INTERNATIONAL IMMUNOPHARMACOLOGY
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2024
·
IF 4.8
Ye Wang,Shao-jie Chen,Ting Ma,Qiu Long,Lan Chen,Ke-xin Xu,Yu Cao
Melanoma is a skin cancer originating from melanocytes. The global incidence rate of melanoma is rapidly increasing, posing significant public health challenges. Identifying effective therapeutic agents is crucial in addressing this growing problem. Natural products have demonstrated promising anti-tumor activity. In this study, a plant flavonoid, taxifolin, was screened using Weighted Correlation Network Analysis (WGCNA) in combination with the Connectivity Map (CMAP) platform. Taxifolin was confirmed to inhibit the proliferation, migration, and invasion ability of melanoma A375 and MV-3 cells by promoting apoptosis. Additionally, it suppressed the Epithelial-Mesenchymal Transition (EMT) process of melanoma cells. Cyber pharmacological analysis revealed that taxifolin exerts its inhibitory effect on melanoma through the PI3K/AKT signaling pathway, specifically by downregulating the protein expression of p-PI3K and p-AKT. Notably, the addition of SC-79, an activator of the PI3K/AKT signaling pathway, reversed the effects of taxifolin on cell migration and apoptosis. Furthermore, in vivo experiments demonstrated that taxifolin treatment slowed tumor growth in mice without significant toxic effects. Based on these findings, taxifolin holds promise as a potential drug for melanoma treatment.
研究领域:
肿瘤学
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药理学
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分子生物学
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癌症研究
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DOI
PubMed
高影响因子
Biomed Research International
·
2021
·
IF 3.411
Ling Kui,Min Li,Xiaonan Yang,Ling Yang,Qinghua Kong,Yunbing Pan,Zetan Xu,Shouling Wang,Dandan Mo,Yang Dong,Yao Liu,Jianhua Miao
Lung cancer is known as the leading cause which presents the highest fatality rate worldwide; non-small-cell lung cancer (NSCLC) is the most prevalent type of lung carcinoma with high severity and affects 80% of patients with lung malignancies. Up to now, the general treatment for NSCLC includes surgery, chemotherapy, and radiotherapy; however, some therapeutic drugs and approaches could cause side effects and weaken the immune system. The combination of conventional therapies and traditional Chinese medicine (TCM) significantly improves treatment efficacy in lung cancer. Therefore, it is necessary to investigate the chemical composition and underlying antitumor mechanisms of TCM, so as to get a better understanding of the potential natural ingredient for lung cancer treatment. In this study, we selected 78 TCM to treat NSCLC cell line (A549) and obtained 92 transcriptome data; differential expression and WGCNA were applied to screen the potential natural ingredient and target genes. The sample which was treated with A. pierreana generated the most significant DEG set, including 6130 DEGs, 2479 upregulated, and 3651 downregulated. KEGG pathway analyses found that four pathways (MAPK, NF-kappa B, p53, and TGF-beta signaling pathway) were significantly enriched; 16 genes were significantly regulated in these four pathways. Interestingly, some of them such as EGFR, DUSP4, IL1R1, IL1B, MDM2, CDKNIA, and IDs have been used as the target biomarkers for cancer diagnosis and therapy. In addition, classified samples into 14 groups based on their pharmaceutical effects, WGCNA was used to identify 27 modules. Among them, green and darkgrey were the most relevant modules. Eight genes in the green module and four in darkgrey were identified as hub genes. In conclusion, we screened out three new TCM (B. fruticose, A. pierreana, and S. scandens) that have the potential to develop natural anticancer drugs and obtained the therapeutic targets for NSCLC therapy. Our study provides unique insights to screen the natural components for NSCLC therapy using high-throughput transcriptome analysis.
研究领域:
癌症生物学
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药理学
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分子生物学
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生物信息学
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传统中药
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DOI
PubMed
高影响因子
Artificial Cells Nanomedicine and Biotechnology
·
2023
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IF 5.8
Jing Wen,Tong Ren,Jinzhen Zheng,Xing Jiang,Yingxia Li,Xilin Jiang,Xin Jin,Hongying Zhao,Jingwen Li
As the main pathological basis for the development of cardiovascular and cerebrovascular diseases, atherosclerosis (AS) seriously affects human health. The key targets of biological information analysis of AS can help exploit therapeutic targets. The expression data of early and progressive atherosclerotic tissues were downloaded from the Gene Expression Omnibus (GEO) database. Based on GSE28829 and GSE120521, 74 key genes were obtained through differential expression analysis and weighted correlation network analysis (WGCNA) analysis, which were mainly enriched in the regulating of inflammatory response, chemokine signalling pathway, apoptosis, lipid and AS, Toll-like receptor signalling pathway and so on according to the results of the enrichment analysis. Cytoscape software was applied to screen four pivotal genes (TYROBP, ITGB2, ITGAM and TLR2) based on PPI. The results of the correlation analysis showed that the expression level of pivotal genes was positively related to macrophages M0, and was negatively related to T cells follicular helper. In addition, the expression of ITGB2 was positively related to Tregs. In this study, bioinformatics was applied to screen pivotal genes affecting the progress of AS, which were significantly related to immune-related biological functions and signal pathways of atherosclerotic tissues and the infiltration level of immune cells. Therefore, pivotal genes were expected to become therapeutic targets for AS.
