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Llinàs-Arias P, Ensenyat-Méndez M, Orozco JIJ, Íñiguez-Muñoz S, Valdez B, Wang C, Mezger A, Choi E, Tran YZ, Yao L, Bonath F, Olsen RA, Ormestad M, Esteller M, Lupien M, Marzese DM. 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer. BMC Genom Data 2023; 24:61. [PMID: 37919672 PMCID: PMC10621134 DOI: 10.1186/s12863-023-01166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
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.
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Affiliation(s)
- Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Miquel Ensenyat-Méndez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Sandra Íñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Betsy Valdez
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Chuan Wang
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Anja Mezger
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Eunkyoung Choi
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yan Zhou Tran
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Liqun Yao
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Franziska Bonath
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Remi-André Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Ormestad
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), 28029, Madrid, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain.
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