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Article ; Online: Machine learning uncovers accumulation mechanism of flavonoid compounds in Polygonatum cyrtonema Hua.

Han, Zhigang / Gong, Qiqi / Huang, Suya / Meng, Xinyue / Xu, Yi / Li, Lige / Shi, Yan / Lin, Junhao / Chen, Xueliang / Li, Cong / Ma, Haijie / Liu, Jingjing / Zhang, Xinfeng / Chen, Donghong / Si, Jinping

Plant physiology and biochemistry : PPB

2023 Volume 201, Page(s) 107839

Abstract: The compositions and yield of flavonoid compounds of Polygonatum cyrtonema Hua (PC) are important ...

Abstract	The compositions and yield of flavonoid compounds of Polygonatum cyrtonema Hua (PC) are important indices of the quality of medicinal materials. However, the flavonoids compositions and accumulation mechanism are still unclear in PC. Here, we identified 22 flavonoids using widely-targeted metabolome analysis in 15 genotypes of PC. Then weighted gene co-expression network analysis based on 45 transcriptome samples was performed to construct 12 co-expressed modules, in which blue module highly correlated with flavonoids was identified. Furthermore, 4 feature genes including PcCHS1, PcCHI, PcCHS2 and PcCHR5 were identified from 94 hub genes in blue module via machine learning methods support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF), and their functions on metabolic flux of flavonoids pathway were confirmed by tobacco transient expression system. Our findings identified representative flavonoids and key enzymes in PC that provided new insight for elite breeding rich in flavonoids, and thus will be beneficial for rapid development of great potential economic and medicinal value of PC.
MeSH term(s)	Flavonoids ; Polygonatum/genetics ; Plant Breeding ; Gene Expression Profiling ; Machine Learning
Chemical Substances	Flavonoids
Language	English
Publishing date	2023-06-18
Publishing country	France
Document type	Journal Article
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2023.107839
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Article ; Online: Evaluating the efficacy and mechanisms of Hua-Zhuo-Ning-Fu-Decoction on psoriasis using integrated bioinformatics analysis and metabolomics.

Man, Shuai / Ma, Wenke / Jiang, Hao / Haider, Ali / Shi, Shasha / Li, Xiao / Wu, Zhuzhu / Song, Yongmei

Journal of ethnopharmacology

2024 Volume 325, Page(s) 117856

Abstract: Ethnopharmacological relevance: Hua Zhuo Ning Fu Decoction (HZD) is an empirical prescription ...

Abstract	Ethnopharmacological relevance: Hua Zhuo Ning Fu Decoction (HZD) is an empirical prescription from traditional Chinese medicine that shows excellent clinical results for psoriasis patients. Uncertainty lingered over HZD's potential anti-psoriasis mechanisms. Aim of the study: The study's objective is to investigate the pharmacological processes and therapeutic effects of HZD on psoriasis. Materials and methods: In the initial phase of the study, an investigation was conducted to assess the effects of HZD on psoriasis-afflicted mice using an imiquimod (IMQ)-induced murine model. The experimental mice were randomly allocated to different groups, including the IMQ-induced model group, the control group, the HZD therapy groups with varying dosage levels (low, medium, and high), and Dexamethasone (DEX, the positive control medicine) group. Bioinformatics analysis and molecular docking were subsequently employed to identify the primary components and molecular targets associated with the therapeutic action of HZD in the context of psoriasis. Additionally, to find the impacts on metabolite regulation, plasma metabolomics based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) was used. It's interesting to note that the combined mechanisms from metabolomics were examined in tandem with the targets. In vivo tests were the last step in validating the potential mechanism. Throughout the trial, the following data were recorded: body weight, psoriasis area and severity index (PASI). The molecular targets connected to HZD's anti-psoriasis activities were revealed using histological examination, western blot (WB), and ELISA investigation. Results: In mice induced with IMQ, HZD shown good anti-psoriasis effects in terms of PASI score and epidermal acanthosis. 95 HZD targets and 77 bioactive chemicals connected to psoriasis were found by bioinformatics research; of these, 7 key targets (EPHX2, PLA2G2A, TBXAS1, MAOA, ALDH1A3, ADH1A, and ADH1B) were linked to the mechanisms of HZD, the combination degree of which was finally expressed by the score of docking. In addition, HZD regulated nine metabolites. In line with this, HZD modified three metabolic pathways. Additionally, a combined examination of 7 key targets and 9 metabolites suggested that the metabolism of arachidonic acid might be the key metabolic route, which was identified by ELISA analysis. The in vivo investigation shown that HZD could control cytokines associated to inflammation (IL-10, TGF-β, IL-17A, and IL-23), as well as important antioxidant system markers (ROS, GSH, and MDA). Moreover, HZD controlled iron levels and the expression of ferroptosis-related proteins (ACSL4 and GPX4), suggesting that ferroptosis played a crucial role in this process. Conclusions: Our findings demonstrated the whole mechanism and anti-psoriasis effectiveness of HZD, which will promote its clinical application and aid in the investigation of new bioactive components of HZD against psoriasis.
MeSH term(s)	Humans ; Mice ; Animals ; Molecular Docking Simulation ; Psoriasis/chemically induced ; Psoriasis/drug therapy ; Psoriasis/pathology ; Medicine, Chinese Traditional ; Drugs, Chinese Herbal/pharmacology ; Drugs, Chinese Herbal/therapeutic use ; Metabolomics ; Imiquimod ; Computational Biology
Chemical Substances	Drugs, Chinese Herbal ; Imiquimod (P1QW714R7M)
Language	English
Publishing date	2024-02-03
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2024.117856
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Article ; Online: Machine learning uncovers accumulation mechanism of flavonoid compounds in Polygonatum cyrtonema Hua

