KRT18 regulates the alternative splicing of cell proliferation and apoptosis genes via splicing factors in gastric cancer cells and clinical samples
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ABSTRACT:
PROVIDER: PRJNA664409 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12673047_1.fastq.gz | Fastqsanger.gz | |||
| SRR12673047_2.fastq.gz | Fastqsanger.gz | |||
| SRR12673048_1.fastq.gz | Fastqsanger.gz | |||
| SRR12673048_2.fastq.gz | Fastqsanger.gz | |||
| SRR12673049_1.fastq.gz | Fastqsanger.gz |
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Project description:We knocked down KRT18 in AGS cells using siRNAs to study KRT18-regulated genes using RNA-seq technology, followed by analysis of KRT18-regulated splicing factors in transcription and posttranscriptional level.
2021-05-25 | GSE158242 | GEO
Project description:27 sample pairs were conducted exon microarrays and 25 sample pairs were retain for our further alternative splicing analysis. 260 genes showed differential expression in more than 50% of our samples and 21 genes among them were validated by real-time PCR. Six genes with splicing events, which were firstly found in gastric cancer, were confirmed by RT-PCR. Keywords: Transcriptome analysis
2009-09-24 | GSE13195 | GEO
Project description:Except for a few genes known to have oncogenic spliceforms in gastric cancer, the full scope of aberrant splicing in gastric oncogenesis remains unclear. In this study, we elucidated the alternative splicing events associated with gastric carcinogenesis and identified upstream regulators governing these events. We performed RNA-seq on 19 matched tumor/normal pairs and a panel of gastric cancer cell lines, and identified 361 tumor associated (TA) alternative splicing events (ASEs), which included known oncogenic ASEs in genes such as INSR, FGFR2, CD44 and KRAS. We further identified 8 splicing factors dysregulated in gastric tumors, the expression of which are correlated to the splice ratio of the TA ASEs. We thereby constructed a dysregulated splicing network in gastric cancer, consisting of alternative splicing changes correlated to their potential regulators. This network featured three potential regulatory modules centered around the splicing factors ESRP2, MBNL1 and PTPB1. Knockdown of each splicing factor led to the expected changes in splicing of approximately half of the ASEs assayed. Thus, dysregulation of the splicing factors indeed was the cause of many of the TA ASEs. Pathway enrichment analysis showed that genes affected by tumor associated splicing were pre-dominantly involved in cytoskeletal organization. Concordant with this, knockdown of the splicing factors regulating the TA ASEs led to the expected changes in trans-well migration activity. Thus, we have established for the first time a comprehensive splicing network that likely drives gastric tumor progression, based on which novel therapeutic targets can be identified for further evaluation.
| EGAS00001002256 | EGA
Project description:Splicing dysregulation, which leads to apoptosis resistance, has been recognized as a major hallmark for tumorigenesis and cancer progression. Targeting alternative splicing by either increasing pro-apoptotic proteins or inhibiting anti-apoptotic proteins in tumor cells may be an effective approach for gastric cancer (GC) therapy. However, the role of modulation of alternative splicing in GC remains poorly understood. In this study, to the best of our knowledge, the unbalanced expression of the myeloid cell leukemia-1 (Mcl-1) splicing variants, Mcl-1L and Mcl-1S, was identified in GC patients for the first time. Increasing anti-apoptotic Mcl-1L and decreasing pro-apoptotic Mcl-1S expression levels were correlated with tumor proliferation and poor survival. In vitro data showed that a shift in splicing from Mcl-1L to Mcl-1S induced by treatment with Mcl-1-specific steric-blocking oligonucleotides (SBOs) efficiently decreased Mcl-1L expression, increased Mcl-1S expression, and accelerated tumor cell apoptosis in a dose-dependent manner. Additionally, mouse xenotransplant models confirmed that modification of Mcl-1 alternative splicing increased tumor cell death and suppressed tumor proliferation. This study demonstrated that the modification of Mcl-1 splicing might stimulate the pro-apoptotic factor and inhibit the anti-apoptotic protein to induce significant apoptosis. Thus, this finding provided a strategy for cancer therapy, according to which SBOs could be used to change the Mcl-1 splicing pattern, thereby inducing apoptosis.
