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Sema3d restrained Hepatocellular carcinoma progression through inactivating Pi3k/Akt signaling via interact with FLNA

ABSTRACT: Purpose: High throughput RNA-seq has provided an efficient and convenient access to screening substantial differentially expressed genes (DEGs). The goals of this study are to screen out Sema3d-regulated DEGs of HCC cells by utilizing RNA-sequencing and to furtherly identify specific biological function-related gene subset from Sema3d-regulated DEGs. Method: Firstly, HCCLM3 cells were seperated into two groups and respectively transfected with lentivirus-delivered Sema3d and control. We cultured these cells with DMEM containing 10% FBS serum. 48 hours later, cells of two groups were harvested by Trizol RNA isolater and examined expression difference of Sema3d, and then analyzed by High througput RNA-sequencing. Conclusion: Using next generation high throughput RNA-sequencing technology and using |log2(FoldChange)|>1 and Qvalue<0.05 as a cutoff for statistic analysis, we identified 75 positive-regulated DEGs and 282 negative-regulated DEGs were identified. Finally, pathway and process enrichment analysis identified a series of Sema3d regulated DEGs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200430 | GEO | 2022/05/25

REPOSITORIES: GEO

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Project description:Purpose: Primary retroperitoneal liposarcomas (RLPSs) are rare heterogeneous tumors for which there are few effective therapies. Certain anti-angiogenic tyrosine kinase inhibitors have demonstrated efficacy against various solid tumors. The aims of this study were to investigate the effect of Apatinib against retroperitoneal liposarcoma cells and its underlying mechanism and to explore the anti-tumor efficacy of a combination of Apatinib and Epirubicin. Methods: SW872 cells were treated with Apatinib(18μM) for 24 h. The RNAs of the control group and experimental group were stored in TRIzol reagent at -80 ℃. Then mRNA extraction and RNA sequencing were performed by Beijing Mygenostics Co. Ltd., Beijing, China. A Bioanalyzer 2100 System (Agilent Technologies, Santa Clara, CA, USA) was used to assay RNA integrity. An AMPureXP system (BeckmanCoulter, Brea, CA, USA) was used to perform PCR on the products. Quality-tested library preparations were sequenced on the Illumina Novaseq platform (Illumina, San Diego, CA, USA). There were three biological replicates per condition. Differential expression analysis of both groups was performed using DESeq2R v. 1.20.0. The Benjamini-Hochberg multiple hypothesis test correction was performed to obtain the false discovery rate (FDR). The criteria used to select the DEGs were |log2(FoldChange)| > 0.5 and FDR < 0.05. When log2(FoldChange) > 0, the gene was considered upregulated. When log2(FoldChange) < 0, the gene was considered downregulated. profiler package in R (R Core Team, Vienna, Austria) was used for GO function and KEGG pathway enrichment analyses of the DEGs. Histograms and bubble graphs were plotted with the ggplot2 package in R v. 3.4.3. Results:To elucidate the mechanisms by which Apatinib inhibited liposarcoma cells, we used RNA-seq to evaluate relative genetic changes in the SW872 cells after being treated with Apatinib for 24 hs, and found 2,038 DEGs, including 1,059 significantly downregulated genes and 979 significantly upregulated genes. The output of the KEGG pathway enrichment analysis suggests that Apatinib might inhibit SW872 cell proliferation through p53, DNA replication, and other important signaling pathways. GO enrichment analysis was performed on the genes that were significantly altered after Apatinib application.High-throughput RNA sequencing showed that Apatinib downregulated the expression of TYMS and RRM2. Conclusions: Apatinib showed strong efficacy against liposarcoma both in vitro and in vivo. Apatinib might inhibit liposarcoma cell proliferation through the RRM2/PI3K/AKT/mTOR signaling pathway and downregulate PD-L1 via the TYMS/STAT3 signaling pathway.

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Sema3d restrained Hepatocellular carcinoma progression through inactivating Pi3k/Akt signaling via interact with FLNA

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