Revealing the potential mechanism of Astragalus membranaceus improving prognosis of hepatocellular carcinoma by combining transcriptomics and network pharmacology

Bioinformatics combined with network pharmacology and experimental validation to identify key biomarkers of hepatocellular carcinoma and corresponding compounds in Radix Astragali and Pueraria Mirifica

The occurrence and death rates of primary hepatocellular carcinoma (HCC) are increasing, and there remains a shortage of effective oral medications with minimal side effects. We aim to identify potential biomarkers and compounds from Radix Astragali (RA) and Pueraria Mirifica (PM) to treat liver cancer and improve prognosis. Differentially expressed genes (DEGs) associated with HCC were identified by bioinformatics analysis of three datasets, GSE112791, GSE101685, and GSE45114. Using public databases to predict the bioactive components and possible targets of RA and PM. Target crossover from Gene Expression Omnibus (GEO) and public databases were used to identify potential biomarkers for HCC. Subsequently, validation and prognostic value analyses were performed using the Gene Expression Profile Interaction Analysis (GEPIA) platform. The Cytoscape software created a network of "compound targets" to pinpoint compounds linked to the biomarkers. Molecular docking techniques were utilized to validate the connection between these compounds and the identified biomarkers. Ultimately, the HepG2 liver cancer cell line was chosen to assess the inhibitory effect of Hederagenin (HDG) and to confirm the expression of ADH1B through Western blot analysis. In this study, four key biomarkers (NR1I2, ADH1B, NQO1, GHR) were identified. Molecular docking showed that these four core targets could form stable conformations with the corresponding compounds. As the drug concentration decreases, the inhibitory effect on HepG2 diminishes, and the survival rate of HepG2 cells significantly declines following the administration of 100 µmol/L HDG. Compared to the control, the expression of ADH1B protein is significantly increased in HepG2 cells treated with 100 µmol/L HDG. The study identified four key biomarkers (ADH1B, GHR, NQO1, NR1I2) that have prognostic ability for HCC. This study provides biomarkers and potential targeted monomeric medicines for treating HCC.

Application of omics technologies in studies on antitumor effects of Traditional Chinese Medicine

Traditional Chinese medicine (TCM) is considered to be one of the most comprehensive and influential form of traditional medicine. It plays an important role in clinical treatment and adjuvant therapy for cancer. However, the complex composition of TCM presents challenges to the comprehensive and systematic understanding of its antitumor mechanisms, which hinders further development of TCM with antitumor effects. Omics technologies can immensely help in elucidating the mechanism of action of drugs. They utilize high-throughput sequencing and detection techniques to provide deeper insights into biological systems, revealing the intricate mechanisms through which TCM combats tumors. Multi-omics approaches can be used to elucidate the interrelationships among different omics layers by integrating data from various omics disciplines. By analyzing a large amount of data, these approaches further unravel the complex network of mechanisms underlying the antitumor effects of TCM and explain the mutual regulations across different molecular levels. In this study, we presented a comprehensive overview of the recent progress in single-omics and multi-omics research focused on elucidating the mechanisms underlying the antitumor effects of TCM. We discussed the significance of omics technologies in advancing research on the antitumor properties of TCM and also provided novel research perspectives and methodologies for further advancing this research field.

Revealing the mechanism of ethyl acetate extracts of Semen Impatientis against prostate cancer based on network pharmacology and transcriptomics

ETHNOPHARMACOLOGICAL RELEVANCE

Prostate cancer (PCa) is the most common malignancy of the male genitourinary system and currently lacks effective treatment. Semen Impatientis, the dried ripe seed of Impatiens balsamina L., is described by the Chinese Pharmacopoeia as a traditional Chinese medicine (TCM) and is used in clinical practice to treat tumors, abdominal masses, etc. In our previous study, the ethyl acetate extracts of Semen Impatientis (EAESI) was demonstrated to be the most effective extract against PCa among various extracts. However, the biological effects of EAESI against PCa in vivo and the specific antitumor mechanisms involved remain unknown.

