{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Xiaoyu Luo"],"organism":["Mus musculus"],"software":["SOAPnuke, RSEM, DESeq2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15788"],"description":["Establishment 615 mouse subcutaneous tumor model using mouse derived gastric cancer cell lines (MFC)，and intervention with traditional Chinese medicine（Sijunzi Decoction）. The mice model were indived into Model group(model), early Sijunzi Decoction (E-SJZD), synchronization Sijunzi Decoction (S-SJZD).The size of GC tumor changes and body weight in these groups of 615 mice were observed. The mRNA-seq analysis of mouse models and the network pharmacology technology based on TCM Systems Pharmacology database and Swiss target prediction were used to predict corresponding potential target genes of SJZD."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - On the terminal day (Day 21 post-MFC inoculation), all mice were euthanized. Gastric carcinoma tumor tissues from the MFC allograft were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80°C until nucleic acid extraction to preserve RNA integrity.","Nucleic Acid Extraction - RNA from snap-frozen tissues samples was extracted using TRIzol (Invitrogen, USA) according to manufacturer’s instructions. mRNA was isolated from total RNA extracts.","Sequencing - The constructed libraries were subjected to high-throughput sequencing on the DNBSEQ platform, following the manufacturer's standard sequencing workflow to generate single-end reads.","Growth Protocol - Four-to-five-week-old inbred 615 mice were maintained under specific pathogen-free (SPF) conditions at 22 °C ± 2 °C, 55% ± 5% humidity, with a 12/12-hour light/dark cycle, and provided with ad libitum access to water and diet. A one-week acclimatization period was provided prior to any experimental procedures.","Sample Treatment - After acclimatization, mice were randomly divided into three groups (n=6/group):  Model group: Received 200μl of 0.9% saline via intragastric gavage on day 1, followed by MFC cell inoculation on day 7.  Early SJZD group (E-SJZD): Received 200μl of Sijunzi Decoction (19,200 mg/kg/bw) via intragastric gavage on day 1, followed by MFC cell inoculation on day 7.  Synchronization SJZD group (S-SJZD): Received 200μl of Sijunzi Decoction (19,200 mg/kg/bw) and MFC cell inoculation simultaneously on day 7. All groups received daily intragastric administration for 3 consecutive weeks.","Library Construction - Strand-specific RNA-seq libraries were constructed from the isolated mRNA."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Gene expression levels were quantified using RSEM (v1.3.1). For differential expression analysis, read counts were normalized using the methods inherent to the DESeq2 (v1.4.5) software, which employs a median-of-ratios method to account for library size and RNA composition."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-T7","SPF Animal Room","Animal Experiment Facility","Centrifuge, Nucleic Acid Quantification Instrument","Dr. Tom Multi-omics Data Mining System","Biosafety Cabinet, Liquid Nitrogen Tank, -80°C Freezer","PCR Thermocycler, Fragment Analyzer"],"pubmed_abstract":["<h4>Background</h4>Gastric cancer (GC) is an importent cause of global cancer mortality, underscoring the need for therapeutic strategies. Traditional Chinese medicine (TCM), particularly Sijunzi Decoction (SJZD), has demonstrated clinical promise as an adjuvant therapy in oncology by improving survival and reducing chemotherapy toxicity. However, the mechanistic basis of SJZD's anti-tumor activity, especially concerning its potential immunomodulatory effects within a competent tumor microenvironment, remains poorly elucidated due to the complexity of its components and limitations of previous preclinical models.<h4>Methods</h4>The subcutaneous tumor models were established in inbred 615 mice with MFC cells, and RNA-sequencing (RNA-Seq) was performed on tumor tissues to characterize treatment-associated differentially expressed genes across three groups (model, early Sijunzi Decoction, and synchronization Sijunzi Decoction). Network pharmacology analysis predicted the bioactive compounds and putative targets of Sijunzi Decoction, and constructed a compound-target-disease network to explore potential GC-related pathways. The expression profile of STAT3 in gastric cancer tissues from three groups of mice model was examined through Western blotting assays and immunohistochemistry to determine its role in Gastric cancer and its regulatory relationship.<h4>Results</h4>SJZD could prevent tumor growth. Additionally, the earlier Chinese medicine intervention, the more definiter tumor inhibition. The RNA-Seq revealed an immunomodulatory gene signature, as evidenced by the 13 common DEGs significant enrichment in the JAK-STAT pathway. Network pharmacology identified 156 overlapping targets between SJZD and GC, among which STAT3 was recognized as a critical hub gene. Forthermore, Western blot and IHC analysis confirmed that SJZD had downregulated STAT3 protein expression in tumor tissues.<h4>Conclusion</h4>SJZD had a definitely inhibitive effect against GC in mice by regulation the STAT3 expression in JAK/STAT signaling pathway, providing a mechanistic rationale for the potential clinical translation of SJZD in GC treatment."],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_title":["STAT3 as a critical target of Sijunzi Decoction in the treatment of gastric cancer: evidence from integrated network pharmacology and experimental validation"],"pubmed_authors":["Xiaoyu Luo","XiaoYu Luo, GuiPing Xie, QianYing Tan, YaoHui Wang, HaiDan Wang, Jing Zhai1"],"additional_accession":[]},"is_claimable":false,"name":"Potential Mechanism of Chinese herbal formula Sijunzi Decoction in Treating Gastric Cancer","description":"Establishment 615 mouse subcutaneous tumor model using mouse derived gastric cancer cell lines (MFC)，and intervention with traditional Chinese medicine（Sijunzi Decoction）. The mice model were indived into Model group(model), early Sijunzi Decoction (E-SJZD), synchronization Sijunzi Decoction (S-SJZD).The size of GC tumor changes and body weight in these groups of 615 mice were observed. The mRNA-seq analysis of mouse models and the network pharmacology technology based on TCM Systems Pharmacology database and Swiss target prediction were used to predict corresponding potential target genes of SJZD.","dates":{"release":"2025-10-31T00:00:00Z","modification":"2026-05-27T17:46:19.292Z","creation":"2025-10-27T06:26:41.331Z"},"accession":"E-MTAB-15788","cross_references":{"ENA":["ERP182504"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.3389/fmolb.2025.1683806"]}}