechanism of SD in treating RA might be achieved by regulating pathways such as PI3K/AKT, IL-17 pathway, apoptosis, and multiple biological processes to exert anti-inflammatory and immunomodulatory effects. Molecular docking confirmed that all core ingredients and key targets had great docking activity. Prangenidin inhibited viability, migration, and invasion, and induced apoptosis in MH7A cells. Prangenidin also reduced the production of IL-1β, IL-6, IL-8, MMP-1, and MMP-3. Molecular analysis showed that Prangenidin exerts its regulatory effect on MH7A cells by inhibiting PI3K/AKT pathway. Treatment with Prangenidin ameliorated synovial inflammation in the joints of mice with CIA. CONCLUSION Our findings provide insights into the therapeutic effects of SD on RA, successfully predicting the effective ingredients and potential targets, which could suggest a novel theoretical basis for further exploration of its molecular mechanisms. It also revealed that Prangenidin inhibited viability, migration, invasion, cytokine, and MMPs expression, and induced apoptosis in RA FLSs via the PI3K/AKT pathway.
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Affiliation(s)
- Yong Jiang
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China; Department of Spine Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, China
| | - Shuxin Zhong
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Huangsheng Tan
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China; Department of Spine Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, China
| | - Yuanfei Fu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China; Department of Spine Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, China
| | - Juyi Lai
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China; Department of Spine Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, China
| | - Lijin Liu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China
| | - Juanling Weng
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China
| | - Hanwei Chen
- Department of Radiology, Panyu Health Management Center (Panyu Rehabilitation Hospital), Guangzhou, 511495, China.
| | - Shenghua He
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China; Department of Spine Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, China.
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Niu J, Wang X, Yue J, Zhou S, Liu Z, Zhou J. The complete chloroplast genome of Ligusticopsis acaulis (Shan et Sheh) Pimenov (Apiaceae), an endemic species from China. MITOCHONDRIAL DNA PART B 2023; 8:451-456. [PMID: 37006959 PMCID: PMC10062233 DOI: 10.1080/23802359.2023.2191750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Ligusticopsis acaulis, belonging to the family Apiaceae (Umbelliferae), is endemic to China. The complete chloroplast genome sequence of L. acaulis was assembled and annotated for the first time in this study. The results showed that the plastome was 148,509 bp in length and consisted of a pair of inverted repeat regions (IRs: 19,468 bp), a large single-copy region (LSC: 91,902 bp), and a small single-copy region (SSC: 17,671 bp). A total of 114 unique genes were annotated, including 80 protein-coding, 30 tRNA, and four rRNA genes. According to the phylogenetic analysis, L. acaulis belongs to the tribe Selineae, with a close relationship to Ligusticum hispidum (Franch.) Wolff.
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Ni Y, Li J, Chen H, Yue J, Chen P, Liu C. Comparative analysis of the chloroplast and mitochondrial genomes of Saposhnikovia divaricata revealed the possible transfer of plastome repeat regions into the mitogenome. BMC Genomics 2022; 23:570. [PMID: 35945507 PMCID: PMC9364500 DOI: 10.1186/s12864-022-08821-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Saposhnikovia divaricata (Turcz.) Schischk. is a perennial herb whose dried roots are commonly used as a source of traditional medicines. To elucidate the organelle-genome-based phylogeny of Saposhnikovia species and the transfer of DNA between organelle genomes, we sequenced and characterised the mitochondrial genome (mitogenome) of S. divaricata. Results The mitogenome of S. divaricata is a circular molecule of 293,897 bp. The nucleotide composition of the mitogenome is as follows: A, 27.73%; T, 27.03%; C, 22.39%; and G, 22.85. The entire gene content is 45.24%. A total of 31 protein-coding genes, 20 tRNAs and 4 rRNAs, including one pseudogene (rpl16), were annotated in the mitogenome. Phylogenetic analysis of the organelle genomes from S. divaricata and 10 related species produced congruent phylogenetic trees. Selection pressure analysis revealed that most of the mitochondrial genes of related species are highly conserved. Moreover, 2 and 46 RNA-editing sites were found in the chloroplast genome (cpgenome) and mitogenome protein-coding regions, respectively. Finally, a comparison of the cpgenome and the mitogenome assembled from the same dataset revealed 10 mitochondrial DNA fragments with sequences similar to those in the repeat regions of the cpgenome, suggesting that the repeat regions might be transferred into the mitogenome. Conclusions In this study, we assembled and annotated the mitogenome of S. divaricata. This study provides valuable information on the taxonomic classification and molecular evolution of members of the family Apiaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08821-0.
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Affiliation(s)
- Yang Ni
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Jingling Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China
| | - Jingwen Yue
- College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shang Xiadian Road, Fuzhou, Fujian Province, 350002, P. R. China
| | - Pinghua Chen
- College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shang Xiadian Road, Fuzhou, Fujian Province, 350002, P. R. China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, P. R. China.