AIM OF THE STUDY

In this study, we aimed to investigate the antitumor effect of EAESI on PCa in vitro and in vivo by performing network pharmacology analysis, transcriptomic analysis, and experiments to explore and verify the underlying mechanisms involved.

MATERIALS AND METHODS

The antitumor effect of EAESI on PCa in vitro and in vivo was investigated via CCK-8, EdU, flow cytometry, and wound healing assays and xenograft tumor models. Network pharmacology analysis and transcriptomic analysis were employed to explore the underlying mechanism of EAESI against PCa. Activating transcription factor 3 (ATF3) and androgen receptor (AR) were confirmed to be the targets of EAESI against PCa by RT‒qPCR, western blotting, and rescue assays. In addition, the interaction between ATF3 and AR was assessed by coimmunoprecipitation, immunofluorescence, and nuclear-cytoplasmic separation assays.

RESULTS

EAESI decreased cell viability, inhibited cell proliferation and migration, and induced apoptosis in AR+ and AR- PCa cells. Moreover, EAESI suppressed the growth of xenograft tumors in vivo. Network pharmacology analysis revealed that the hub targets of EAESI against PCa included AR, AKT1, TP53, and CCND1. Transcriptomic analysis indicated that activating transcription factor 3 (ATF3) was the most likely critical target of EAESI. EAESI downregulated AR expression and decreased the transcriptional activity of AR through ATF3 in AR+ PCa cells; and EAESI promoted the expression of ATF3 and exerted its antitumor effect via ATF3 in AR+ and AR- PCa cells.

CONCLUSIONS

EAESI exerts good antitumor effects on PCa both in vitro and in vivo, and ATF3 and AR are the critical targets through which EAESI exerts antitumor effects on AR+ and AR- PCa cells.

Shen-Qi-Ling-Bi Decoction Inhibits Colorectal Cancer Cell Growth by Inducing Ferroptosis Through Inactivation of PI3K/AKT Signaling Pathway

Colorectal cancer (CRC) is a common malignancy with poor prognosis. Shen-Qi-Ling-Bi Decoction (SQLB), a classic traditional Chinese medicine (TCM) formula, was found to exert antitumor effects in CRC. This study aimed to explore the biological functions of SQLB in CRC. Cell Counting Kit 8 (CCK-8), wound healing, and transwell invasion assays in vitro were used to evaluate the antitumor effects of SQLB in CRC cells. In addition, ferroptosis in CRC cells was determined by evaluating Fe2+ content and lipid ROS, MDA, and GSH levels. SQLB treatment partially reduced CRC cell proliferation, migration, and invasion; however, a ferroptosis inhibitor, ferrostatin-1 (Fer-1), abolished these effects. In addition, SQLB treatment triggered CRC cell ferroptosis, as evidenced by increased Fe2+, lipid ROS, and MDA levels and decreased GSH levels; conversely, these levels were reversed by Fer-1. Furthermore, SQLB notably suppressed tumor growth in nude mice in vivo. Meanwhile, SQLB decreased phosphorylated PI3K and AKT levels, downregulated Nrf2, GPX4, and SLC7A11 levels, and upregulated ACSL4 levels in CRC cells and in tumor tissues; however, these effects were reversed by Fer-1. Collectively, SQLB inhibited CRC cell proliferation, invasion, and migration by triggering ferroptosis through inactivation of the PI3K/AKT signaling pathway. These findings demonstrate a novel mechanism of action for SQLB in the treatment of CRC.

Targeting ferroptosis unveils a new era for traditional Chinese medicine: a scientific metrology study

