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Genome-wide maps of SNAI2 binding in undifferentiated and differentiated keratinocytes

ABSTRACT: We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium. Examination of SNAI2 binding sites across the genome using the 6 different conditions

ORGANISM(S): Homo sapiens

SUBMITTER: George Sen

PROVIDER: E-GEOD-55421 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide maps of SNAI2 binding in undifferentiated and differentiated keratinocytes

Project description:We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium.

2014-10-15 | GSE55421 | GEO

Gene expression data on human keratinocytes with knockdown or overexpression of SNAI2

Project description:1. Keratinocytes infected with retroviruses expressing control or SNAI2 shRNAs were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles. 2. Keratinocytes infected with retroviruses overexpressing LACZ or SNAI2 were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.

2014-10-15 | GSE55269 | GEO

Gene expression data on human keratinocytes with knockdown or overexpression of SNAI2

2014-10-15 | E-GEOD-55269 | biostudies-arrayexpress

Genome Wide Expression of Mammary Epithelial Populations in Slug (SNAI2) WT vs Slug Null Mice

Project description:This experiment shows differential expression of genes in the luminal, basal and stromal subpopulations from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells.

2014-03-08 | GSE55620 | GEO

Genome Wide Expression of Mammary Epithelial Populations in Slug (SNAI2) WT vs Slug Null Mice

Project description:This experiment shows differential expression of genes in the luminal, basal and stromal subpopulations from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells. Luminal, basal and stromal populations were sorted from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells based on expression of CD49f and Epcam.

2014-03-08 | E-GEOD-55620 | biostudies-arrayexpress

The effects of SNAI2 overexpression on the transcriptional program in HaCaT cells

Project description:Investigation of the transcriptional profile of SNAI2-overexpressing HaCaT cells.

2021-09-01 | GSE166199 | GEO

PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib

Project description:The synthetic lethal association between BRCA deficiency and poly (ADP-ribose) polymerase (PARP) inhibition supports PARP inhibitor (PARPi) clinical efficacy in BRCA-mutated tumors. PARPis also demonstrate activity in non-BRCA mutated tumors presumably through induction of PARP1-DNA trapping. Despite pronounced clinical response, therapeutic resistance to PARPis inevitably develops. An abundance of knowledge has been built around resistance mechanisms in BRCA-mutated tumors, however, parallel understanding in non-BRCA mutated settings remains insufficient. In this study, we find a strong correlation between the epithelial-mesenchymal transition (EMT) signature and resistance to a clinical PARPi, Talazoparib, in non-BRCA mutated tumor cells. Genetic profiling demonstrates that SNAI2, a master EMT transcription factor, is transcriptionally induced by Talazoparib treatment or PARP1 depletion and this induction is partially responsible for the emerging resistance. Mechanistically, we find that the PARP1 protein directly binds to SNAI2 gene promoter and suppresses its transcription. Talazoparib treatment or PARP1 depletion lifts PARP1-mediated suppression and increases chromatin accessibility around SNAI2 promoters, thus driving SNAI2 transcription and drug resistance. We also find that depletion of the chromatin remodeler CHD1L suppresses SNAI2 expression and reverts acquired resistance to Talazoparib. The PARP1/CHD1L/SNAI2 transcription axis might be therapeutically targeted to re-sensitize Talazoparib in non-BRCA mutated tumors.

2022-07-08 | PXD033530 | Pride

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell Renal Cell Carcinoma

Project description:In this study we performed a genome wide analysis of the entire complement of mRNAs in clear cell renal cell carcinomas (ccRCC) by means of the Affymetrix Exon Array platform. The analyses were performed both at gene and exon level. Under our parameters over 2,000 genes resulted differentially expressed, and about 250 genes resulted alternative spliced showing differential inclusion of specific cassette exons comparing tumor and non tumoral tissues. 20 total samples were used for exon array analysis: 10 ccRCC tumor sample (T) and their matched non-tumor (NT) kidney tissues samples. All exon array data were analyzed using Partek Genomic Suite 6.4 software (Partek). The robust multi-array average (RMA) algorithm was used for the gene- and exon-level intensity analyses. Data were M-oM-,M-^Altered to consider only those probe sets included in the M-bM-^@M-^\Core Meta-ProbesetM-bM-^@M-^]. Lists of genes and exons with significant variation of the expression levels were generated by using a 0.01 FDR criterion as a significant cutoff. Partek list of significant exon-level probesets (FDR corrected p-value < 0.01) and exon level ANOVA test list were used to create - by an ad hoc Python script - a database of significant probesets from Exon Array experiments. To make more stringent the analysis criteria we excluded from the final exon lists all those cases in which Exon Array revealed a significant change at gene-level. This database we created has been used to explore simple exon skipping events using as reference ASPicDB single exon skipping splicing events after mapping Affymetrix probesets on ASPicDB .gtf files. A single exon from the Partek list was defined significantly skipped only if its adjacent exons were not, by using 0.01 and 0.05 p-value criterions as a significant cutoff for the M-bM-^@M-^\skippedM-bM-^@M-^] and adjacent exons, respectively.

2013-09-06 | E-GEOD-47032 | biostudies-arrayexpress

Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations

Project description:The resistance of CML leukemic stem cells (LSC) to tyrosine kinase inhibitor therapies targeting BCR-ABL leads to persistence of disease in most cases. We have identified novel putative therapeutic targets that are differentially expressed in CML LSCs compared to normal hematopoietic stem cells (HSC) by transciptional profiling of stem and progenitor cell populations from CML patients and normal donors. These data are used to obtain 97 genes that are differentially expressed in CML vs. normal stem and progenitor cells and 236 transcripts that show evidence of alternative exon usage in CML vs. normal stem cells. Bone marrow stem and progenitor cell fractions from 5 patients with newly diagnosed and untreated chronic phase CML and 5 healthy donors were analyzed. Contrasts between CML vs. normal stem and progenitors overall and CML vs. normal stem cells were performed using Partek Genomic Suite software. Genes with |log2(fold-change) > 1| and false discovery rate (FDR) of 0.05 were identified as significantly differentially expressed. To identify genes with evidence of alternative exon useage, contrasts between CML and normal stem cell populations were performed, and genes with an alternative splicing FDR of 0.01 were considered to be alternatively spliced.

2013-05-08 | E-GEOD-43754 | biostudies-arrayexpress

Snai2 influences breast cancer evolution in a non-cell autonomous manner

Project description:SNAI2 is a transcription factor involved in multiple processes in both physiology and pathology, including apoptosis, epithelial-mesenchymal transition and tumorigenesis. The effects of SNAI2 on the epithelial compartment have been interpreted as an effect of its expression and action in that compartment. In this work, we demonstrated that the absence of Snai2 in other compartments has repercussions in different aspects of the behavior of the epithelial cells of luminal breast tumors, developed by MMTV-ErbB2/Neu transgenic mice that do not express SNAI2 in the epithelial component. The absent of SNAI2 in the stroma of these tumors is accompanied by different characteristics at histopathological and molecular levels than those having functional SNAI2. These results indicate that the expression of SNAI2 in the tumor niche contributes to the luminal tumor development and behavior.

2018-03-20 | GSE112052 | GEO

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