研究领域:
心血管病学
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生物信息学
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DOI
PubMed
高影响因子
Frontiers in Nutrition
·
2024
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IF 4
She Jiarong,Li Qingyang,Cui Maokai,Zheng Qiong,Yang Jie,Chen Tiantian,Shen Danyu,Peng Shaofeng,Li Chi,Liu Yihua
Less research has been conducted on the association between camellia oil’s (CO) phenolic composition and antioxidant capability. In this study, the phenolic profile of CO and its connection to antioxidant capacity were examined utilizing a combination of widely-targeted phenolic metabolomics and multivariate statistical analysis. A total of 751 phenolics were discovered. The WGCNA was used to link phenols to antioxidants, yielding 161 antioxidant-related phenols from the blue module. In response to several antioxidant assays, 59 (FRAP), 59 (DPPH), and 53 (ABTS) phenolics were identified as differential phenolic markers (DPMs). Further stepwise multiple linear regression revealed six DPMs that substantially influenced the antioxidant capacities. Nine metabolic pathways and their associated network mechanisms for the most significant phenolics were developed. This study sheds light on the phenolic content of CO, elucidates their role in antioxidant activity, and lays the groundwork for improving extraction techniques and generating improved product.
研究领域:
食品科学
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分析化学
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营养学
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产品关联
DOI
PubMed
高影响因子
Foods
·
2026
·Vol. 15
·期 9
·1475
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IF 6
Ying Liang,Yaqian Yuan,Jia Wang,Wenxue Chen,Weijun Chen,Qiuping Zhong,Jianfei Pei,Chun Chen,Xiong Fu,Rongrong He,Haiming Chen
The primary processing shapes the taste characteristics of coffee beans, while the regulation pathways remain unclear. Coffee beans processed by five methods—dry processing (DP), wet processing (WP), red honey (RH), black honey (BH) and anaerobic fermentation (AF)—were evaluated using electronic tongue analysis, sensory evaluation, and untargeted metabolomics. Sensory evaluation scores for mouthfeel, balance, and overall were higher in BH and AF. Conversely, the WP and DP exhibited heightened bitterness and astringency responses on the electronic tongue sensors, particularly for the former. The multigroup metabolomic comparison identified 808 DMs, and WGCNA revealed eight sensory-related modules containing 467 hub metabolites, mainly amino acids and derivatives, organic acids, alkaloids, and phenolic acids. KEGG analysis demonstrated that pathways such as caffeine metabolism and glycerophospholipid metabolism were the main pathways responsible for the metabolic differences. Further correlation analysis revealed potential flavor components closely associated with key taste characteristics. 1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and Tyr demonstrated positive associations with bitterness, while TPC, TFC, Gly, and Met exhibited negative correlations with bitterness and astringency. Glu demonstrated a positive correlation with umami. These findings elucidate the material basis by which the primary processing modulates non-volatile compounds and taste perception, offering new insights into enhancing coffee quality.
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DOI
PubMed
高影响因子
JOURNAL OF ETHNOPHARMACOLOGY
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2025
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IF 5.4
Changqing Wen,Hang Su,Jiaxuan Li,Jia Zou,Mingxu Gong,Fujiang Wang,Haitao Ge
Ethnopharmacological relevance IgA nephropathy (IgAN) is characterized by the deposition of thylakoid Gd-IgA1 and progresses to kidney dysfunction and failure. Thousands of years ago, Abelmoschus manihot (L.) Medic has been used as a traditional Chinese medicine to treat kidney diseases. The total flavonoid (TFA) of Abelmoschus manihot (L.) Medic is the main active ingredient of the medicine, which is known to have therapeutic effects on kidney diseases. However, the mechanism of action is still not further explored. Aim of study We aim to reveal the targets and potential mechanisms of TFA through comprehensive proteomics and Weighted Gene Co-expression Network Analysis (WGCNA), and to provide new ideas for the treatment of IgAN. Materials and methods In this study, we constructed a model of IgA nephropathy in rats and evaluated the efficacy of TFA in the IgAN model by assessing renal function, renal Gd-IgA1/IgA and serum markers. Integrated proteomics and WGCNA analysis identified core targets associated with TFA, and target validation was performed by immunohistochemistry. Results Kidney function (Scr, PCR, BUN) and serum markers (TGF-β1, TNF-α, BAFF, MCP-1) were significantly reduced after TFA treatment. Proteomics identified 2,757 differential expressed genes (DEGs). WGCNA highlighted four key modules associated with TFA effects. Six core targets (C1QBP, CYC1, Phab, VDAC2, CDH2, Dbn1) were validated by immunohistochemistry, confirming their roles in TFA renoprotection. Conclusion Induction of rat IgAN model, proteomics and WGCNA analyses demonstrated that TFA improves renal function, reduces histopathological damage and modulates inflammation. These findings further elucidate the treatment mechanism of TFA and provide new insights into the treatment of IgA nephropathy.