In the past 11 years, there has been a surge in studies exploring the regulatory effect of Traditional Chinese Medicine (TCM) on ferroptosis. However, a significant gap persists in comprehensive scientometric analysis and scientific mapping research, especially in tracking the evolution, primary contributors, and emerging research focal points. This study aims to comprehensively update the advancements in targeting ferroptosis with various TCMs during the previous 11 years. The data, covering the period from 1 January 2012, to 30 November 2023, were retrieved from the Web of Science database. For in-depth scientometric and visualized analyses, a series of advanced analytical instruments were employed. The findings highlight China's predominant role, accounting for 71.99% of total publications and significantly shaping research in this domain. Noteworthy productivity was observed at various institutions, including Guangzhou University of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, and Zhejiang University. Thomas Efferth emerged as the foremost author within this field, while Frontiers in Pharmacology boasted the highest publication count. This study pinpointed hepatocellular carcinoma, chemical and drug-induced liver injury, mitochondrial diseases, acute kidney injury, and liver failure as the most critical disorders addressed in this research realm. The research offers a comprehensive bibliometric evaluation, enhancing our understanding of the present status of TCM therapy in managing ferroptosis-related diseases. Consequently, it aids both seasoned researchers and newcomers by accelerating access to vital information and fostering innovative concept extraction within this specialized field.

Exploring the mechanism of Jianpi Huatan recipe in protecting hepatocellular carcinoma based on network pharmacology

ETHNOPHARMACOLOGICAL RELEVANCE

Jianpi Huatan Recipe (JPHTR) is an effective prescription for delaying progression of hepatocellular carcinoma (HCC) provided by Longhua Hospital affiliated to Shanghai University of traditional Chinese Medicine, and it is consisted of nine traditional Chinese drugs, but the protective mechanism of JPHTR against HCC progression is unclear.

AIM OF THE STUDY

To study the mechanism of JPHTR preventing the progression of HCC based on the network pharmacology.

MATERIALS AND METHODS

The chemical component and potential gene targets of JPHTR and the important gene targets of HCC were obtained by retrieving traditional Chinese medicine network pharmacology analysis system (TCMNPAS) database. The data obtained from the database are used to construct the drugs-chemical component-targets network and protein-protein interaction network by using Cytoscape software and STRING database. The potential targets of JPHTR and HCC targets were imported into TCMNPAS-related modules in order to obtain the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Finally, we used HCC rat model to verify the vital signaling pathways predicted by network pharmacology.

RESULTS

A total of 197 potential compounds and 721 potential targets of JPHTR and 611 important gene targets of HCC were obtained. Through the experiment in vivo, it was found that JPHTR can reduce the serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, reduce the lipid droplets and inflammatory injury of liver tissue, and reduce the mRNA expression of Interleukin-6 (Il-6), Janus tyrosine Kinase2 (Jak2) and Forkhead box O3 (Foxo3) in FOXO pathway in the liver, thus delaying the development of HCC.

CONCLUSION

Through network pharmacology and rat experiments, it is preliminarily confirmed that JPHTR may delay the progression of HCC by regulating the expression of Il-6/Jak2/Foxo3 in FOXO signal pathway, which is expected to be a new therapeutic target for the protection of HCC.

Effects of Natural Products on Enzymes Involved in Ferroptosis: Regulation and Implications

Ferroptosis is a form of regulated cell death that is characterized by the accumulation of iron-dependent lipid peroxides. The regulation of ferroptosis involves both non-enzymatic reactions and enzymatic mechanisms. Natural products have demonstrated potential effects on various enzymes, including GPX4, HO-1, NQO1, NOX4, GCLC, and GCLM, which are mainly involved in glutathione metabolic pathway or oxidative stress regulation, and ACSL3 and ACSL4, which mainly participate in lipid metabolism, thereby influencing the regulation of ferroptosis. In this review, we have provided a comprehensive overview of the existing literature pertaining to the effects of natural products on enzymes involved in ferroptosis and discussed their potential implications for the prevention and treatment of ferroptosis-related diseases. We also highlight the potential challenge that the majority of research has concentrated on investigating the impact of natural products on the expression of enzymes involving ferroptosis while limited attention is given to the regulation of enzyme activity. This observation underscores the considerable potential and scope for exploring the influence of natural products on enzyme activity.

Anhydroicaritin suppresses tumor progression via the PI3K/AKT signaling pathway in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the most malignant tumors. The in vitro experiments on the application of Anhydroicaritin (AHI), the active ingredient of Bushen Huayu Decoction, in HCC treatment remain limited, particularly regarding its molecular mechanism.

