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Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE167154 | GEO | 2022/05/06

REPOSITORIES: GEO

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Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [Hi-C]

Project description:Triple-negative breast cancer (TNBC) is malignant cancer with a high risk of recurrence. To date, the underlying 3D chromatin organizations of TNBC have remained unclear. Here, using in situ Hi-C, we characterized the 3D chromatin organizations in cells representing five distinct subtypes of breast cancer (including TNBC) and TNBC tissues, compared to normal cells/tissues. We found that the global and local 3D architectures are severely disrupted in TNBC cells. Importantly, we detected CTCF-dependent TNBC-susceptible loss/gain of 3D chromatin organizations and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulations. Although some discrepancies exist between TNBC cell lines and tissues, we observed that perturbed local 3D architectures found in TNBC cells are partially conserved in TNBC tissues. Furthermore, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. Collectively, our findings provide important features of 3D chromatin organization in TNBC.

2022-05-06 | GSE167150 | GEO

Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ATAC-seq]

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Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ChIP-seq]

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Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [RNA-seq]

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Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers

Project description:Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers

| PRJNA703390 | ENA

Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [RNA-seq]

Project description:Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [RNA-seq]

| PRJNA703394 | ENA

Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [Hi-C]

Project description:Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [Hi-C]

| PRJNA703392 | ENA

Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ChIP-seq]

Project description:Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ChIP-seq]

| PRJNA703393 | ENA

Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ATAC-seq]

Project description:Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ATAC-seq]

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Molecular Characterization of Basal-like and Non-Basal-like Triple-Negative Breast Cancers

Project description:Triple-negative (TN) and Basal-like (BL) breast cancer definitions have been used interchangeably to identify breast cancers that lack expression of the hormonal receptors (HR) and overexpression and/or amplification of HER2. However, both classifications when compared to each other, show substantial discordance rates. Here, we molecularly characterize TN tumors, and Basal-like tumors, and compare and contrast the results in terms of common patterns and distinct patterns for each. In total, when testing 412 TN and 473 Basal-like tumors, 21.4% and 31.5% were identified as non-Basal-like and non-TN, respectively. TN tumors identified as Luminal or HER2-enriched showed undistinguishable overall gene expression profiles when compared versus Luminal or HER2-enriched tumors that were not TN. Similar findings were observed within Basal-like tumors regardless of the TN status. Interestingly, most TN tumors identified as HER2-enriched showed low HER2 expression and lack of HER2 amplification despite the similar overall gene expression profiles to HER2-E tumors that were not TN. Lastly, additional genomic classifications are examined within TN and Basal-like cancers, most of which are largely concordant with tumor intrinsic subtype. These results suggest that future clinical trials focused on TN disease should consider stratifying patients based on Basal-like versus non-Basal-like gene expression profiles as this appears to be the main biological difference seen within TN breast cancer patients. reference x sample

| S-ECPF-GEOD-41119 | biostudies-other

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