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Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance [T47D]

ABSTRACT: To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer T47D cells and Tamoxifen resistant breast cancer T47D cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119890 | GEO | 2019/04/09

REPOSITORIES: GEO

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Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance

Project description:To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer MCF7 cells and Tamoxifen resistant breast cancer MCF7 cells.

2019-04-09 | GSE108787 | GEO

Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance [T47D]

Project description:Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance [T47D]

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Gene expression in human breast cancer T47D cells associated with expression of PTH-AS, a lncRNA downstream of parathyroid hormone

Project description:To comprehensively analyze the effect of PTH-AS on gene expression, microarray analysis was performed using human breast cancer T47D cells expressing PTH-AS. The gene expression levels of full-length PTH-AS expressing T47D cells (T47D-PA6) and vector control (T47D-VC1) or incomplete PTH-AS expressing T47D cells (T47D-PA5) were compared. As a result, 1453 genes were differentially expressed in his T47D-PA6 compared to T47D-VC1. Except for genes whose expression was altered in T47D-PA5 cells expressing incomplete PTH-AS, PTH-AS expression in T47D cells upregulated 914 genes and downregulated 600 genes. Many of the altered genes have been classified as immune-related biological processes. Particularly striking was the significant upregulation of JAK-STAT pathway-related genes, including the interferon-related DNA damage resistance signature (IRDS) that promotes cancer.

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TCC in pluripotent and differentiated cells

Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked. Recently CTCF anchored loops have been described as major features of chromatin organisation. However, the dynamics and role for these structures in differentiation is unknown. We used Tethered Chromatin Conformation Capture (TCC) to assess for the dynamics of CTCF-anchor loop formation upon differentiation of mouse embryonic stem cells (ESC) and neural stem cells (NSC).

2018-11-08 | E-MTAB-4870 | biostudies-arrayexpress

Mass Spectrometry of T47D cells treated with PTK6 PROTAC

Project description:PTK6 PROTAC treatment of T47D breast cancer cells were analyzed with mass spectrometry for determining PTK6 PROTAC specificity and global proteomic changes.

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T47D shNT versus T47D shRON

Project description:T47D shNT versus T47D shRON

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Identification of AGR2 interacting proteins in T47D cells using label-free quantification

Project description:LC-MS/MS analysis with label-free quantification to identify proteins interacting with AGR2 protein in T47D breast cancer cells

2022-01-03 | PXD012690 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of human breast cancer cell T47D and T47D-TR Transcriptomes

Project description:To gain new insight into the resistance to hormonal therapy in breast cancer, we generated a tamoxifen-resistant human breast cancer cell line T47D-TR by exposing estrogen-sensitive cell line T47D to increasing concentrations of 4-hydroxy tamoxifen (4-OHT) and identified its resistance with different ways. What we interested is the underlying mechanisms of breast cancer tamoxifen resistance which was not reported yet.Here, we detect the RNA sequence of both the two cell lines hoping to find some evidence.

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RNA-seq analysis of hormone receptor positive breast cancer cell line T47D with 24h hormone treatment

Project description:T47D cells treated with hormones 24h

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Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation

Project description:The three-dimensional (3D) organization of the genome within the cell nucleus contributes to cell-specific gene expression in different cell types1. High-throughput 3CM-bM-^@M-^Sderived methods have revealed that the genome is segmented into contiguous topologically associating domains (TADs), which help to orchestrate gene expression changes during differentiation and development2-5. Using ChIP-Seq, Hi-C and 3D modelling techniques, we reveal that TADs regulate the rapid gene expression changes induced by progestin in T47D breast cancer cells. In response to the hormone, TADs maintain their borders and operate as discrete regulatory units in which the majority of the genes are either transcriptionally activated or repressed. Additionally, the epigenetic signatures of the TADs are coordinately modified by hormone in correlation with the transcriptional changes. Hormone-induced changes in gene activity and chromatin remodelling are accompanied by structural changes that are distinct for activated or repressed TADs. Integrative 3D modelling revealed that TADs are structurally expanded if active and compacted if repressed, and that this is accompanied by differential changes in accessibility. We thus propose that TADs function as M-bM-^@M-^\regulonsM-bM-^@M-^] to enable spatially proximal genes to be coordinately transcribed in response to hormones. T47D-MTVL human breast cancer cells were incubated with the progestin R5020 for different times at 37M-BM-:C and prepared for ChIP-Seq or Hi-C according published protocols

2014-10-06 | E-GEOD-53463 | biostudies-arrayexpress

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