METHODS

The TCMSP platform was used for drug ingredient screening. The GeneCards database and DisGeNET database are used to collect liver cancer targets. PPI network construction of active component-target intersection target was completed with string database. The GO and KEGG pathway analyses were performed via bioinformatics analysis. The molecular docking was used to confirm AHI's target proteins. The in vitro experiments were performed to validate the effect of AHI on HCC cell and explore the molecular mechanism by western blotting analysis.

RESULTS

Through the intersection, 155 intersection targets are finally obtained. The top 15 active ingredients were quercetin, kaempferol, beta-sitosterol, luteolin, beta-carotene, Stigmasterol, naringenin, formononetin, baicalein, Anhydroicaritin, isorhamnetin, licochalcone, 7-O-methylisomucronulatol, aloe-emodin and 8-O-Methylreyusi. The molecular mocking analysis showed that the four active components (quercetin, kaempferol, luteolin and AHI) and targets had a good binding activity (affinity ≤ 5 kcal/mol). In vitro experiments reveled that AHI could suppress tumor proliferation, invasion and metastasis of HCC cells. Further analysis showed that AHI inhibited tumor growth by PI3K/AKT signal pathway in HCC.

CONCLUSIONS

The Bushen Huayu Decoction and its active ingredient AHI could fight HCC. The potential mechanism may be associated with inhibiting the activation of PI3K/AKT signal pathway, which may serve as a potential treatment for HCC therapy.

Huanglian-Houpo extract attenuates DSS-induced UC mice by protecting intestinal mucosal barrier and regulating macrophage polarization

ETHNOPHARMACOLOGICAL RELEVANCE

Huanglian-Houpo Decoction (HLHP), a classical prescription, has been used to treat gastrointestinal diseases for hundreds of years in TCM. However, the effective constituents and underlying mechanisms of HLHP in the treatment of ulcerative colitis (UC) have not been fully investigated.

AIM OF THE STUDY

This study aimed to reveal the potential anti-UC mechanisms of 50% ethanol extraction of HL and HP (EHLHP), combining transcriptomes and network pharmacology, as well as the animal experiment verification.

METHODS

Primarily, we identified the chemical composition of EHLHP via UPLC-QE-MS analysis. A visualization network with components-targets-pathways on UC treatment were constructed using network pharmacology. And then, the transcriptomics sequencing method was applied to screen out the differentially expressed genes (DEGs) of EHLHP in the treatment of UC. The key targets and pathways of EHLHP were selected by the combination of the network pharmacology and transcriptomics results. Ultimately, the potential mechanisms of EHLHP on DSS-induced UC mice were verified.

RESULTS

A total of 34 components of EHLHP were identified by UPLC-QE-MS analysis. Combined with the analysis of network pharmacology and transcriptomics, there were 262 DEGs between the normal group and the model group, and 151 DEGs between the model group and the EHLHP group. At the same time, there are 79 interaction paths, such as PI3K-Akt signaling pathway, MAPK signaling pathway, etc. These results indicated that the anti-UC mechanisms would be involved in calcium signaling pathway, inflammatory signaling pathway (JAK-STAT, TNF-α, cGMP-PKG) and immune regulation (IL-17, B cell receptor). After 160 mg/kg and 320 mg/kg EHLHP were given to DSS induced UC mice, these typical symptoms could be significantly alleviated, such as the decrease of DAI value and inflammation level. The IHC staining results of ZO-1, Occludin and Claudin-1 suggested that the intestinal barrier of UC mice was enhanced by EHLHP. The expression of macrophages and immune cells in F4/80⁺, CD11c⁺, Gr-1⁺, NK1.1⁺ by FCM determination indicated that EHLHP could suppress UC by immunosuppression and macrophage polarization M1 to M2.

CONCLUSION

The potential mechanisms of HLHP extract on DSS-induced UC mice were revealed, by the prediction of integrated analysis of transcriptomes and network pharmacology, and subsequently animal test verification. It would provide a viable strategy to elucidate the mechanisms of TCM classical formula.