| S-EPMC7732305 | biostudies-literature
Project description:Keratin 18 (KRT18), one of the most abundant keratins in epithelial and endothelial cells, has been reported to be aberrantly expressed in many malignancies and extensively regarded as a biomarker and important regulator in multiple cancers, including gastric cancer (GC). But the molecular regulatory mechanisms of KRT18 in GC patients and cells are largely unknown. In the present study, we analyzed the expression level of KRT18 in 450 stomach adenocarcinoma tissue samples from TCGA database and found a significantly higher expression level in tumor tissues. We then explored the potential functions of KRT18 in AGS cells (human gastric adenocarcinoma cell line) by KRT18 knockdown using siRNA and whole transcriptome RNA-seq analysis. Notably, KRT18 selectively regulates expression of cell proliferation and apoptotic genes. Beyond this, KRT18 affects the alternative splicing of genes enriched in apoptosis, cell cycle, and other cancer-related pathways, which were then validated by reverse transcription-quantitative polymerase chain reaction approach. We validated KRT18-KD promoted apoptosis and inhibited proliferation in AGS cells. We then used RNA-seq data of GC samples to further demonstrate the modulation of KRT18 on alternative splicing regulation. These results together support the conclusion that KRT18 extensively modulates diverse alternative splicing events of genes enriched in proliferation and apoptosis processes. And the dysregulated splicing factors at transcriptional or posttranscriptional level by KRT18 may contribute to the alternative splicing change of many genes, which expands the functional importance of keratins in apoptotic and cell cycle pathways at the posttranscriptional level in GC.
| S-EPMC8287183 | biostudies-literature
Project description:The major treatment strategies for gastric cancer (GC) including surgery, chemotherapy, and molecular-targeted therapy are limited by tumor recurrence and chemoresistance. Isorhamnetin (ISO) derives from the total flavones of Hippophae rhamnoides L. and has been used as potential antitumor medicine in several types of cancer. However, the antitumor effect of ISO on GC cells remains unclear. Here, we investigated the effects of ISO on two types of GC cells and explored its apoptotic mechanisms underlying such effects. The transcriptomic analysis of ISO-treated GC cells enriched multiple targets on cell growth and apoptosis. The CCK-8, colony formation and morphology observation assays demonstrated that ISO treatment significantly inhibited the growth and proliferation of GC cells in time- and dose-dependent manners. In addition, we also found that ISO treatment inhibited cell migration and invasion. Furthermore, ISO increased TUNEL positive apoptotic bodies as well as severe cell apoptosis. Intriguingly, ISO treatment significantly increased the expression of mitochondria-associated Bax/Bcl-2, cytosolic Cytochrome c and activated the cleavage of Caspase-3 and PARP, followed by severe reduction of mitochondrial potential. Moreover, the apoptosis of ISO-treated GC cells was blocked by the specific inhibitor of Caspase-3. Therefore, we demonstrated that ISO could induce apoptosis of GC cells through mitochondria-dependent apoptotic pathway. In summary, we reported for the first time the antitumor function of ISO in GC via intervening apoptosis, indicating a potential application in GC therapy.
2022-05-30 | GSE204967 | GEO
Project description:Objective: To determine the effect and mechanism of the long non-coding RNA (lncRNA) ncRuPAR (non-protein coding RNA, upstream of coagulation factor II thrombin receptor [F2R]/protease-activated receptor-1 [PAR-1]) in human gastric cancer. Methods: HGC-27-ncRuPAR overexpression and MGC-803-ncRuPAR-RNAi knockdown gastric cancer cell lines were established. We assessed the effect of ncRuPAR on cell proliferation, apoptosis, migration, and invasion using Cell Counting Kit 8, flow cytometry, scratch and transwell assays, respectively. Differentially expressed genes in HGC-27-ncRuPAR overexpression and HGC-27-empty vector cell lines were identified using Affymetrix GeneChip microarray analysis. Ingenuity Pathway Analysis (IPA) of the microarray results was subsequently conducted to identify ncRuPAR-enriched pathways, followed by validation using real time-quantitative PCR (RT-qPCR). As one of the top enriched pathways, phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway was further examined by western blotting to determine its role in ncRuPAR-mediated regulation of gastric cancer pathogenesis. Results: ncRuPAR inhibited human gastric cancer cell proliferation and induced G1/S phase arrest and apoptosis, but did not affect migration or invasion in vitro. Overexpression of ncRuPAR in vitro was found to inhibit its known target PAR-1, as well as PI3K/Akt signaling. The downstream targets of PI3K/Akt, cyclin D1 was downregulated, but there was no change in expression level of B-cell lymphoma 2 (Bcl-2). Conclusions: We showed that lncRNA-ncRuPAR could inhibit tumor cell proliferation and promote apoptosis of human gastric cancer cells, potentially by inhibiting PAR-1, PI3K/Akt signaling, and cyclin D1. The results suggest a potential role for lncRNAs as key regulatory hubs in GC progression.
