Chapter 27
Analysis of Cellular EMT States Using Molecular Biology
and High Resolution FISH Labeling
Noe ´ mie Kempf, Fatima Moutahir, Isabelle Goiffon, Sylvain Cantaloube,
Kerstin Bystricky, and Anne-Claire Lavigne
Abstract
Metastasis results from the ability of cancer cells to grow and to spread beyond the primary tumor to distant
organs. Epithelial-to-Mesenchymal Transition (EMT), a fundamental developmental process, is reactivated
in cancer cells, and causes epithelial properties to evolve into mesenchymal and invasive ones. EMT changes
cellular characteristics between two distinct states, yet, the process is not binary but rather reflects a broad
spectrum of partial EMT states in which cells exhibit various degrees of intermediate epithelial and
mesenchymal phenotypes. EMT is a complex multistep process that involves cellular reprogramming
through numerous signaling pathways, alterations in gene expression, and changes in chromatin morphology. Therefore, expression of key proteins, including cadherins, occludin, or vimentin must be precisely
regulated. A comprehensive understanding of how changes in nuclear organization, at the level of single
genes clusters, correlates with these processes during formation of metastatic cells is still missing and yet
may help personalized prognosis and treatment in the clinic. Here, we describe methods to correlate
physiological and molecular states of cells undergoing an EMT process with chromatin rearrangements
observed via FISH labeling of specific domains.
Key words Epithelial-mesenchymal transition, Hybrid EMT, Plasticity, Cancer, DNA-FISH, Highthroughput microscopy, Chromatin reorganization, Genome, Metastasis
1 Introduction
Epithelial-to-Mesenchymal Transition (EMT) is a fundamental
development process in which cells lose their epithelial characteristics and acquire mesenchymal features. EMT has long been
viewed as a binary process defined by the two extreme phenotypes,
epithelial and mesenchymal. It is now clearly recognized that this
process is set up gradually with the sequential appearance of different intermediate states (partial or hybrid EMT states) from a morphological, transcriptional, or epigenetic point of view [1]. These
partial EMT states have become significant in recent years because
of their contribution to carcinogenesis. The EMT process is
Kyra Campbell and Eric Theveneau (eds.), The Epithelial-to Mesenchymal Transition: Methods and Protocols,
Methods in Molecular Biology, vol. 2179, https://doi.org/10.1007/978-1-0716-0779-4_27,
© Springer Science+Business Media, LLC, part of Springer Nature 2021
353
Analysis of Cellular EMT States Using Molecular Biology
and High Resolution FISH Labeling
Noe ´ mie Kempf, Fatima Moutahir, Isabelle Goiffon, Sylvain Cantaloube,
Kerstin Bystricky, and Anne-Claire Lavigne
Abstract
Metastasis results from the ability of cancer cells to grow and to spread beyond the primary tumor to distant
organs. Epithelial-to-Mesenchymal Transition (EMT), a fundamental developmental process, is reactivated
in cancer cells, and causes epithelial properties to evolve into mesenchymal and invasive ones. EMT changes
cellular characteristics between two distinct states, yet, the process is not binary but rather reflects a broad
spectrum of partial EMT states in which cells exhibit various degrees of intermediate epithelial and
mesenchymal phenotypes. EMT is a complex multistep process that involves cellular reprogramming
through numerous signaling pathways, alterations in gene expression, and changes in chromatin morphology. Therefore, expression of key proteins, including cadherins, occludin, or vimentin must be precisely
regulated. A comprehensive understanding of how changes in nuclear organization, at the level of single
genes clusters, correlates with these processes during formation of metastatic cells is still missing and yet
may help personalized prognosis and treatment in the clinic. Here, we describe methods to correlate
physiological and molecular states of cells undergoing an EMT process with chromatin rearrangements
observed via FISH labeling of specific domains.
Key words Epithelial-mesenchymal transition, Hybrid EMT, Plasticity, Cancer, DNA-FISH, Highthroughput microscopy, Chromatin reorganization, Genome, Metastasis
1 Introduction
Epithelial-to-Mesenchymal Transition (EMT) is a fundamental
development process in which cells lose their epithelial characteristics and acquire mesenchymal features. EMT has long been
viewed as a binary process defined by the two extreme phenotypes,
epithelial and mesenchymal. It is now clearly recognized that this
process is set up gradually with the sequential appearance of different intermediate states (partial or hybrid EMT states) from a morphological, transcriptional, or epigenetic point of view [1]. These
partial EMT states have become significant in recent years because
of their contribution to carcinogenesis. The EMT process is
Kyra Campbell and Eric Theveneau (eds.), The Epithelial-to Mesenchymal Transition: Methods and Protocols,
Methods in Molecular Biology, vol. 2179, https://doi.org/10.1007/978-1-0716-0779-4_27,
© Springer Science+Business Media, LLC, part of Springer Nature 2021
353