Ferroptosis in gastrointestinal cancer: From mechanisms to implications

Ferroptosis is a form of regulated cell death that is initiated by excessive lipid peroxidation that results in plasma membrane damage and the release of damage-associated molecular patterns. In recent years, ferroptosis has gained significant attention in cancer research due to its unique mechanism compared to other forms of regulated cell death, especially caspase-dependent apoptotic cell death. Gastrointestinal (GI) cancer encompasses malignancies that arise in the digestive tract, including the stomach, intestines, pancreas, colon, liver, rectum, anus, and biliary system. These cancers are a global health concern, with high incidence and mortality rates. Despite advances in medical treatments, drug resistance caused by defects in apoptotic pathways remains a persistent challenge in the management of GI cancer. Hence, exploring the role of ferroptosis in GI cancers may lead to more efficacious treatment strategies. In this review, we provide a comprehensive overview of the core mechanism of ferroptosis and discuss its function, regulation, and implications in the context of GI cancers.

The Role of Ferroptosis and Cuproptosis in Curcumin against Hepatocellular Carcinoma

BACKGROUND

Among cancer-related deaths, hepatocellular carcinoma (HCC) ranks fourth, and traditional Chinese medicine (TCM) treatment is an important complementary alternative therapy for HCC. Curcumin is a natural ingredient extracted from Curcuma longa with anti-HCC activity, while the therapeutic mechanisms of curcumin remain unclear, especially on ferroptosis and cuproptosis.

METHODS

Differentially expressed genes (DEGs) of curcumin treatment in PLC, KMCH, and Huh7 cells were identified, respectively. The common genes among them were then obtained to perform functional enrichment analysis and prognostic analysis. Moreover, weighted gene co-expression network analysis (WGCNA) was carried out for the construction of the co-expression network. The ferroptosis potential index (FPI) and the cuproptosis potential index (CPI) were subsequently used to quantitatively analyze the levels of ferroptosis and cuproptosis. Finally, single-cell transcriptome analysis of liver cancer was conducted.

RESULTS

We first identified 702, 515, and 721 DEGs from curcumin-treated PLC, KMCH, and Huh7 cells, respectively. Among them, HMOX1, CYP1A1, HMGCS2, LCN2, and MTTP may play an essential role in metal ion homeostasis. By WGCNA, grey60 co-expression module was associated with curcumin treatment and involved in the regulation of ion homeostasis. Furthermore, FPI and CPI assessment showed that curcumin had cell-specific effects on ferroptosis and cuproptosis in different HCC cells. In addition, there are also significant differences in ferroptosis and cuproptosis levels among 16 HCC cell subtypes according to single-cell transcriptome data analysis.

CONCLUSIONS

We developed CPI and combined it with FPI to quantitatively analyze curcumin-treated HCC cells. It was found that ferroptosis and cuproptosis, two known metal ion-mediated forms of programmed cell death, may have a vital effect in treating HCC with curcumin, and there are significant differences in various liver cancer cell types and curcumin treatment which should be considered in the clinical application of curcumin.

Toxicologic, transcriptomic, and metabolomic insights into the effect of a mixture of 26 veterinary antimicrobials on rat liver

To evaluate the maximum possible hazard of veterinary antimicrobial mixtures at doses accessible to humans, Sprague-Dawley male rats were orally dosed with a mixture of 26 commonly used veterinary antimicrobials for 90 consecutive days. The daily dosage of each component was 100 times (G1), 10 times (G2) and, 1 time (G3) of acceptable daily intake (ADI) in China. Hematology analysis and biochemical analysis found significant changes of several parameters, suggesting liver damage. Histopathological examination further indicated that mixtures of veterinary drugs at three levels caused obvious hepatotoxicity, and the severity of damage increased with dosage. LC-MS-based metabolomics analysis was carried out to detect metabolite changes in liver tissue. In G1, G2, and G3, 208, 165, and 195 differential accumulated metabolites (DAMs) compared with the Ctrl group were filtered, respectively. Similarly, RNA-seq helped us to filter a total of 183, 118, and 38 differentially expressed genes (DEGs) in G1, G2, and G3 compared with the Ctrl group, respectively. By integrating with the transcriptomic and metabolomic data, we revealed that mineral absorption, ascorbate and aldarate metabolism may be the major pathways affected by the veterinary antimicrobial mixtures in our study. This study provided useful data for the risk assessment of multiple chemicals.

