Similar Datasets
Project description:RNA-seq and miRNA-seq of gastric cancer cell lines after overexpression of FN1 3' UTR
| PRJNA810186 | ENA
Project description:As a key protein in the tumor microenvironment, FN1 has been proven to promote cancer in a variety of cancer species. However, in our previous study on gastric cancer, it was found that FN1 protein expression in patient tissues was not significantly correlated with prognosis, and clinical data analysis was only correlated with T stage of gastric cancer. Analysis of the relationship between FN1 mRNA expression level and prognosis by TCGA-STAD database revealed that high FN1 mRNA expression was significantly correlated with poor prognosis. Moreover, many miRNA binding sites were found on FN1 3' UTR by database prediction, so we speculated that FN1 played different functions at mRNA and protein levels, and FN1 3' UTR might function as ceRNA. At present, FN1 3' UTR overexpression has been proved to significantly promote the invasion and metastasis of gastric cancer in vivo and in vitro, and its effect is stronger than FN1 protein. Therefore, in this study, miRNA sequencing, which was used to find those miRNAs bound to FN1 3’UTR, was carried out to further explore its cancer-promoting mechanism.
2022-02-27 | GSE197423 | GEO
Project description:As a key protein in the tumor microenvironment, FN1 has been proven to promote cancer in a variety of cancer species. However, in our previous study on gastric cancer, it was found that FN1 protein expression in patient tissues was not significantly correlated with prognosis, and clinical data analysis was only correlated with T stage of gastric cancer. Analysis of the relationship between FN1 mRNA expression level and prognosis by TCGA-STAD database revealed that high FN1 mRNA expression was significantly correlated with poor prognosis. Moreover, many miRNA binding sites were found on FN1 3' UTR by database prediction, so we speculated that FN1 played different functions at mRNA and protein levels, and FN1 3' UTR might function as ceRNA. At present, FN1 3' UTR overexpression has been proved to significantly promote the invasion and metastasis of gastric cancer in vivo and in vitro, and its effect is stronger than FN1 protein. Therefore, in this study, transcriptome sequencing of FN1 3' UTR after overexpression was carried out to further explore its cancer-promoting mechanism.
2022-02-27 | GSE197422 | GEO
Project description:miRNA-sequencing of HGC27 and AGS cells with FN1 3' UTR overexpression
| PRJNA810188 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-01-23 | E-GEOD-54301 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-10-01 | E-GEOD-49052 | biostudies-arrayexpress
Project description:Cancer cell lines are not homogeneous nor are they static in their genetic state and biological properties. Genetic, transcriptional and phenotypic diversity within cell lines contributes to the lack of experimental reproducibility frequently observed in tissue-culture-based studies. While cancer cell line heterogeneity has been generally recognized, there are no studies which quantify the number of clones that coexist within cell lines and their distinguishing characteristics. We used a single-cell DNA sequencing approach to characterize the cellular diversity within nine gastric cancer cell lines and integrated this information with single-cell RNA sequencing. Overall, we sequenced the genomes of 8824 cells, identifying between 2 and 12 clones per cell line. Using the transcriptomes of more than 28 000 single cells from the same cell lines, we independently corroborated 88% of the clonal structure determined from single cell DNA analysis. For one of these cell lines, we identified cell surface markers that distinguished two subpopulations and used flow cytometry to sort these two clones. We identified substantial proportions of replicating cells in each cell line, assigned these cells to subclones detected among the G0/G1 population and used the proportion of replicating cells per subclone as a surrogate of each subclone's growth rate.
| S-EPMC7079336 | biostudies-literature
Project description:Somatic mutations in 3'-untranslated regions (3'UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA⁻mRNA interactions. We identified 67,159 somatic mutations located in the 3'UTRs of messenger RNAs (mRNAs) which can alter miRNA⁻mRNA interactions (functional somatic mutations, funcMutations), and 69.3% of these funcMutations (the degree of energy change > 12 kcal/mol) were identified to significantly promote loss of miRNA-mRNA binding. By integrating mRNA expression profiles of 21 cancer types, we found that the expression of target genes was positively correlated with the loss of absolute affinity level and negatively correlated with the gain of absolute affinity level. Functional enrichment analysis revealed that genes carrying funcMutations were significantly enriched in the MAPK and WNT signaling pathways, and analysis of regulatory modules identified eighteen miRNA modules involved with similar cellular functions. Our findings elucidate a complex relationship between miRNA, mRNA, and mutations, and suggest that 3'UTR mutations may play an important role in tumor development.
| S-EPMC6267165 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-01-23 | GSE54301 | GEO
Project description:MiR-145 is a tumor suppressor miRNA that its ubiquitously expressed in the body but in numerous types of cancers such as GC, its expression became reduced or sometimes ceased in many subjects. This study aimed at restoring the function of the miR-145 in MKN-45 cells and investigating the function of this miRNA in proliferation, apoptosis, and migration of GC cells. MKN-45 cells were transfected using the PCMV-miR-145 plasmid vector. The MTT, DAPI staining, and wound healing assays were applied to estimate the impacts of ectopic expression of miR-145 in vitro. Moreover, alterations in the expression levels of K-Ras, c-Myc, caspase-3, caspase-9, Bax, Bcl-2, and MMP-9 mRNA were measured by qRT-PCR analysis. The findings designated that high expression of miR-145 reduced the proliferation and migration and increased the apoptosis of the MKN-45 cells. These effects occur with concurrent suppression of c-Myc, K-Ras, Bcl-2, and MMP-9 as well as induction of caspase-3, caspase-9, and Bax expression. Exogenous miR-145 influences multiple oncogenic pathways and can be regarded as a promising avenue of future therapeutic interventions for GC therapy.
| S-EPMC7689247 | biostudies-literature