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The long noncoding RNA HOTAIR has tissue and cell type dependent effects on HOX gene expression and phenotype of cancer cells

ABSTRACT: HOTAIR was found to be overepressed in a subset of urothelial cancer tissues and cell lines compared to normal controls. Ectopic HOTAIR expression in urothelial cancer cells in vitro demonstrated cell type dependent changes in phenotype. While some cell lines showed increased proloferation activity and induction of an aggressive phenotypes (e.g. stable transfected VM-CUB1 cells), others displayed rather a reduction of proliferation and migration. Stable transfection of 5637 cells resulted in induction of an immune response. Results of microarray analysis of stable transfected VM-CUB1 and 5637 cells concurred well with observed phenotypical cell type-specific changes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57672 | GEO | 2015/06/05

SECONDARY ACCESSION(S): PRJNA247558

REPOSITORIES: GEO

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The long noncoding RNA HOTAIR has tissue and cell type dependent effects on HOX gene expression and phenotype of cancer cells

Project description:HOTAIR was found to be overepressed in a subset of urothelial cancer tissues and cell lines compared to normal controls. Ectopic HOTAIR expression in urothelial cancer cells in vitro demonstrated cell type dependent changes in phenotype. While some cell lines showed increased proloferation activity and induction of an aggressive phenotypes (e.g. stable transfected VM-CUB1 cells), others displayed rather a reduction of proliferation and migration. Stable transfection of 5637 cells resulted in induction of an immune response. Results of microarray analysis of stable transfected VM-CUB1 and 5637 cells concurred well with observed phenotypical cell type-specific changes. For differential gene expression analyses three independent high quality RNA preparations from VM-CUB1 cells, stably transfected with HOTAIR (clone 20), and 5637 cells, stably transfected with HOTAIR (clone 4), were compared to the respective vector control cells.

2015-06-05 | E-GEOD-57672 | biostudies-arrayexpress

HOTAIR reprograms gene expression profiling in esophageal squamous cell carcinoma (ESCC) KYSE180 cells

Project description:To investigate the functional role of HOTAIR in esophageal squanmous cell carcinoma (ESCC) cells, RNAi-mediated knockdown of HOTAIR and overexpression of HOTAIR were carried out using KYSE180 cells. Gene expression microarray analysis revealed that a number of reported HOTAIR target genes were regulated by HOTAIR. Moreover, gene ontology analysis revealed enrichment of genes closely related to tumorigenesis, such as cell migration, regulation of cell cycles. For RNAi-mediated knockdown of HOTAIR, two different stealth siRNAs against HOTAIR were generated by Invitrogen, after which a mixture of the two was used for transfection. KYSE180 cells in 6-well plates were transfected with 100 pmol of Stealth siRNA (Invitrogen) or a Stealth RNAi Negative Control Medium GC (Invitrogen) using Lipofectamine2000 (Invitrogen). For HOTAIR overexpression, KYSE180 cells were transfected with LZRS_HOTAIR vector using Polyfect Transfection Reagent (Qiagen). Total RNA was extracted 48 h after transfection.

2013-06-05 | E-GEOD-47638 | biostudies-arrayexpress

Gene expression altered by HOTAIR knockdown in MCF-7-TNR

Project description:The human HOTAIR-specific siRNA and control siRNA were transfected into MCF-7-TNR cells. RNA was collected at 72 hrs after transfection. RNA-SEQ was carried out to profile the gene expression altered by HOTAIR knockdown.

2019-01-11 | GSE124934 | GEO

Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays

Project description:To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells.

2013-06-05 | GSE47637 | GEO

Gene expression signatures in GIST-T1 cells transfected with siRNA targeting HOTAIR

Project description:To analyze the effect of HOTAIR depletion in a gastrointestinal stromal tumor (GIST) cells, RNAi-mediated knockdown of HOTAIR was carried out using GIST-T1 cells. Gene expression microarray analysis revealed that a number of reported HOTAIR target genes were upregulated by knockdown of HOTAIR. Moreover, we found that 1424 genes were upregulated by siHOT (>2-fold), and Gene Ontology analysis revealed enrichment of genes related to “nucleus”, “chromosome” and “membrane-bounded organelle.” For RNAi-mediated knockdown of HOTAIR, three different Stealth siRNAs against HOTAIR were generated by Invitrogen, after which a mixture of the three was used for transfection. GIST-T1 cells in 6-well plates were transfected with 100 pmol of Stealth siRNA (Invitrogen) or a Stealth RNAi Negative Control Medium GC (Invitrogen) using Lipofectamine2000 (Invitrogen). Total RNA was extracted 48 h after transfection.

2011-12-01 | E-GEOD-32064 | biostudies-arrayexpress

Role of Lsd1 in HOTAIR function

Project description:HOTAIR is a scafold long non-coding RNA tethering PRC2 and Lsd1/REST/coREST complexes to gene promoters to repress transcription of genes involved in epithelial to mesenchymal transition (EMT). To decipher a role of the Lsd1 in HOTAIR function we generated epithelial cell lines expressing full length and truncated versions of HOTAIR missing first 5'-300 (Epi-HOTΔP) and last 3'-500 bp (Epi-HOTΔL) interacting with HOTAIR partners. These cell lines were further used to determine Lsd1 binding sites using chromatin immunoprecipitation approach.

2021-04-22 | GSE106262 | GEO

Long non-coding RNA HOTAIR is expressed in small cell lung cancer and is relevant to cellular proliferation, invasiveness and clinical relapse: tissue and cell-line analyses

Project description:LincRNA HOTAIR was expressed in pure SCLC and higher expression was significantly related to lymphatic invasion and relapse. Multivariate analyses demonstrated that HOTAIR expression correlated with RFS. In vitro experiments demonstrated that half of SCLC cell lines expressed HOTAIR at higher levels than normal cells and that, using cells of SBC-3, knockdown of HOTAIR decreased proliferative activity and cellular invasiveness with altered expression of cell adhesion-related genes. Total RNAs from one siHOTAIR-transfected SBC-3 cells and control cells (siGFP-transfected cells), were extracted using RNeasy mini kit Plus (Qiagen) and hybridized to the microarrays, Sure Print G3 Human GE 8x60K microarrays (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. Subsequently, data analysis was carried out using the GeneSpring GX 12 software (Agilent Technologies), with a stringency of P<0.1 and a 2-fold or more change using gene ontology analysis.

2014-03-05 | E-GEOD-43877 | biostudies-arrayexpress

Effects of HOTAIR RNAi on Transcriptomes in T47D Cells

Project description:We profiled transcriptomes in human breast cancer cell line T47D when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).

2018-09-06 | GSE119511 | GEO

Effects of HOTAIR RNAi on Transcriptomes in H23 Cells

Project description:We profiled transcriptomes in human lung cancer cell line H23 when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).

2018-09-06 | GSE119510 | GEO

In-Vitro Identification and In-Vivo Confirmation of DNA Methylation Biomarkers for Urothelial Cancer

Project description:DNA-methylation targets specific for urothelial cancer (UC) were identified by genome-wide methylation difference analysis of human urothelial (RT4, J82, 5637), prostate (LNCAP, DU-145, PC3) and renal (RCC-KP, CAKI-2, CAL-54) cancer cell lines with their respective primary epithelial cells

2020-07-28 | GSE149387 | GEO

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