IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos

Forsyth, Jessica E. and Al-Anbaki, Ali H. and de la Fuente, Roberto and Modare, Nikkinder and Perez-Cortes, Diego and Rivera, Isabel and Seaton Kelly, Rowena and Cotter, Simon and Plusa, Berenika and Brickman, Joshua Mark (2021) IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos. PLOS Biology, 19 (7). e3001345. ISSN 1545-7885

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Abstract

Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.

Item Type: Article
Subjects: Academic Digital Library > Biological Science
Depositing User: Unnamed user with email info@academicdigitallibrary.org
Date Deposited: 17 Jan 2023 08:29
Last Modified: 20 Sep 2023 07:41
URI: http://publications.article4sub.com/id/eprint/89

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