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The Chloroplast Genome of Wild Saposhnikovia divaricata: Genomic Features, Comparative Analysis, and Phylogenetic Relationships. Genes (Basel) 2022; 13:genes13050931. [PMID: 35627316 PMCID: PMC9141249 DOI: 10.3390/genes13050931] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
Saposhnikovia divaricata, a well-known Chinese medicinal herb, is the sole species under the genus Saposhnikovia of the Apiaceae subfamily Apioideae Drude. However, information regarding its genetic diversity and evolution is still limited. In this study, the first complete chloroplast genome (cpDNA) of wild S. divaricata was generated using de novo sequencing technology. Similar to the characteristics of Ledebouriella seseloides, the 147,834 bp-long S. divaricata cpDNA contained a large single copy, a small single copy, and two inverted repeat regions. A total of 85 protein-coding, 8 ribosomal RNA, and 36 transfer RNA genes were identified. Compared with five other species, the non-coding regions in the S. divaricata cpDNA exhibited greater variation than the coding regions. Several repeat sequences were also discovered, namely, 33 forward, 14 reverse, 3 complement, and 49 microsatellite repeats. Furthermore, phylogenetic analysis using 47 cpDNA sequences of Apioideae members revealed that L. seseloides and S. divaricata clustered together with a 100% bootstrap value, thereby supporting the validity of renaming L. seseloides to S. divaricata at the genomic level. Notably, S. divaricata was most closely related to Libanotis buchtormensis, which contradicts previous reports. Therefore, these findings provide a valuable foundation for future studies on the genetic diversity and evolution of S. divaricata.
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Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
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Cruz J, Trombley J, Carrington L, Cheng X. Properties of the Novel Chinese Herbal Medicine Formula Qu Du Qiang Fei I Hao Fang Warrant Further Research to Determine Its Clinical Efficacy in COVID-19 Treatment. Med Acupunct 2021; 33:71-82. [PMID: 33613814 PMCID: PMC7894031 DOI: 10.1089/acu.2020.1466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction: COVID-19, the infectious disease induced by the virus severe acute respiratory syndrome-related coronavirus-2, has caused increasing global health concerns, and novel strategies to prevent or ameliorate the condition are needed. Traditional Chinese Medicine (TCM) herbal formulas have been used in the treatment of epidemics in China for over 2000 years. This study investigated the therapeutic effects of Qu Du Qiang Fei I Hao Fang (QDQF1) "Eliminating Virus and Strengthening Lung-No.1 Formula," in the treatment and prevention of COVID-19. QDQF1 consists of Shēng Huáng Qí, Běi Shā Shēn, Chuān Jié Gěng, Zhì Fáng Fēng, Qīng Lián Qiáo, Jīn Yín Huā, Bǎn Lán Gēn, Chǎo Cāng Zhú, Zǐ Huā Dì Dīng, and Shēng gān căo. Materials and Methods: A literature survey was performed by conducting systematic electronic searches in PubMed, Science Direct, Google Scholar, and in books. Results: Each herb in this formula has long been used to treat various diseases due to their pharmacologic, antiviral, anti-inflammatory, and antimicrobial effects that inhibit microbial adherence to mucosal or epithelial surfaces, inhibit endotoxin shock, and selectively inhibit microbial growth. Conclusion: The herbs chosen for the QDQF1 formula have been historically paired, and cast a wide net over the potential COVID-19 symptomatology. Their combined functions provide comprehensive and balanced therapeutics from both TCM and allopathic perspectives. Individual herbs and herbal combinations are analyzed for their applicability to pertinent TCM patterns of COVID-19 presentations, including heat and cold patterns, damp and phlegm syndromes, toxicity, and deficiency patterns. A further study in a randomized, double-blind, and placebo-controlled trial of QDQF1 is recommended to assess its therapeutic efficacy in the treatment of COVID-19.
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Affiliation(s)
- Jennifer Cruz
- Institute of Clinical Immunology, Yue-yang Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Doctoral Program of Acupuncture & Oriental Medicine, The Atlantic Institute of Oriental Medicine, Fort Lauderdale, FL, USA
| | - Jason Trombley
- Institute of Clinical Immunology, Yue-yang Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Doctoral Program of Acupuncture & Oriental Medicine, The Atlantic Institute of Oriental Medicine, Fort Lauderdale, FL, USA
| | - Linda Carrington
- Doctoral Program of Acupuncture & Oriental Medicine, The Atlantic Institute of Oriental Medicine, Fort Lauderdale, FL, USA
| | - Xiaodong Cheng
- Institute of Clinical Immunology, Yue-yang Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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