Plant Physiology and Biochemistry. 2023 Aug., v. 201 p.107839-

2023

Abstract: The compositions and yield of flavonoid compounds of Polygonatum cyrtonema Hua (PC) are important ...

Abstract	The compositions and yield of flavonoid compounds of Polygonatum cyrtonema Hua (PC) are important indices of the quality of medicinal materials. However, the flavonoids compositions and accumulation mechanism are still unclear in PC. Here, we identified 22 flavonoids using widely-targeted metabolome analysis in 15 genotypes of PC. Then weighted gene co-expression network analysis based on 45 transcriptome samples was performed to construct 12 co-expressed modules, in which blue module highly correlated with flavonoids was identified. Furthermore, 4 feature genes including PcCHS1, PcCHI, PcCHS2 and PcCHR5 were identified from 94 hub genes in blue module via machine learning methods support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF), and their functions on metabolic flux of flavonoids pathway were confirmed by tobacco transient expression system. Our findings identified representative flavonoids and key enzymes in PC that provided new insight for elite breeding rich in flavonoids, and thus will be beneficial for rapid development of great potential economic and medicinal value of PC.
Keywords	Polygonatum cyrtonema ; flavonoids ; genes ; metabolomics ; plant physiology ; tobacco ; transcriptome ; Polygonatum cyrtonema Hua ; Flavonoid compounds ; Machine learning ; Metabolome ; Biosynthesis
Language	English
Dates of publication	2023-08
Publishing place	Elsevier Masson SAS
Document type	Article ; Online
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2023.107839
Database	NAL-Catalogue (AGRICOLA)

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Article: Comparatively Evaluating the Role of Herb Pairs Containing Angelicae Sinensis Radix in Xin-Sheng-Hua Granule by Withdrawal Analysis.

Pang, Han-Qing / Xu, Ding-Qiao / Tang, Yu-Ping / Zhou, Gui-Sheng / Xu, Hui-Qin / Jin, Yi / Zhu, Zhen-Hua / Shi, Xu-Qin / Yue, Shi-Jun / Chen, Yan-Yan / Huang, Sheng-Liang / Duan, Jin-Ao

Evidence-based complementary and alternative medicine : eCAM

2020 Volume 2020, Page(s) 9456350

Abstract: ... Danggui) in Xin-Sheng-Hua Granule (XSHG) on hemolytic and aplastic anemia (HAA) mice. HAA model mice were ...

Abstract	The present study aims to investigate the roles of herb pairs containing Angelicae Sinensis Radix (Danggui) in Xin-Sheng-Hua Granule (XSHG) on hemolytic and aplastic anemia (HAA) mice. HAA model mice were induced by acetyl phenylhydrazine and cyclophosphamide; then the samples of XSHG and its decomposed recipes (DY, DC, DT, DH, DJ, and DZ) were orally administrated to these mice. Indicators of peripheral blood routine, organ index, and ATPase activities were tested. Moreover, the main effective components in these samples were also analyzed by UHPLC-TQ-MS/MS. Clear separation between the control and model groups from score plot of principal component analysis (PCA) was easily seen, indicating that HAA model was successfully conducted. Afterwards, relative distance calculation method between dose groups and control group from PCA score plot was adopted to evaluate the integrated effects of hematinic function of different samples. And the orders of hematinic effects were as follows: XHSG > DJ > DT > DZ > DH > DC > DY. Further analysis of these samples by UHPLC-TQ-MS/MS revealed that XSHG underwent complicated changes when herb pairs containing Danggui were excluded from XSHG, respectively. Compared with XSHG, the vast majority of active compounds in sample DY (formula minus herb pair Danggui-Yimucao) decreased significantly, which could partly explain why herb pair Danggui-Yimucao made great contribution to XSHG. These findings showed that withdrawal analysis method is a valuable tool to analyze the impacts of herb pairs containing Danggui on XSHG, which could lay foundation to reveal the compatibility rules of this formula.
Language	English
Publishing date	2020-09-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2020/9456350
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: GC-MS Profile of Hua-Feng-Dan and RNA-Seq Analysis of Induced Adaptive Responses in the Liver.

