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Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle

ABSTRACT: Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle

PROVIDER: PRJNA517432 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8495210_1.fastq.gz	Fastqsanger.gz
	SRR8495210_2.fastq.gz	Fastqsanger.gz
	SRR8495220_1.fastq.gz	Fastqsanger.gz
	SRR8495220_2.fastq.gz	Fastqsanger.gz
	SRR8495230_1.fastq.gz	Fastqsanger.gz

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Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle

Project description:We have used computational and experimental biology approaches to identify candidate mechanisms of action of a traditional Chinese medicine; Compound Kushen Injection (CKI), in a breast cancer cell line in which CKI has been shown to cause apoptosis. Because CKI is a complex mixture of plant secondary metabolites, we used a high-performance liquid chromatography (HPLC) fractionation and reconstitution approach to define chemical fractions required for CKI to induce apoptosis in MDA-MB-231 cells. Our initial fractionation separated major from minor compounds, and showed that the major compounds accounted for little of the activity of CKI. By systematically perturbing the major compounds in CKI we found that removal of no single major compound could alter the effect of CKI on cell viability and apoptosis. However, simultaneous removal of two major compounds identified oxymatrine and oxysophocarpine as critical compounds with respect to CKI activity. We then used RNA sequencing and transcriptome analysis to correlate compound removal with gene expression and phenotype data. We determined that many compounds in CKI are required for its effectiveness in triggering apoptosis but that significant modulation of its activity is conferred by a small number of compounds. In conclusion, CKI may be typical of many plant based extracts that contain many compounds in that no single compound is responsible for all of the bioactivity of the mixture and that many compounds interact in a complex fashion to influence a network containing many targets.

2019-05-29 | GSE125743 | GEO

Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection with Transcriptome Analysis

Project description:Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. We have used transcriptome analysis to explore the effects and interactions of two plant extracts (Kushen and Baituling) combined in Compound Kushen Injection (CKI). Based on shared chemical compounds and in vitro cytotoxicity comparisons, we found that both the major compounds in CKI, and the cytotoxicity effects of CKI were mainly derived from the extract of Kushen (Sophorae flavescentis). We generated and analyzed transcriptome data from MDA-MB-231 cells treated with single-herb extracts or CKI and results showed that Kushen contributed to the perturbation of the majority of cytotoxicity/cancer related pathways in CKI such as cell cycle and DNA replication. We also found that Baituling (Heterosmilax yunnanensis Gagnep) could not only enhance the cytotoxic effects of Kushen in CKI, but also activate immune-related pathways. Our analyses predicted that IL-1[beta] gene expression was upregulated by Baituling in CKI and we confirmed that IL-1[beta] protein expression was increased using an ELISA assay. Altogether, these findings help to explain the rationale for combining Kushen and Baituling in CKI, and show that transcriptome analysis using single herb extracts is an effective method for understanding herbal compatibility in TCM.

2019-08-20 | GSE130358 | GEO

Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle.

Project description:We used computational and experimental biology approaches to identify candidate mechanisms of action of aTraditional Chinese Medicine, Compound Kushen Injection (CKI), in a breast cancer cell line (MDA-MB-231). Because CKI is a complex mixture of plant secondary metabolites, we used a high-performance liquid chromatography (HPLC) fractionation and reconstitution approach to define chemical fractions required for CKI to induce apoptosis. The initial fractionation separated major from minor compounds, and it showed that major compounds accounted for little of the activity of CKI. Furthermore, removal of no single major compound altered the effect of CKI on cell viability and apoptosis. However, simultaneous removal of two major compounds identified oxymatrine and oxysophocarpine as critical with respect to CKI activity. Transcriptome analysis was used to correlate compound removal with gene expression and phenotype data. Many compounds in CKI are required to trigger apoptosis but significant modulation of its activity is conferred by a small number of compounds. In conclusion, CKI may be typical of many plant based extracts that contain many compounds in that no single compound is responsible for all of the bioactivity of the mixture and that many compounds interact in a complex fashion to influence a network containing many targets.

| S-EPMC6775143 | biostudies-literature

Survival Benefit of Compound Kushen Injection in the Treatment of Advanced Colorectal Cancer

Project description:To clarify the effectiveness and safety of compound kushen injection in the treatment of advanced colorectal cancer.