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产品关联
DOI
PubMed
高影响因子
PLANT GROWTH REGULATION
·
2023
·Vol. 100
·期 3
·633-646
·
IF 4.2
Wang Jie,Jia Jingyu,Sun Jiaju,Pang Xinyue,Li Bairu,Yuan Jiangfeng,Chen Enyan,Li Xin
Trypsin can significantly improve the storage quality of Cucumis sativus ( C. sativus ) due to its novel superoxide scavenging activity. Based on the results of physiological indices, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out, gene function was further confirmed by VIGS, a potential molecular mechanism of resistance improvement of C. sativus due to flavonoid biosynthesis induced by trypsin was proposed and discussed. Transcriptomic results showed that 1,068 genes highly related to flavonoid biosynthesis gathered in the brown module were obtained by the advanced method WGCNA. An isomeric compound of dihydrochalcone, trilobatin, was likely to be the key metabolite regulated by trypsin. Results of O2PLS and co-expression network illustrated that CsUGT91C1 acted as the hub gene which regulated the biosynthesis of flavonoids, especially trilobatin, in C. sativus . CsUGT91C1 also played as a hub node in the Protein-Protein Interactions network of WGCNA screened genes (WSGs). GO and KEGG analyses of WSGs enriched the transferase activities, especially UDP-glycosyltransferase activity and KEGG pathways of “Phenylpropanoid biosynthesis (map00940)” and “Flavonoid biosynthesis (map00941)”. Results of webtools of the PlantCARE database identified the G-box region of CsUGT91C1 , which can bind to the transcription factor CsMYC2. The expression and biological effects of CsUGT91C1 were significantly impeded by the silencing of CsMYC2 through VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus . Graphical abstract
研究领域:
植物科学
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分子生物学
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生物化学
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基因组学
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产品关联
DOI
高影响因子
FOOD CHEMISTRY
·
2025
·
IF 9.8
Dianhui Wu,Ziqiang Chen,Mingtao Ma,Wenzhe Li,Zhengcong Peng,Zhenbao Shi,Jinglong Zhang,Hua Liu,Guangfa Xie,Jian Lu
Aging plays a crucial role in enhancing the flavor of Huangjiu. This study aims to elucidate the changes in taste attributes of aged Huangjiu and explore the correlation between non-volatile compounds. It showed that aging made the sourness, bitterness, and astringency more pronounced. The content of organic acids and amino acids exhibited specific patterns with aging years. The total taste activity value of organic acids showed an increasing trend, peaking at 54.40 in Huangjiu aged 15 years, which served as a key indicator of sourness intensity. A total of 22 potential contributors to umami and 18 to bitterness were screened based on weighted gene coexpression network analysis. The total content of potential umami contributors was significantly higher in fresh Huangjiu and aging stage I, but declined in later periods, while bitterness contributors increased gradually throughout the aging process. This study provided theoretical support for the taste characteristics of aged Huangjiu.
