Similar Datasets
Project description:RNA binding proteins (RBPs) took a critical part in genome regulation. kpna2, as an essential member of the RBP family, was found to be highly expressed and associated with lymph node metastasis in gastric cancer (GC). Transcriptional sequencing data were used to find that KPNA2 primarily regulated alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), exon skipping (ES) and cassette exon. Vitally, KPNA2 was involved in the transcriptional regulation of cancer-related genes. Therefore, we screened potential targets in AGS cells with differential expression and alternative splicing (AS) levels regulated by KPNA2, further identifying that KPNA2 was engaged in biological processes concerning immune response, cell proliferation and apoptosis in GC through transcriptional regulation. Besides, the binding sites of KPNA2 to spliceosomes were identified using improved RNA immunoprecipitation sequencing techniques, and KPNA2 was preferentially bound to the intron region. Notably, KPNA2 regulated the A3SS AS mode of WDR62, which may increase the malignancy of GC. Finally, we also discovered that AS of immune-related molecules can be regulated by KPNA2. Overall, for the first time, our results demonstrated that KPNA2 served as an oncogenic splicing factor in GC regulating AS and differential expression of GC-related genes and may represent a potential target for GC therap
2024-08-02 | GSE201418 | GEO
Project description:RNA binding proteins (RBPs) took a critical part in genome regulation. kpna2, as an essential member of the RBP family, was found to be highly expressed and associated with lymph node metastasis in gastric cancer (GC). Transcriptional sequencing data were used to find that KPNA2 primarily regulated alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), exon skipping (ES) and cassette exon. Vitally, KPNA2 was involved in the transcriptional regulation of cancer-related genes. Therefore, we screened potential targets in AGS cells with differential expression and alternative splicing (AS) levels regulated by KPNA2, further identifying that KPNA2 was engaged in biological processes concerning immune response, cell proliferation and apoptosis in GC through transcriptional regulation. Besides, the binding sites of KPNA2 to spliceosomes were identified using improved RNA immunoprecipitation sequencing techniques, and KPNA2 was preferentially bound to the intron region. Notably, KPNA2 regulated the A3SS AS mode of WDR62, which may increase the malignancy of GC. Finally, we also discovered that AS of immune-related molecules can be regulated by KPNA2. Overall, for the first time, our results demonstrated that KPNA2 served as an oncogenic splicing factor in GC regulating AS and differential expression of GC-related genes and may represent a potential target for GC therap
2024-08-02 | GSE201419 | GEO
Project description:RNA Binding protein KPNA2 promotes the progress of gastric cancer by regulating alternative splicing of related genes
| PRJNA831664 | ENA
Project description:RNA Binding protein KPNA2 promotes the progress of gastric cancer by regulating alternative splicing of related genes [RIP-seq]
| PRJNA831667 | ENA
Project description:RNA Binding protein KPNA2 promotes the progress of gastric cancer by regulating alternative splicing of related genes [RNA-seq]
| PRJNA831668 | ENA
Project description:BackgroundThe high prevalence of alternative splicing among genes implies the importance of genomic complexity in regulating normal physiological processes and diseases such as gastric cancer (GC). The standard form of stem cell marker CD44 (CD44S) and its alternatives with additional exons are reported to play important roles in multiple types of tumors, but the regulation mechanism of CD44 alternative splicing is not fully understood.MethodsHere the expression of hnRNPK was analyzed among the Cancer Genome Atlas (TCGA) cohort of GC. The function of hnRNPK in GC cells was analyzed and its downstream targeted gene was identified by chromatin immunoprecipitation and dual luciferase report assay. Finally, effect of hnRNPK and its downstream splicing regulator on CD44 alternative splicing was investigated.ResultsThe expression of hnRNPK was significantly increased in GC and its upregulation was associated with tumor stage and metastasis. Loss-of-function studies found that hnRNPK could promote GC cell proliferation, migration, and invasion. The upregulation of hnRNPK activates the expression of the splicing regulator SRSF1 by binding to the first motif upstream the start codon (-?65 to -?77 site), thereby increasing splicing activity and expression of an oncogenic CD44 isoform, CD44E (has additional variant exons 8 to 10, CD44v8-v10).ConclusionThese findings revealed the importance of the hnRNPK-SRSF1-CD44E axis in promoting gastric tumorigenesis.