2022-08-19 | GSE211598 | GEO
Project description:Isorhamnetin Inhibits Proliferation and Invasion and Induces Apoptosis Through the Mitochondria‑Dependent Apoptosis in Human Gastric Cancer Cells
| PRJNA842914 | ENA
Project description:Post-transcriptional mechanisms is an important means for the body to fight against cancer, and it may also be hijacked by tumor cells to help them adapt to local microenvironment. Filamin B (FLNB), an actin-binding protein and providing crucial scaffolds for cell motility and signaling, was also identified as one of RNA binding proteins (RBPs). Recent works showed that FLNB might play important role not only in skeletal development but also in the regulation of tumorigenesis. However, the effects of dysregulated expression of FLNB at a molecular level are unclear. In this study, we used RNA-seq to analyze the global transcriptional level changes and alternative splicing between the knocked-down FLNB and the control in Hela cells. Reduced levels of FLNB led to a significant decrease in cell apoptosis, compared with control cells. FLNB knockdown extensively regulated the expression of genes in cell apoptosis, tumorigenesis, metastases, transmembrane transport, cartilage and nerve development. Moreover, FLNB regulated alternative splicing of a large number of genes enriched in cell death and apoptotic process. Meanwhile, some genes and alternative splicing related to skeletal development were enriched and regulated by FLNB. Quantitative RT-PCR confirmed the FLNB-regulated transcription and alternative splicing. This study provides the first transcriptome-wide analysis of FLNB. Our findings indicated that FLNB may play an important regulatory role in cancer cell apoptosis via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of FLNB mediated gene regulation.
2020-05-19 | GSE134769 | GEO
Project description:Accumulating evidence indicates that RNA-binding proteins (RBPs) are involved in tumorigenesis. As a member of DEAD-box RBPs, DDX17 has a significant role in various contexts, such as mRNA translation, pre-mRNA splicing, ribosome biogenesis, and DNA repair. However, whether DDX17 is involved in the regulation of gene expression and alternative splicing in lung adenocarcinoma (LUAD) remains unclear. Methods: CCK-8 assay was used to evaluate cells proliferation. Cell apoptosis was evaluated by an Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) apoptosis detection kit. We used high-throughput RNA sequencing (RNA-seq) to determine differentially expressed genes (DEGs) and alternative splicing (AS) events in DDX17 knockdown LUAD cells. Functional and pathway enrichment analysis was also performed. Results: Knockdown of DDX17 by siRNA significantly inhibited the proliferation and induced apoptosis in A549 cells. 5243 DEGs were identified. Functional enrichment analyses indicated that these genes were mainly enriched in biological processes including regulation of transcription, regulation of cell growth, DNA repair. DDX17 knockdown increased the level of pro-apoptotic gene expression and decreased the expression of pro-proliferation genes. We also showed that DDX17-regulated AS events revealed by computational analysis using ABLas software in A549 cells were highly validated by RT-qPCR, and also validated by TCGA-LUAD dataset. Functional enrichment analyses showed regulated alternatively spliced genes (RASGs) were mainly enriched in biological processes related to apoptotic process, DNA repair, positive regulation of translation, positive regulation of apoptotic process. Conclusion: The present findings suggest that DDX17 may function as an oncogene by regulating both the expression and the alternative splicing of genes associated with proliferation, invasion and apoptosis in LUAD cells. Our findings may bring new insights into understanding the molecular mechanisms of LUAD and provide a new direction for LUAD treatment.
2022-07-28 | GSE196835 | GEO