2026-04-17T06:44:11Zhttps://recercat.cat/oai/request

oai:recercat.cat:10230/608752025-12-12T01:40:31Zcom_2072_6col_2072_452952

00925njm 22002777a 4500 dc Ramírez Cuéllar, Angélica Julieta author Ferrari, Roberto author Sanz, Rosario T. author Valverde Santiago, Marta author García García, Judith author Nacht, A. Silvina author Castillo, David author Le Dily, François author Neguembor, Maria Victoria author Malatesta, Marco author Bonnin, Sarah author Marti-Renom, Marc A. author Beato, Miguel author Vicent, Guillermo Pablo author 2024-08-01T11:55:10Z 2024-08-01T11:55:10Z 2024 The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal. The authors would like to thank Jianrong Lu (University of Florida College of Medicine, USA) for generously sharing the CTCF constructs. Additionally, we also would like to thank Dr. Julia Ponomarenko (Bioinformatics Unit, CRG) for their valuable advice, technical assistance and involvement in processing the RNA-seq, ChIP-seq, and ATAC-seq data. The experimental work was supported by grants from the Departament d’Innovació Universitat i Empresa (DIUiE), the Spanish Ministry of Economy and Competitiveness (SAF2016-75006-P, PID2019-105173RB-I00, and PID2022-137045OB-I00) and Consejo Superior de Investigaciones Científicas (Ref# 201820I131), ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-2018 and ERC Synergy Grant “4DGenome” nr: 609989. MAM-R acknowledges support by the Spanish Ministerio de Ciencia e Innovación (PID2020-115696RB-I00). This work has benefited from the equipment and framework of the COMP-HUB and COMP-R Initiatives, funded by the ‘Departments of Excellence’ program of the Italian Ministry for University and Research (MIUR, 2018-2022 and MUR, 2023-2027) and from the HPC (High-Performance Computing) facility of the University of Parma, Italy. Breast Cancer CTCF LATS1 Kinase and Hormonal Response Three-dimensional Cell Growth LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells