Optimized ChIP-seq procedure facilitates hormone receptor profiling in human tumors
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ABSTRACT:
PROVIDER: PRJNA472620 | ENA |
REPOSITORIES: ENA
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Project description:Performing ChIP-seq analyses in clinical specimens has remained largely challenging due to multiple technical limitations and low quantities of starting material, resulting in low enrichments and poor signal-to-noise ratio. Here, we refined the original protocols for transcription factor ChIP-seq analyses in breast, prostate, and endometrial tumor tissue. In addition to the standard fixative formaldehyde, a second crosslinker Disuccinimidyl glutarate (DSG) was included in the procedure.
2018-12-27 | GSE114737 | GEO
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Project description:Our study represents the first detailed analysis of thyroid hormone binding to the genome in the intestine of wild-type and TRα (-/-) tadpoles, with biological replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of TR binding profiles.
2022-07-19 | GSE161718 | GEO
Project description:Purpose: Androgen-deprivation therapy is the standard treatment for prostate cancer but fails in hormone-refractory prostate cancer. The anti-inflammatory plant Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Here, we evaluated the systemic antitumor effects of a standardized and effect-optimized Wedelia chinensis herbal extract (WCE) on hormone-refractory prostate cancer. Methods: Hormone-refractory PC-3 orthotopic tumor mouse models were orally administered with WCE. The tumor transcriptomes were studied using RNA sequencing and Ingenuity Pathway Analysis to identify the molecular mechanisms. Results: WCE significantly attenuated tumor growth and metastasis in orthotopic PC-3 xenografts. Transcriptomic analysis of genome-wide gene expression in the tumors revealed that WCE suppressed the expression of HIF1α, IKKα/β phosphorylation, and the downstream cytokines/chemokines. Conclusions: A standardized preparation of Wedelia chinensis improved prostate cancer therapy through repressing NFκB-mediated cytokine expression in tumor cells and modulating the inflammatory tumor microenvironment. These data suggest that WCE functions through immunomodulation and has potential application as an adjuvant agent for the treatment of castration-resistant prostate cancer.
2017-12-01 | GSE99820 | GEO
Project description:Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ?100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.
| S-EPMC6311467 | biostudies-literature
Project description:Total RNA was extracted from FFPE samples of 139 chemotherapy-naïve hormone-receptor-negative breast cancers pooled from three sample sources and assayed for the expression of 21 genes within two previously reported microarray-derived prognostic signatures in 6 RT-PCR multiplexes.
2013-10-25 | GSE51630 | GEO
Project description:BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH. METHODS: In this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use. RESULTS: Our protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method. CONCLUSION: This report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility. In this study, we optimized the BAC araay-CGH protocol for automated hybridization for FFPE breast cancer samples. We have tested hybridization temperature and duration, different hybridization buffer conditions, and post-hybridization washing.
2010-06-12 | E-GEOD-7122 | biostudies-arrayexpress
Project description:Total RNA was extracted from FFPE samples of 139 chemotherapy-naïve hormone-receptor-negative breast cancers pooled from three sample sources and assayed for the expression of 21 genes within two previously reported microarray-derived prognostic signatures in 6 RT-PCR multiplexes. RT-PCR gene expression profiling. Total RNA was extracted from 10 micron FFPE sections, and expression levels of the 21 genes of interest plus two reference genes were quantified with 6 multiplex RT-PCR TaqMan assays.
2013-10-25 | E-GEOD-51630 | biostudies-arrayexpress