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Integrative assessment of classical and molecular phenotypes in MCF10A cells [ATAC-seq]

ABSTRACT: Maintenance of proper phenotypic state of mammary epithelial cells is crucial for normal function, however the molecular networks underlying control of various cellular phenotypes are not well understood. To date most studies have assessed the impact of extracellular signals on a single phenotypic response, such as proliferation, or have focused on elucidation of molecular changes associated with single perturbations. However, these approaches ignore that ligands frequently induce multiple phenotypic changes and that similar phenotypic responses can be induced by multiple ligands. As a consequence, little is known about the core molecular mechanisms that drive cells to different phenotypic states. Here we deeply profiled the phenotypic and molecular responses of MCF10A mammary epithelial cells to a diverse panel of ligands known to have a role in the normal mammary gland. These ligands elicited multiple phenotypic responses, including changes in proliferation, migration, and differentiation status. Analysis of companion RNAseq, ATACseq, and proteomic data identified distinct molecular features associated with ligand treatments and phenotypic changes. These data provide a robust resource to address questions about how environmental signals are encoded into molecular and phenotypic responses, the associations between molecular modalities, and temporal encoding of molecular and phenotypic responses.

ORGANISM(S): Homo sapiens

PROVIDER: GSE152408 | GEO | 2021/04/15

REPOSITORIES: GEO

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Project description:The activation of receptors displayed on the surface of cells typically initiates cytoplasmic signalling cascades that lead to changes in cellular transcriptional responses so that a cell expresses proteins that enable it to behave appropriately as a function of their position within an organism. Understanding these signals and learning how to either prevent or ectopically activate them could have many therapeutic benefits and applications. In some cases these signals are highly localised, being delivered by directly neighbouring cells that express ligands which specifically bind to and activate receptors; for example, stem cells display receptors for ligands provided by cells within their niche to both ensure continual production of cells, and that their cellular progeny are directed towards appropriate fates. While for some cell types we know something of these signals enabling the in vitro differentiation of stem cells towards certain cellular fates, the differentiation processes is often not complete and so immature cell types which are not fully functional are produced, implying that some important signals are missing. Here, we propose to systematically identify receptor-triggered signalling pathways by stimulating receptors on the surface of human stem cells by using a library of soluble recombinant oligomerised protein ligands and measuring the consequent transcriptional perturbations using RNA-seq. We propose to screen an existing library of ~50 oligomerised human ligands previously used in receptor protein interaction screens and first test them for their ability to bind to human stem cells to identify those ligands for which the stem cells express a cell surface receptor. For those ligands which interact with the stem cells (we estimate between 2 and 5), they will be added to stem cell cultures and their effects on transcription quantified. The budget requested is sufficient for us to include controls and test important parameters such different time points after addition of the proteins. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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Integrative assessment of classical and molecular phenotypes in MCF10A cells [ATAC-seq]

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