Network pharmacology-based analysis of heat clearing and detoxifying drug JC724 on the treatment of colorectal cancer

BACKGROUND

Heat-clearing and detoxifying drugs has protective effect on colorectal cancer (CRC). Given the complicated features of Traditional Chinese medicine formulas, network pharmacology is an effective approach for studying the multiple interactions between drugs and diseases.

AIM

To systematically explore the anticancer mechanism of heat-clearing and detoxifying drug JC724.

METHODS

This study obtained the active compounds and their targets in JC724 from Traditional Chinese Medicine System Pharmacology Database. In addition, the CRC targets were obtained from Drugbank, TTD, DisGeNET and GeneCards databases. We performed transcriptome analysis of differentially expressed genes in CRC treated with JC724. Venn diagram was used to screen the JC724-CRC intersection targets as candidate targets. Core targets were selected by protein-protein interaction network and herb ingredient-target-disease network analysis. The functional and pathway of core targets were analysed by enrichment analysis.

RESULTS

We found 174 active ingredients and 283 compound targets from JC724. 940 CRC-related targets were reserved from the four databases and 304 CRC differentially expressed genes were obtained by transcriptome analysis. We constructed the network and found that the five core ingredients were quercetin, β Beta sitosterol, wogonin, kaempferol and baicalein. The core JC724-CRC targets were CYP1A1, HMOX1, CXCL8, NQO1 and FOSL1. JC724 acts on multiple signaling pathways associated with CRC, including the Nrf2 signaling pathway, oxidative stress, and the IL-17 signaling pathway.

CONCLUSION

In this study, we systematically analyzed the active ingredients, core targets and main mechanisms of JC724 in the treatment of CRC. This study could bring a new perspective to the heat-clearing and detoxifying therapy of CRC.

Adjuvant effects of Chinese medicinal tonics on gastric, liver, and colorectal cancers—OMICs-based contributions to understanding their mechanism of action

Gastric, liver, and colorectal cancers belong to gastrointestinal (GI) cancers, one of the most threatening diseases in the world. The tonics class in Chinese medicines plays a critical role in antigastrointestinal cancer as adjuvants. However, it is a challenge to study the effects and underlying mechanisms of tonics due to their multiple components and multiple targets; OMICs were introduced to facilitate the investigation of the complex mixture of tonics. In this review, the online databases PubMed, ProQuest, Web of Knowledge, China National Knowledge Infrastructure (CNKI), Chongqing VIP, and Wanfang were retrieved from 1 January 2011 to 31 May 2022, in an aim to summarize and discuss the research progress of the effects and, especially, the underlying mechanisms of tonics for antigastrointestinal cancers via OMICs. The results showed that through the combination of OMICs and other technologies, tonics have been used for gastrointestinal cancer by targeting cancer hallmarks, enhancing body resistance to carcinogenesis, enhancing therapeutic effects, and/or decreasing side effects. In conclusion, tonics may play a promising role in gastric, liver, and colorectal cancers as adjuvants and can be well investigated via the combination of OMICs and other technologies, which deserves further study.

The Role of Ferroptosis in the Treatment and Drug Resistance of Hepatocellular Carcinoma

Cell death is a fundamental feature of multicellular organisms’ development and a key driver of degenerative diseases. Ferroptosis is a new regulatory cell death mediated by iron-dependent lipid peroxidation, which is different from apoptosis and necrosis in morphology, pathophysiology and mechanism. Recent studies have found that ferroptosis is involved in the development of many diseases including hepatocellular carcinoma (HCC). As further research progresses, specific mechanisms of ferroptosis in HCC are being revealed. In this review, we summarize these recent advances about the treatment of drug-resistance in HCC and the latest ferroptosis-related treatment for HCC.