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Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell

ABSTRACT: The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using ChIP-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2-HA protein. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 3 treatments (Veh, Dox, DoxTam) were performed in duplicates. After treatments, cells were collected for ChIP experiment with HA antibody. ChIP-seq libraries were sequenced and data analysis showed almost no binding in Veh treatment, indicating low backgroud and good quality of the data. PAX transcription factor motif were enriched in PAX2 peaks, indicating the reliability of the data. When crossing the ChIP-seq data with genes regulated by PAX2 in MCF-7, we could observe high level binding of PAX2 to prmoters of PAX2 up-regulated genes and the center of intergenic transcripts induced by PAX2, suggesting the role of PAX2 in regulating transcription activation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE140060 | GEO | 2019/11/08

REPOSITORIES: GEO

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Genome wide analysis of transcripts regulated by PAX2 and Tamoxifen in MCF-7 cells

Project description:The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using GRO-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 4 treatments (Veh, Tam, Dox, DoxTam) were performed in duplicates. After treatments, nuclei were isolated and used for nuclear run-on and subsequent GRO-seq library preparation. Libraries were sequenced and data analysis showed that PAX2 could repress estrogen target genes and induce genes enriched in cytokine (TNF-alpha and INF-gamma) related pathways. When combined with tamoxifen, PAX2 could further repress estrogen target genes to a higher degree, and induce genes enriched in p53 related pathway. Moreover, PAX2 could induce the transcription of some intergenic transcripts (potential enhancers) to activate the transcription of nearby genes with could predict good outcome in estrogen receptor positive breast cancer. Overall our finding suggests that PAX2 could benifit ER positive breast cancer by 1) repressing estrogen target genes, and this effect is enhanced by tamoxifen 2) activating cell death/growth arrest related pathways, which is enhanced by potential enhancer transcription induced by PAX2 itself.

2019-11-06 | GSE139928 | GEO

Pax2 Dependent Expression in the Intermediate Mesoderm at E11.5

Project description:Heterozygous and homozygous Pax2 E11.5 embryos were collected and the intermediate mesoderm was dissected and dispersed into single cells. The Pax2 positive cells also expressed EGFP, which was knocked into the Pax2 locus. EGFP positive cells were sorted by FACS and RNA isolated. We compared RNA expression levels in EGFP positive cells from Pax2 null and Pax2 heterozygote embryos.

2014-12-13 | E-GEOD-64129 | biostudies-arrayexpress

Down-regulation of PAX2 affects ovarian cancer cell growth and migration

Project description:PAX2 is one of nine PAX genes that regulate tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell lineage specification, migration, and survival. In our previous study, we found that PAX2 is highly expressed in low-grade ovarian serous carcinoma, but its expression in clear cell, endometrioid, and mucinous cell ovarian carcinomas have not been studied. More importantly, the functional role of PAX2 in ovarian cancer is not known. Downregulation of PAX2 in PAX2-expressing ovarian cancer cells inhibits cell proliferation and migration. This growth inhibition is due to the upregulation of the tumor suppressor gene G0S2 and subsequent induction of apoptosis. The PAX2 pathway thus represents a potential therapeutic target for PAX2-expressing ovarian carcinomas. Knockdown PAX2 expression in these cell lines was achieved by lentiviral shRNAs targeting the PAX2 gene. PAX2 stable knockdown cells were characterized for cell proliferation, migration, apoptosis, and gene expression profiles.

