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Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this work is comprehensive analysis of target genes co-regulated by CREB1 and FoxA1 in prostate cancer cell models, tissues, and circulating tumor cells (CTCs). Expression of CREB1/FoxA1 target genes corresponds with disease recurrence and aggressive clinical features. Methods: LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. For RNA-seq, cells are transfected with FoxA1,CREB1 specific or nonspecific siRNA and total RNA is extracted with Qiangen RNeasy Mini kit(cat 74104) and library is generated with TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001). For Chip-seq, LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. After crosslinking with 1% formaldehyde, ChIP was performed. the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63034 | GEO | 2016/01/13

SECONDARY ACCESSION(S): PRJNA266510

REPOSITORIES: GEO

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Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this work is comprehensive analysis of target genes co-regulated by CREB1 and FoxA1 in prostate cancer cell models, tissues, and circulating tumor cells (CTCs). Expression of CREB1/FoxA1 target genes corresponds with disease recurrence and aggressive clinical features. Methods: LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. For RNA-seq, cells are transfected with FoxA1,CREB1 specific or nonspecific siRNA and total RNA is extracted with Qiangen RNeasy Mini kit(cat 74104) and library is generated with TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001). For Chip-seq, LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. After crosslinking with 1% formaldehyde, ChIP was performed. the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. LNCaP cells and LNCaP cells were used as cell model. Library was sequenced using Illumina HISeq 2500.

2016-01-13 | E-GEOD-63034 | biostudies-arrayexpress

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [ChIP_seq, DHS_seq]

2011-09-14 | E-GEOD-30623 | biostudies-arrayexpress

Microarray screening of RNA samples from low-, intermediate- and high-passage human prostate LNCaP cells

2011-04-29 | GSE28927 | GEO

FoxA1 inhibits androgen receptor expression and suppresses prostate cancer metastasis [LNCaP, ChIP-seq]

Project description:FoxA1 has been shown critical for prostate development and prostate-specific gene expression regulation. In addition to its well-established role as an AR pioneering factor,several studies have recently revealed significant AR binding events in prostate cancer cells with FoxA1 knockdown. Furthermore, the role of FoxA1 itself in prostate cancer has not been carefully examined. Thus, it is important to understand the role of FoxA1 in prostate cancer and how it interacts with AR signaling. To address these questions, we generated LNCaP cells with stable FoxA1 knockdown. We performed AR/FoxA1 ChIP-seq and microarray analysis of these cells. ChIP_Seq examination of AR and FoxA1 binding sites in LNCaP shCtrl and shFoxA1 cells

2014-06-02 | E-GEOD-37345 | biostudies-arrayexpress

Proteomic analysis of castrate resistant prostate cancer cell lines

Project description:In this study the development of androgen independence in a cell model of disease was selected as a mirror of to the events at play in the development of Castrate Resistant Prostate Cancer in-vivo. LNCaP cells which are androgen dependent and androgen independent sublines; LNCaP-Abl and LNCaP-Abl-Hof were subject to extensive fractionation by 1-D SDS PAGE and accurate mass-high resolution mass spectrometry (Q Exactive) to identify proteins whose expression was changes significantly in response to androgen independent growth.

2022-02-28 | PXD000751 | Pride

LNCap cell chromatin accessibility regulator of pioneer factor GATA2 binding model

Project description:Purpose: The dynamic chromatin accessibility was regulated by pioneer factors. The goals of this study are revealing the mechanism of GATA2 and SOX9 required for the change of nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by Tn5 transposase and ChIP was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and SOX9 is recruit for unwrapped the nucleosomes. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and mechanism underlining GATA2 and nucleosome reorganization in whole genomic DNA.

2021-12-09 | GSE182529 | GEO

Microarray screening of RNA samples from low-, intermediate- and high-passage human prostate LNCaP cells

Project description:This laboratory studies the structures, biosynthesis, and functions of mucin glycans The low-(<33) and high-(>80)passage human prostate LNCaP cells developed by Dr. Ming-Fong Lin (Lin et al, Urology 166:1943, 2001) have been considered as the best in vitro model that reflects the progression of prostate cancer from androgen-dependent to androgen-independent stage (Parajuli et al, Cancer Res. 61:8227, 2001; Demeade et al, The Prostate 54:249, 2003; Unni et al, Cancer Res. 64:7156, 2004). The high-passage cells are metastatic while the low-passage cells are not. RT-PCR analysis of these two cell clones for 25 glycogenes among 8 different groups of glycogenes showed that only high-passage cells expressed two (isozymes 1 and 5) of the five known GlcNAc6ST genes. In addition, P-selectin blot analysis showed qualitative and quantitative differences between these clones. They included 3 higher intensity bands and 3 lower intensity bands in high-passage cells as compared to low-passage cells. The difference in P-selectin-specific glycoconjugates between low and high-passage LNCaP cells should help identify the glycans that distinguish high- from low-passage LNCaP cells. RNA preparations from low-, intermediate-, and high-passage human prostate LNCaP cells were sent to Microarray Core (E). *Concurrent analysis of glycan profiles in these cells was performed in Core C*. Three replicate samples from each condition were used in the study. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to identify the glycogenes, glycans, and/or carbohydrate binding proteins responsible for the difference in metastatic property between low- and high-passage LNCaP cells. The intermediate-passage cells were used for identifying changes in glycogene, glycan, and/or carbohydrate binding protein expression that may be responsible for the earliest change of the metastatic property.

2011-04-29 | E-GEOD-28927 | biostudies-arrayexpress

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [ChIP_seq, DHS_seq]

2011-09-14 | GSE30623 | GEO

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [Expression Array]

2011-09-14 | GSE30622 | GEO

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [Expression Array]

Project description:We report the dual role of FoxA1 in androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell line LNCaP-1F5 using ChIP-sequencing. Depletion of FoxA1 reprograms both androgen and glucocorticoid receptor recruitment and subsequent gene expression. The ChIP-seq has been performed using AR, FoxA1, GR, H3K4me2 antibodies. We have also mapped the DNaseI-hypersensitive sites (DHS) using deep sequencing. LNCaP-1F5 cells were depleted of FoxA1 using siRNAs. Parental cells and FoxA1 depleted cells (siFoxA1) were treated with vehicle or 100 nM DHT or (100 nM DEX) for 24 hours followed by RNA isolation and hybridization to Illumina arrays. All the experiments have been performed in biological duplicates. Parental cells treated with DHT (or DEX) were analyzed for differentially expressed genes compared to vehicle treated parental cells. Similarly siFoxA1 cells treated with DHT (or DEX) were analyzed for differentially expressed genes compared to vehicle treated siFoxA1 cells.

2011-09-13 | E-GEOD-30622 | biostudies-arrayexpress

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