Liu, Jia-Jia / Liang, Yan / Zhang, Ya / Wu, Rui-Xia / Song, Ying-Lian / Zhang, Feng / Shi, Jing-Shan / Liu, Jie / Xu, Shang-Fu / Wang, Zhang

Frontiers in pharmacology

2022 Volume 13, Page(s) 730318

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2022-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.730318
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Article ; Online: The underlying mechanisms of Jie-Du-Hua-Yu granule for protecting rat liver failure.

Qiu, Hua / Mao, Dewen / Tang, Nong / Long, Fuli / Zhang, Rongzhen / Wang, Minggang / Shi, Qinglan / Li, Jiahuan / Jiang, Qin / Chen, Yueqiao / Wang, Xiufeng

Drug design, development and therapy

2019 Volume 13, Page(s) 589–600

Abstract: Objectives: Jie-Du-Hua-Yu (JDHY) granule is a combination of six traditional Chinese medicines ...

Abstract	Objectives: Jie-Du-Hua-Yu (JDHY) granule is a combination of six traditional Chinese medicines with known therapeutic effect in treating acute liver failure (ALF). The aim of this study was to investigate the amelioration efficacy of JDHY in lipopolysaccharide/D-galactosamine (LPS/D-GalN)-induced ALF in rat and explore the possible molecular mechanism underlying the therapeutic efficacy. Materials and methods: The efficacy of JDHY was determined by assessing hepatic pathology and function in LPS and D-GalN challenged Wistar rat. We also evaluated the effect of JDHY on LPS-induced Kupffer cells by measuring inflammatory cytokines and determining the phenotypic function. By means of bioinformatics analysis of liver tissue and validation in Kupffer cells, we identified possible pathways involved in the pharmacologic action of mechanism of JDHY. Results: JDHY could attenuate LPS-induced liver injury in rat by inhibiting apoptosis and increasing hepatic activity. In vitro study showed that JDHY could decrease the production of proinflammatory cytokines (tumor necrosis factor-α, IL6, and interferon-γ), increase anti-inflammatory cytokines (IL10, IL13), and promote cell survival and proliferation, possibly due to inhibition of IκB/nuclear factor-κB (NF-κB) signaling pathway and expression of CD14 and CXCL2, which was consistent with the findings from bioinformatics analysis. Conclusion: Our results revealed that JDHY protected against LPS-induced liver damage both in vitro and in vivo, by inhibiting the NF-κB-mediated inflammatory pathway, indicating its potential function to treat liver diseases.
MeSH term(s)	Animals ; Cell Proliferation/drug effects ; Drugs, Chinese Herbal/chemistry ; Drugs, Chinese Herbal/isolation & purification ; Drugs, Chinese Herbal/pharmacology ; Galactosamine/pharmacology ; Lipopolysaccharides/pharmacology ; Liver Failure, Acute/chemically induced ; Liver Failure, Acute/pathology ; Liver Failure, Acute/prevention & control ; Male ; Medicine, Chinese Traditional ; Rats ; Rats, Wistar
Chemical Substances	Drugs, Chinese Herbal ; Lipopolysaccharides ; Galactosamine (7535-00-4)
Language	English
Publishing date	2019-02-11
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2451346-5
ISSN	1177-8881 ; 1177-8881
ISSN (online)	1177-8881
ISSN	1177-8881
DOI	10.2147/DDDT.S180969
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transcriptome analysis of Polygonatum cyrtonema Hua

Chenkai Wang / Daiyin Peng / Jinhang Zhu / Derui Zhao / Yuanyuan Shi / Shengxiang Zhang / Kelong Ma / Jiawen Wu / Luqi Huang

Plant Methods, Vol 15, Iss 1, Pp 1-

identification of genes involved in polysaccharide biosynthesis

2019 Volume 14

Abstract: Abstract Background Polygonatum cyrtonema Hua (P. cyrtonema) is one of the most important herbs ...