| S-EPMC6909542 | biostudies-literature
Project description:Polyadenylate-binding protein cytoplasmic 1 (PABPC1) is dysregulated in malignancies, which is considered as a potential therapeutic target for many cancer types. By alternative splicing (AS) for gastric cancer (GC), we described PABPC1-modulated AS events in this study. PABPC1 expression was analyzed in 408 GC tissues from The Cancer Genome Altas (TCGA) database. Human gastric adenocarcinoma (AGS) cells were transfected with PABPC1-specific small interfering RNA (siPABPC1) with siCtrl as a negative control. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was done for the determination of transcripts. To detect the differentially expressed genes (DEGs) and 10 different types of AS events, RNA sequencing (RNA-seq) was performed. DEGs were analyzed for functional categories including gene ontology, and the Kyoto encyclopedia of genes and genomes pathway were analyzed for DEGs. GC displayed an elevated expression of PABPC1. PABPC1 was efficiently knocked down in AGS cells. Here, we excavated 1234 PABPC1-regulated DEGs, among which 502 were down-regulated and 732 were up-regulated compared to the siCtrl group. A total of 94 DEGs were involved in inflammation and immune response. Results from qRT-PCR validated the up-regulation of 10 immune and inflammation-related DEGs in the siPABPC1 group. PABPC1 deficiency causes 1304 AS events differentially occurred in AGS cells. The most common type of AS events regulated by PABPC2 is alternative 5' splice sites. qRT-PCR confirmed the transcription level of five immune-related genes, in which AS events were detected in the siPABPC1 group. PABPC1 knockdown mediates AS events and thus the transcript level of immune and inflammation-related genes in AGS cells. PABPC1-regulated oncogenic AS events display potential as targets for therapeutic development.
| S-EPMC9742748 | biostudies-literature
Project description:Angiogenesis is involved in many pathological and physiological processes and is mainly driven by hypoxia. Karyopherin subunit alpha 2 (KPNA2), a member of the nuclear transport protein family, was recently shown to be induced by hypoxia in various types of tumours, so we aimed to investigate the role and mechanism of KPNA2 in angiogenesis under hypoxia. After overexpression or knockdown of KPNA2 in human umbilical vein endothelial cells (HUVEC) by adenovirus vector infection, the tube formation, proliferation and migration of HUVEC under hypoxia were detected by tubule formation assay, 5-ethynyl-2'-deoxyuridine (EdU) staining and Transwell assay, respectively. After overexpression or knockdown of KPNA2 in a murine hindlimb ischemia model by local injection of purified adenovirus vector into the gastrocnemius muscle, blood flow changes were examined with a laser Doppler system. Changes in KPNA2-binding proteins under hypoxia were detected by immunoprecipitation-mass spectrometry (IP-MS) and co-immunoprecipitation (Co-IP). The effect of KPNA2 on signal transducer and activator of transcription 3 (STAT3) was detected by Western blotting and quantitative RT‒PCR. KPNA2 was upregulated in the HUVEC hypoxia model and murine hindlimb ischemia model. Overexpression of KPNA2 increased the proliferation, migration and tube formation of HUVEC under hypoxia, while knockdown of KPNA2 reduced the proliferation, migration and tube formation of HUVEC. Overexpression of KPNA2 promoted the restoration of blood flow in the murine hindlimb ischemia model, while knockout of KPNA2 inhibited the restoration of blood flow in the murine hindlimb ischemia model. Mechanistically, hypoxia promoted the binding of STAT3 to KPNA2. Overexpression of KPNA2 promoted STAT3 phosphorylation and then upregulated vascular endothelial growth factor (VEGF) and angiopoietin 2(ANGPT2), whereas knockdown of KPNA2 inhibited STAT3 phosphorylation and then downregulated VEGF and ANGPT2. Our study demonstrates that hypoxia promotes the binding of STAT3 to KPNA2 and KPNA2 promotes angiogenesis under hypoxia by promoting the binding of STAT3 and JAK1 and regulating STAT3 phosphorylation.
| S-EPMC9798605 | biostudies-literature
Project description:Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
| S-EPMC10722200 | biostudies-literature
Project description:BackgroundThis study sought to identify the downstream target genes of enolase 1 (ENO1), clarify the role of ENO1 in gastric cancer (GC), and provide novel insights into the regulatory mechanisms of ENO1 in the occurrence and development of GC.MethodsWe performed RNA-immunoprecipitation sequencing in MKN-45 cells to study the types and abundance of pre-messenger RNA (mRNA)/mRNA bound by ENO1, the binding sites and motifs, the relationship between ENO1 binding and its regulation of transcription level, and alternative splicing level by combining with RNA-sequencing (RNA-seq) data to further clarify the role of ENO1 in GC.ResultsWe found that ENO1 stabilized the expression of SRY-box transcription factor 9 (SOX9), vascular endothelial growth factor A (VEGFA), G protein-coupled receptor class C group 5 member A (GPRC5A), and myeloid cell leukemia-1 (MCL1) by binding to their mRNA, which increased the growth of GC. In addition, ENO1 interacted with some other long non-coding RNAs (lncRNAs) or small-molecule kinases, such as NEAT1, LINC00511, CD44, and pyruvate kinase M2 (PKM2), to regulate their expression to affect cell proliferation, migration, and apoptosis.ConclusionsENO1 may play a role in GC by binding to and regulating GC-related genes. Our findings extend understandings of its mechanism as a clinical therapeutic target.
| S-EPMC10186516 | biostudies-literature