Transcriptome analysis of A549 cells upon lncRNA ectopic LETS1 expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE203159 | GEO | 2023/04/28
REPOSITORIES: GEO
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Project description:We identified a tumor-supressing long non-coding RNA (lncRNA) named lncRNA induced by TGF-beta and antagonizes TGF-beta signaling 1 (LITATS1). It was found to mitigate epithelial-to-mesenchymal transition (EMT), cell migration and extravasation in a zebrafish exnograft model. To better dissect the downstream target genes and elucidate the signaling pathways altered by LITATS1, we depleted LITATS1 by specific shRNAs in A549 cells. Total RNA was collected and sent for RNA sequencing analysis. Afterwards, differentially expressd genes were used for the pathway enrichment analysis and gene set enrichment analysis (GSEA).
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Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
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Project description:ARHGAP8 was expressed at negligible levels in normal melanocytes but was ectopically activated in approximately 10% of melanoma specimens and melanoma cell lines. ARHGAP8 was ectopically expressed in ARHGAP8-negative M14 melanoma cells using the pIRES2 vector (Clontech), producing a bicistronic ARHGAP8-ires-eGFP mRNA. M14 cells stably transfected with vector control or N-terminally FLAG-tagged ARHGAP8 were cultured in 2D or 3D embedded growth conditions and then subjected to gene expression profiling using Affymetrix U133_Plus_2 gene chips. M14 cells stably transfected with pIRES2 alone or pIRES2 containing N-terminally FLAG-tagged ARHGAP8 were cultured in 2D or 3D conditions for 4 d as described. Total RNA was isolated using Trizol reagent (Invitrogen) and processed for application to Affymetrix gene chips.
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Project description:Transforming growth factor- (TGF-) signaling is a critical driver of epithelial–mesenchymal transition (EMT) and cancer progression. However, the regulatory roles of long non-coding RNAs (lncRNAs) in TGF--induced EMT and cancer progression are not well understood. Here, we identified an unannotated nuclear lncRNA LETS1 (LncRNA Enforcing TGF- Signaling 1) as a novel TGF-/SMAD target gene. Loss of LETS1 attenuates TGF--induced EMT, migration and extravasation in breast and lung cancer cells. LETS1 potentiates TGF-/SMAD signaling by stabilizing cell surface TGF- type I receptor (TRI) and thereby forms a positive feedback loop. Mechanistically, LETS1 inhibits TRI polyubiquitination by inducing the orphan nuclear receptor 4A1 (NR4A1) expression, a critical determinant of a destruction complex for inhibitory SMAD7. An unbiased interactome analysis identified the Nuclear Factor of Activated T Cells (NFAT5) as a protein partner of LETS1 to mediate activation of NR4A1 promoter. Overall, our findings characterize LETS1 as an EMT-promoting lncRNA and elucidate the mechanism by which nuclear LETS1 potentiates TGF- receptor signaling.
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Project description:Interventions: Gold Standard:Colonoscopy and tissue case biopsy;Index test:EVs nucleic acid combination (miRNA, lncRNA, circRNA) detection system.
Primary outcome(s): RNA;SEN, SPE, ACC, AUC of ROC
Study Design: Factorial
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Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
| 98681 | ecrin-mdr-crc