2011-12-05 | E-GEOD-30501 | biostudies-arrayexpress

Down-regulation of PAX2 affects ovarian cancer cell growth and migration

2011-12-05 | GSE30501 | GEO

Pax2 Dependent Expression in the Intermediate Mesoderm at E11.5

2014-12-13 | GSE64129 | GEO

Genetic deletion of Pax2 and Pax8 in adult mice

Project description:Background: The mammalian kidneys maintain salt and water homeostasis for proper electrolyte balance and hydration. As the glomerular filtrate passes through the nephron and into the renal medulla, electrolytes, water, and urea are reabsorbed through the concerted actions of solute carrier channels and aquaporins located at various positions along the nephron and in the outer and inner medulla. Renal epithelial cells develop from Pax2 positive proliferating stem cells that suppress Pax2 expression once differentiated into mature proximal and distal tubules, but continue to express the related Pax8 protein. The collecting tubules and renal medulla are derived from a Pax2 positive ureteric bud epithelia that continue to express Pax2 and Pax8 in adult kidneys. Despite the necessity for Pax2 in renal development, functions for Pax2 or Pax8 in adult renal epithelia have not been established. Methods: In this report, we deleted either Pax2, Pax8, or both genes in adult mice and examined the phenotypes and changes in gene expression patterns. The mechanism of Pax8 mediated activation of potential target genes was described in inner medullary collecting duct cells. Results: Mice with induced deletions of both Pax2 and Pax8 exhibit severe polyuria that can be attributed to significant changes in the expression of solute carriers, such as the urea transporter UTA1, and aquaporins within the inner and outer medulla. Furthermore, Pax8 expression is induced by high salt in collecting duct cells and activates the UTA1 gene by recruiting a histone methyltransferase complex to the promoter. Conclusions: These data uncover novel functions for Pax proteins, in adult renal epithelia, that are essential for retaining water and concentrating urine.

2019-12-05 | GSE141455 | GEO

Single cell- and Clumps-RNA seq from the trunk of E9.5 Pax2-GFP and Pax2-GFP; Gata3 knockout embryos

Project description:To study cell heterogeneity and state transitions in the developing urinary tract we isolated Pax2-GFP positive single cells or clumps of cells by Fluorescence-activated cell sorting (FACS) from the trunk of E9.5 Pax2-GFP BAC transgenic embryos and performed 10X Genomics single cell and Clumps RNA sequencing

2021-02-16 | GSE143806 | GEO

Expression data from M0505 (with and without PAX2) murine ovarian surface epithelial cell lines

Project description:Our lab established the M0505 cell line from the ovarian surface epithelium (OSE) of FVB/N mice in May 2005 in order to study OSE biology. This cell line was infected with PAX2 to study the biological consequences of PAX2 expression in normal mOSE cells We used microarrays to try to determine the downstream targets of PAX2 in mOSE (M0505) cells to gain information that may lead to a greater understanding of its oncongenic potential. Two biological replicates of M0505+WPI, M0505+PAX2 and M0505+PAX2+Cre cells were collected for RNA extraction and subesequent hybridization on the Affymetrix MoGene-1_0-st-v1 platform.

2015-05-27 | E-GEOD-69238 | biostudies-arrayexpress

Unravelling the role of PAX2 mutation in human Focal Segmental Glomerulosclerosis

Project description:We performed a genomewide differential gene expression analysis by Ion AmpliSeqTM Transcriptome sequencing that targets more than 20,000 human genes to gain insights into the genes and pathways involved in the onset of familial steroid-resistant Focal Segmental Glomerulosclerosis (FSGS) driven by the presence of a heterozygous mutation in the PAX2 gene (PAX2G189R/+). Using a stepwise protocol, we differentiated control and PAX2G189R/+ induced pluripotent stem cells into podocytes and we performed whole-transcriptomic analysis on control and patient cells on days 6, 13 and 18 of differentiation. Our data indicated that the PAX2 mutation mainly affects the focal adhesion pathway and the expression of IGF1, a PAX2 target, in adult podocytes that are more susceptible to cell death by environmental triggers.

2021-11-30 | GSE185558 | GEO

Expression analysis of Human esophagus cancer cell line TE-1 transfected with PCDNA3.1 and PCDNA3.1-Pax2

Project description:Investigation of whole genome gene expression level changes of TE-1 transfected with PCDNA3.1-Pax2 ,compared to TE-1 transfected with PCDNA3.1. Compare PAX2 activated genes by analyzing mRNA profilings between pcDNA3.1 and pcDNA3.1-PAX2- transfected TE-1 cells.

2014-12-12 | E-GEOD-64093 | biostudies-arrayexpress

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