Cargando…
3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer
OBJECTIVES: Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epige...
Autores principales: | , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621134/ https://www.ncbi.nlm.nih.gov/pubmed/37919672 http://dx.doi.org/10.1186/s12863-023-01166-x |
_version_ | 1785130350022754304 |
---|---|
author | Llinàs-Arias, Pere Ensenyat-Méndez, Miquel Orozco, Javier I. J. Íñiguez-Muñoz, Sandra Valdez, Betsy Wang, Chuan Mezger, Anja Choi, Eunkyoung Tran, Yan Zhou Yao, Liqun Bonath, Franziska Olsen, Remi-André Ormestad, Mattias Esteller, Manel Lupien, Mathieu Marzese, Diego M. |
author_facet | Llinàs-Arias, Pere Ensenyat-Méndez, Miquel Orozco, Javier I. J. Íñiguez-Muñoz, Sandra Valdez, Betsy Wang, Chuan Mezger, Anja Choi, Eunkyoung Tran, Yan Zhou Yao, Liqun Bonath, Franziska Olsen, Remi-André Ormestad, Mattias Esteller, Manel Lupien, Mathieu Marzese, Diego M. |
author_sort | Llinàs-Arias, Pere |
collection | PubMed |
description | OBJECTIVES: Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epigenetic changes that aid in the understanding of the dissemination process of these cancers. DATA DESCRIPTION: Using CRISPR/Cas9, our experimental approach led us to identify and disrupt an insulator element, IE8, whose activity seemed relevant for cell invasion. The experiments were performed in two well-established TNBC cellular models, the MDA-MB-231 and the MDA-MB-436. To gain insights into the underlying molecular mechanisms of TNBC invasion ability, we generated and characterized high-resolution chromatin interaction (Hi-C) and chromatin accessibility (ATAC-seq) maps in both cell models and complemented these datasets with gene expression profiling (RNA-seq) in MDA-MB-231, the cell line that showed more significant changes in chromatin accessibility. Altogether, our data provide a comprehensive resource for understanding the spatial organization of the genome in TNBC cells, which may contribute to accelerating the discovery of TNBC-specific alterations triggering advances for this devastating disease. |
format | Online Article Text |
id | pubmed-10621134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-106211342023-11-03 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer Llinàs-Arias, Pere Ensenyat-Méndez, Miquel Orozco, Javier I. J. Íñiguez-Muñoz, Sandra Valdez, Betsy Wang, Chuan Mezger, Anja Choi, Eunkyoung Tran, Yan Zhou Yao, Liqun Bonath, Franziska Olsen, Remi-André Ormestad, Mattias Esteller, Manel Lupien, Mathieu Marzese, Diego M. BMC Genom Data Data Note OBJECTIVES: Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epigenetic changes that aid in the understanding of the dissemination process of these cancers. DATA DESCRIPTION: Using CRISPR/Cas9, our experimental approach led us to identify and disrupt an insulator element, IE8, whose activity seemed relevant for cell invasion. The experiments were performed in two well-established TNBC cellular models, the MDA-MB-231 and the MDA-MB-436. To gain insights into the underlying molecular mechanisms of TNBC invasion ability, we generated and characterized high-resolution chromatin interaction (Hi-C) and chromatin accessibility (ATAC-seq) maps in both cell models and complemented these datasets with gene expression profiling (RNA-seq) in MDA-MB-231, the cell line that showed more significant changes in chromatin accessibility. Altogether, our data provide a comprehensive resource for understanding the spatial organization of the genome in TNBC cells, which may contribute to accelerating the discovery of TNBC-specific alterations triggering advances for this devastating disease. BioMed Central 2023-11-02 /pmc/articles/PMC10621134/ /pubmed/37919672 http://dx.doi.org/10.1186/s12863-023-01166-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Data Note Llinàs-Arias, Pere Ensenyat-Méndez, Miquel Orozco, Javier I. J. Íñiguez-Muñoz, Sandra Valdez, Betsy Wang, Chuan Mezger, Anja Choi, Eunkyoung Tran, Yan Zhou Yao, Liqun Bonath, Franziska Olsen, Remi-André Ormestad, Mattias Esteller, Manel Lupien, Mathieu Marzese, Diego M. 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title | 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title_full | 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title_fullStr | 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title_full_unstemmed | 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title_short | 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
title_sort | 3-d chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621134/ https://www.ncbi.nlm.nih.gov/pubmed/37919672 http://dx.doi.org/10.1186/s12863-023-01166-x |
work_keys_str_mv | AT llinasariaspere 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT ensenyatmendezmiquel 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT orozcojavierij 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT iniguezmunozsandra 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT valdezbetsy 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT wangchuan 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT mezgeranja 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT choieunkyoung 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT tranyanzhou 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT yaoliqun 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT bonathfranziska 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT olsenremiandre 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT ormestadmattias 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT estellermanel 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT lupienmathieu 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer AT marzesediegom 3dchromatinconformationaccessibilityandgeneexpressionprofilingoftriplenegativebreastcancer |