研究领域:
食品科学
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代谢组学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
Brain Sciences
·
2022
·Vol. 12
·期 9
·1138
·
IF 3.333
Ming-Chun Yang,Di Wu,Hui Sun,Lian-Kun Wang,Xiao-Feng Chen
Background: Glioma is one of the major health problems worldwide. Biomarkers for predicting the prognosis of Glioma are still needed. Methods: The transcriptome data and clinic information on Glioma were obtained from the CGGA, TCGA, GDC, and GEO databases. The immune infiltration status in the clusters was compared. The genes with differential expression were identified, and a prognostic model was developed. Several assays were used to detect RPH3A’s role in Glioma cells, including CCK-8, colony formation, wound healing, and transwell migration assay. Results: Lower Grade Glioma (LGG) was divided into two clusters. The immune infiltration difference was observed between the two clusters. We screened for genes that differed between the two groups. WGCNA was used to construct a co-expressed network using the DEGs, and four co-expressed modules were identified, which are blue, green, grey, and yellow modules. High-risk patients have a lower overall survival rate than low-risk patients. In addition, the risk score is associated with histological subtypes. Finally, the role of RPH3A was detected. The overexpression of RPH3A in LGG cells can significantly inhibit cell proliferation and migration and regulate EMT-regulated proteins. Conclusion: Our study developed a metabolic-related model for the prognosis of Glioma cells. RPH3A is a potential therapeutic target for Glioma.Keywords:glioma;metabolic signature;prognosis
研究领域:
肿瘤学
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分子生物学
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生物信息学
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癌症生物学
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产品关联
DOI
PubMed
高影响因子
LWT-FOOD SCIENCE AND TECHNOLOGY
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2023
·
IF 6
Dahe Qiao,Junyan Zhu,Xiaozeng Mi,Hui Xie,Mingtao Shu,Minyi Chen,Rui Li,Shengrui Liu,Chaoling Wei
Withering time of fresh leaves is a key factor affecting the stability of flavor quality of Taiping Houkui tea (TPHK). It's effect and mechanism on the formation of flavor in TPHK remain unelucidated. Here, metabolomics and transcriptomics were combined to comprehensively investigate changes in the main flavor compounds and the expression patterns of related genes under different withering times. The results showed that withering had the greatest influence on the content of most amino acids and aroma volatiles. The relative content of most volatiles was observed to be highest at 6–8 h of withering time, which was consistent with the results from the sensory evaluation of aroma quality. Plant hormone signal transduction pathways played a key role in the variation of the flavor compound content under different withering times, especially ABA and JA signals. WGCNA demonstrated that ABA, JA, IAA, SA and different flavor substances were significantly associated with specific modules. JA may be involved in the metabolism of theanine during withering, while ABA may be involved in the accumulation of aromatic amino acids and main aroma components of TPHK. This research may serve as a reference for the optimization of the processing technology for TPHK.
研究领域:
植物学
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遗传学
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食品科学
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分子生物学
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产品关联
DOI
高影响因子
PHYTOMEDICINE
·
2024
·
IF 6.7
Qiong Liu,Aizhen Zhao,Xiaopeng Wu,Xin Zhang,Xiaoru Li,Wenwen Yang,Wangrui Lei,Hui Liu,Huadong Zhao,Shuai Jiang,Yang Yang,Mingzhi Shen
Background Septic heart failure has been recognized as a puzzle since antiquity and poses a major challenge to modern medicine. Our previous work has demonstrated the potential effects of lycorine (LYC) on sepsis and septic myocardial injury. Nonetheless, further exploration is needed to elucidate the underlying cellular and molecular mechanisms. Methods In this study, we conducted transcriptome analysis and weighted gene co-expression network analysis (WGCNA) to identify the key genes and reveal the mechanism of LYC against septic heart failure. Purpose This study aims to apply bioinformatic analysis and experimental validations to explore the protective effects and underlying mechanism of LYC on the cecal ligation and puncture (CLP)-induced sepsis model mice. Results Transcriptome analysis revealed the differentially expressed genes (DEGs) following LYC treatment. WGCNA analysis identified gene modules associated with LYC-mediated protection, with BCL3 emerging as a core gene within these modules. Notably, BCL3 was an overlapping gene of DEGs and WGCNA core genes induced by LYC treatment, and is highly negatively correlated with cardiac function indicator. In vivo and in vitro study further prove that LYC exerted a protective effect against septic myocardial injury through inhibiting BCL3. BCL3 siRNA ameliorated LPS-induced cardiac injury and inflammation, while BCL3 overexpression reversed the protective effect of LYC against LPS injury. Conclusion In summary, our findings demonstrate the significant attenuation of septic myocardial disorder by LYC, with the identification of BCL3 as a pivotal target gene. This study is the first to report the role of BCL3 in sepsis and septic myocardial injury. Furthermore, the strategy for hub genes screening used in our study facilitates a comprehensive exploration of septic targets and reveals the potential targets for LYC effect. These findings may offer a new therapeutic strategy for the management of septic heart failure, highlighting the cardioprotective effect of LYC as adjunctive therapy for sepsis management.
研究领域:
心脏病学
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药理学
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分子生物学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF PROTEOME RESEARCH
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2023
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IF 4.4
Jiahao Yan,Yuhe Ding,Zhao Peng,Lu Qin,Jingyu Gu,Cuihong Wan
The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish’s embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish’s early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.
研究领域:
发育生物学
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蛋白质组学
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分子生物学
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基因组学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）