Abstract	Abstract Background Polygonatum cyrtonema Hua (P. cyrtonema) is one of the most important herbs in traditional Chinese medicine. Polysaccharides in P. cyrtonema plants comprise a class of important secondary metabolites and exhibit a broad range of pharmacological functions. Results In order to identify genes involved in polysaccharide biosynthesis, we performed RNA sequencing analysis of leaf, root, and rhizome tissues of P. cyrtonema. A total of 164,573 unigenes were obtained by assembling transcripts from all three tissues and 86,063 of these were annotated in public databases. Differentially expressed genes (DEGs) were determined based on expression profile analysis, and DEG levels in rhizome tissues were then compared with their counterparts in leaf and root tissues. This analysis revealed numerous genes that were either up-regulated or uniquely expressed in the rhizome. Multiple genes encoding important enzymes, such as UDP glycosyltransferases (UGTs), or transcription factors involved in polysaccharide biosynthesis were identified and further analyzed, while a few genes encoding key enzymes were experimentally validated using quantitative real-time PCR. Conclusion Our results substantially expand the public transcriptome dataset of P. cyrtonema and provide valuable clues for the identification of candidate genes involved in metabolic pathways.
Keywords	Polygonatum cyrtonema Hua ; RNA-Seq ; Transcriptome ; Polysaccharides ; Metabolic pathways ; Gene expression ; Plant culture ; SB1-1110 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Broad Anti-Viral Capacities of Lian-Hua-Qing-Wen Capsule and Jin-Hua-Qing-Gan Granule and Rational use Against COVID-19 Based on Literature Mining.

Shi, Mingfei / Peng, Bo / Li, An / Li, Ziyun / Song, Ping / Li, Jing / Xu, Ruodan / Li, Ning

Frontiers in pharmacology

2021 Volume 12, Page(s) 640782

Abstract: ... relatively better clinical outcomes. Both Lian-Hua-Qing-Wen Capsule (LHQWC) and Jin-Hua-Qing-Gan Granule ...

Abstract	The novel coronavirus disease 2019 (COVID-19) has become a matter of international concern as the disease is spreading exponentially. Statistics showed that infected patients in China who received combined treatment of Traditional Chinese Medicine and modern medicine exhibited lower fatality rate and relatively better clinical outcomes. Both Lian-Hua-Qing-Wen Capsule (LHQWC) and Jin-Hua-Qing-Gan Granule (JHQGG) have been recommended by China Food and Drug Administration for the treatment of COVID-19 and have played a vital role in the prevention of a variety of viral infections. Here, we desired to analyze the broad-spectrum anti-viral capacities of LHQWC and JHQGG, and to compare their pharmacological functions for rational clinical applications. Based on literature mining, we found that both LHQWC and JHQGG were endowed with multiple antiviral activities by both targeting viral life cycle and regulating host immune responses and inflammation. In addition, from literature analyzed, JHQGG is more potent in modulating viral life cycle, whereas LHQWC exhibits better efficacies in regulating host anti-viral responses. When translating into clinical applications, oral administration of LHQWC could be more beneficial for patients with insufficient immune functions or for patients with alleviated symptoms after treatment with JHQGG.
Language	English
Publishing date	2021-05-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2021.640782
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ling-Gui-Qi-Hua formula alleviates left ventricular myocardial fibrosis in rats with heart failure with preserved ejection fraction by blocking the transforming growth factor-β1 /Smads signaling pathway.

Shi, Yujiao / Liu, Chunqiu / Xiong, Shuang / Yang, Ling / Yang, Chenguang / Qiao, Wenbo / Liu, Yongcheng / Liu, Siyu / Liu, Jiangang / Dong, Guoju

Journal of ethnopharmacology

2023 Volume 317, Page(s) 116849

Abstract: Ethnopharmacological relevance: Ling-Qui-Qi-Hua (LGQH) decoction, composed of Poria cocos (Schw ...