| 62736 | ecrin-mdr-crc

Compound kushen injection and YFSJ reduce gefitinib resistance in gefitinib resistant lung cancer cell lines

Project description:Compound Kushen Injection (CKI) has been used in clinics for nearly 20 years to treat different kinds of cancers. In this study, we found that CKI inhibited gefitinib resistant cell line proliferation, reduced drug resistance and improved anti-cancer effects when associated with gefitinib in a dose-dependent fashion. We also identified candidate CKI associated molecular mechanisms that might reduce drug resistance using transcriptome analysis methods, including gene differential expression analysis and pathway over-representation analysis. Multiple pathways were perturbed and the PI3K/AKT/MTOR and autophagy pathways were identified as the potential primary target pathways of CKI in this context. We also investigated the molecular mechanisms of another TCM, Yifei-Sanjie Wan (YFSJ) on reducing gefitinib resistance using transcriptome analysis.

2022-01-15 | GSE125933 | GEO

Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection with Transcriptome Analysis

Project description:Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection with Transcriptome Analysis

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The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms

Project description:Compound Kushen Injection (CKI) is a TCM fomula has been in use in hospitals in China for over twenty years for the integrated treatment of cancer.There is little evidence based medicine supporting such complex mixture. Because TCM preparations are often combinations of multiple herbs containing hundreds of compounds, they have been difficult to study. The development of high throughput -omics methods has allowed better characterization of TCM. We have applied high-throughput transcriptome data in two additional cancer cell lines and integrated our differential expression results across cell lines to identify a reduced set of differentially expressed (DE) candidate genes as well as a reproducible set of candidate pathways that are perturbed by CKI. In our results,CKI induced cell-cycle arrest and apoptosis. We identified 363 core candidate genes that were associated with cell cycle, apoptosis, DNA replication/repair and various cancer pathways. Of these, 7 are known to be clinically relevant to cancer diagnosis or therapy and 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes.By identifying a number of promising candidate pathways and genes associated with CKI based on our transcriptome based analysis, we have shown this type of approach is useful for the systematic analysis of molecular changes resulting from complex mixtures of bioactives in the context of cancer therapy.

2020-08-05 | GSE124715 | GEO

Identification Of Candidate Anti-Cancer Molecular Mechanisms Of Compound Kushen Injection Using Functional Genomics

Project description:Compound Kushen Injection (CKI) has been clinically used in China for over 15 years to treat various types of solid tumours. However, because such Traditional Chinese Medicine (TCM) preparations are complex mixtures of plant secondary metabolites, it is essential to explore their underlying molecular mechanisms in a systematic fashion. We have used the MCF-7 breast cancer cell line as an initial in vitro model to identify CKI induced changes in gene expression. Cells were treated with CKI for 24 and 48 hours at two concentrations (1.0 and 2.0 mg/mL), and 5-Fluorouracil (5-FU) was used to treat cells as a positive control. Cell proliferation and apoptosis activity were measured with XTT and Caspase-3 assays respectively. Transcriptome data of cells treated with CKI or 5-FU for 24 and 48 hours were acquired using high-throughput Illumina RNA-seq technology. In this report we show that CKI inhibited MCF-7 cell proliferation and induced apoptosis in a dose-dependent fashion. We integrated and applied a series of transcriptome analysis methods, including gene differential expression analysis, pathway over-representation analysis, de novo identification of long non-coding RNAs (lncRNA) as well as co-expression network reconstruction, to identify candidate anti-cancer molecular mechanisms of CKI. Multiple pathways were perturbed and the cell cycle was identified as the potential primary target pathway of CKI in MCF-7 cells. CKI may also induce apoptosis in MCF-7 cells via a p53 independent mechanism. In addition, we identified novel lncRNAs and showed that many of them might be expressed as a response to CKI treatment. Overall, we have comprehensively investigated the utility of transcriptome analysis with high-throughput sequencing to characterise the molecular response of cancer cells to a TCM drug, and provided a practical guideline for future molecular studies of TCM.

2016-09-14 | GSE78512 | GEO

The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms

Project description:The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms

| PRJNA513201 | ENA

Compound kushen injection and YFSJ reduce gefitinib resistance in gefitinib resistant lung cancer cell lines

Project description:Compound kushen injection and YFSJ reduce gefitinib resistance in gefitinib resistant lung cancer cell lines

| PRJNA518027 | ENA