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Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1

ABSTRACT: We conducted gene expression profilling of common prostate cell lines for comparison with genome-wide DNA methylation profiles for the same cell lines to study the impact of differential DNA methylation in prostate cancer. Total RNA was extracted from 3 biological replicate sets of PrEC, RWPE-1, DU 145, and LNCaP cells. This Series represents the gene expression profiling data only. The methyl-Seq data were submitted directly to SRA and are represented by accession SRA049689.1.

ORGANISM(S): Homo sapiens

SUBMITTER: Angela Ting

PROVIDER: E-GEOD-35401 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1.

Lee Byron H BH Taylor Margaret G MG Robinet Peggy P Smith Jonathan D JD Schweitzer Jessica J Sehayek Ephraim E Falzarano Sara M SM Magi-Galluzzi Cristina C Klein Eric A EA Ting Angela H AH

Cancer research 20121211 3

Recent epidemiologic data show that low serum cholesterol level as well as statin use is associated with a decreased risk of developing aggressive or advanced prostate cancer, suggesting a role for cholesterol in aggressive prostate cancer development. Intracellular cholesterol promotes prostate cancer progression as a substrate for de novo androgen synthesis and through regulation of AKT signaling. By conducting next-generation sequencing-based DNA methylome analysis, we have discovered marked ...[more]

PMID: 23233737

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Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1

Project description:We conducted gene expression profilling of common prostate cell lines for comparison with genome-wide DNA methylation profiles for the same cell lines to study the impact of differential DNA methylation in prostate cancer.

2012-12-19 | GSE35401 | GEO

Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 1)

Project description:Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after toxicant-induced malignant transformation. This study also puts the DNA methylation changes into context with respect to the aberrant DNA methylation events that occur in bladder and prostate carcinogenesis not associated with toxicant exposure. Immortalized UROtsa (n=3) and RWPE-1 (n=2) are compared to normal HUC (n=2) and PrEC (n=2), respectively. Arsenite (n=1), monomethylarsonous acid (n=2) or cadmium (n=1) transformed UROtsa are compared to parental UROtsa (n=3). Arsenite (n=2), cadmium (n=1) or MNU (n=1) transformed RWPE-1 cells are compared to parental RWPE-1 cells (n=2). Clinical bladder tumor biopsies (n=6), urothelial carcinoma cell lines (n=2) and prostate cancer cell lines (n=3) are compared to thier normal tissue counterparts HUC (n=2) and PrEC (n=2). Immunoprecipitation using anti-methylcytosine (5MeC) antibody.

2012-06-25 | E-GEOD-38926 | biostudies-arrayexpress

Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 2)

2012-06-25 | E-GEOD-38928 | biostudies-arrayexpress

miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines

Project description:MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. This series is meant to identify miRNAs deregulated in prostate cancer (PCa) by comparing the PCa cell lines LNCaP, PC3 and Du-145 to the normal prostate epithelial cell line RWPE-1. We analyzed three arrays each for LNCaP, PC3, Du-145 and RWPE-1 cell lines

2012-03-08 | E-GEOD-17317 | biostudies-arrayexpress

miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines

2012-03-08 | GSE17317 | GEO

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Project description:Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after arsenic-induced malignant transformation. Arsenite-transformed RWPE-1 cells (n=2) are compared to parental RWPE-1 cells (n=2). Normal PrEC (n=2) are included for comparison. Immunoprecipitation using anti-methylcytosine (5MeC) antibody.

2012-06-25 | E-GEOD-38929 | biostudies-arrayexpress

miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines

Project description:This SuperSeries is composed of the following subset Series: GSE17315: mRNA expression upon reconstitution of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP GSE17317: miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines GSE22979: Profiling of direct mRNA targets of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP Refer to individual Series

2012-03-07 | E-GEOD-17362 | biostudies-arrayexpress

Dysregulation of transcription factor activity during formation of cancer associated fibroblasts.

Project description:Introduction: The reciprocal interactions between cancer cells and the CAFs serve an important role in cancer progression. Those feedback loops depend on tumor developmental stage and the tissue microenvironment and may promote different CAFs subpopulations in different types of malignancy. Here, we investigated the activation of transcription factors (TFs) in cocultures of fibroblasts with normal prostate or tumorous cells with mRNA sequencing. Materials and Methods: Coculture of WPMY-1 (normal prostate fibroblasts) with RWPE-1 (normal prostate epithelial cells) or RWPE-2 (cancer prostate epithelial cells) were done using transwell inserts. As a control, we used WPMY-1 culture alone. After 6h and 24h of coculture, we performed mRNA-sequencing., We used SEPIRA (Systems EPigenomics Inference of Regulatory Activity) package and mRNA-seq data of 483 cultured fibroblasts from GTEx to calculate the TFs activity score from mRNA-seq expression in our samples. Results: We determined changes in TFs activity between time points in each group. We found 5 TFs (RUFY3, SCMH1, NFIX, ZBTB25, NFE2L1), that increase activity between 6h and 24h in each condition (control, coculture with RWPE1 and coculture with RWPE2). Only one TF (RNF4) increased activity in RWPE-1 coculture, while dysregulation of 45 TFs (7 decreased activity and 38 increased activity) was observed in coculture with RWPE-2. Pathway analysis showed that these 45 dysregulated TFs in fibroblasts after coculture with RWPE2 cells may be associated with RUNX1 and PTEN pathways. Conclusion: Our results demonstrate that CAFs transformation can be orchestrated by dysregulation of multiple TFs, therefore may suggest multiple signaling pathways that participate in CAFs transformation. Moreover, we show potential pathways, that could be involved in feedback loop between fibroblast and epithelial cells in tumors.

2020-12-07 | GSE159493 | GEO

Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling [WGBS]

Project description:Genome wide DNA methylation profiling of a suite of biological samples for technical evaluation of the HumanMethylationEPIC v2.0 BeadChip. Samples include prostate (LNCaP, PrEC) and breast cancer (MCF7, TAMR) cell lines, as well as primary tumour samples from prostate (SYN*) and breast (FD*).

2024-03-07 | GSE240481 | GEO

Characterisation and reproducibility of theHumanMethylationEPIC v2.0 BeadChip for DNAmethylation profiling [EPIC v2]

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