Abstract	Ethnopharmacological relevance: Ling-Qui-Qi-Hua (LGQH) decoction, composed of Poria cocos (Schw.) Wolf, Cinnamomum cassia (L.) J. Presl, Paeonia veitchii Lynch, and Atractylodes macrocephala Koidz., is a compound formula derived from Ling-Gui-Zhu-Gan decoction recorded in the Treatise on Febrile and Miscellaneous. It has shown cardioprotective effects on patients or rats with heart failure with preserved ejection fraction (HFpEF). Nevertheless, the active ingredients of LGQH and its anti-fibrotic mechanism remain unknown. Aim of the study: To determine the active ingredients in LGQH decoction and verify that LGQH decoction may inhibit left ventricular (LV) myocardial fibrosis in HFpEF rats by blocking the transforming growth factor-β1 (TGF-β1)/Smads signaling pathway from the perspective of animal experiments. Materials and methods: First, liquid chromatography-mass spectrometry (LC-MS) technology was used to identify active components in the LGQH decoction. Secondly, a rat model of the metabolic syndrome-associated HFpEF phenotype was established and subsequently received LGQH intervention. The mRNA and protein expression of targets in the TGF-β1/Smads pathway were detected by quantitative real-time polymerase chain reaction and western blot analysis. Finally, molecular docking was conducted to examine the interactions between the active ingredients in the LGQH decoction and key proteins of the TGF-β1/Smads pathways. Results: According to LC-MS analysis, the LGQH decoction contained 13 active ingredients. In animal experiments, LGQH attenuated LV hypertrophy, enlargement, and diastolic function in HEpEF rats. Mechanically, LGQH not only down-regulated TGF-β1, Smad2, Smad3, Smad4, α-SMA, Coll I, and Coll III mRNA expressions and TGF-β1, Smad2, Smad3, P-Smad2/Smad3, Smad4, α-SMA, and Coll I protein expressions, but also up-regulated Smad7 mRNA and protein expressions, which ultimately led to myocardial fibrosis. Furthermore, molecular docking confirmed that 13 active ingredients in the LGQH decoction have excellent binding activities to the critical targets of the TGF-β1/Smads pathway. Conclusion: LGQH is a modified herbal formulation with multiple active ingredients. It might alleviate LV remodeling and diastolic dysfunction and inhibit LV myocardial fibrosis by blocking TGF-β1/Smads pathways in HFpEF rats.
MeSH term(s)	Rats ; Animals ; Transforming Growth Factor beta1/metabolism ; Heart Failure/drug therapy ; Molecular Docking Simulation ; Stroke Volume ; Fibrosis ; Signal Transduction ; Cardiomyopathies/metabolism ; RNA, Messenger/metabolism
Chemical Substances	Transforming Growth Factor beta1 ; RNA, Messenger
Language	English
Publishing date	2023-06-28
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2023.116849
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comparatively Evaluating the Role of Herb Pairs Containing Angelicae Sinensis Radix in Xin-Sheng-Hua Granule by Withdrawal Analysis

Han-Qing Pang / Ding-Qiao Xu / Yu-Ping Tang / Gui-Sheng Zhou / Hui-Qin Xu / Yi Jin / Zhen-Hua Zhu / Xu-Qin Shi / Shi-Jun Yue / Yan-Yan Chen / Sheng-Liang Huang / Jin-Ao Duan

Evidence-Based Complementary and Alternative Medicine, Vol

2020 Volume 2020

Abstract: ... Danggui) in Xin-Sheng-Hua Granule (XSHG) on hemolytic and aplastic anemia (HAA) mice. HAA model mice were ...

Abstract	The present study aims to investigate the roles of herb pairs containing Angelicae Sinensis Radix (Danggui) in Xin-Sheng-Hua Granule (XSHG) on hemolytic and aplastic anemia (HAA) mice. HAA model mice were induced by acetyl phenylhydrazine and cyclophosphamide; then the samples of XSHG and its decomposed recipes (DY, DC, DT, DH, DJ, and DZ) were orally administrated to these mice. Indicators of peripheral blood routine, organ index, and ATPase activities were tested. Moreover, the main effective components in these samples were also analyzed by UHPLC-TQ-MS/MS. Clear separation between the control and model groups from score plot of principal component analysis (PCA) was easily seen, indicating that HAA model was successfully conducted. Afterwards, relative distance calculation method between dose groups and control group from PCA score plot was adopted to evaluate the integrated effects of hematinic function of different samples. And the orders of hematinic effects were as follows: XHSG > DJ > DT > DZ > DH > DC > DY. Further analysis of these samples by UHPLC-TQ-MS/MS revealed that XSHG underwent complicated changes when herb pairs containing Danggui were excluded from XSHG, respectively. Compared with XSHG, the vast majority of active compounds in sample DY (formula minus herb pair Danggui-Yimucao) decreased significantly, which could partly explain why herb pair Danggui-Yimucao made great contribution to XSHG. These findings showed that withdrawal analysis method is a valuable tool to analyze the impacts of herb pairs containing Danggui on XSHG, which could lay foundation to reveal the compatibility rules of this formula.
Keywords	Other systems of medicine ; RZ201-999
Subject code	630
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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