Learning the rules of collective cell migration using deep attention networks.

TitleLearning the rules of collective cell migration using deep attention networks.
Publication TypeJournal Article
Year of Publication2022
AuthorsLaChance, J, Suh, K, Clausen, J, Cohen, DJ
JournalPLoS Comput Biol
Volume18
Issue4
Paginatione1009293
Date Published2022 04
ISSN1553-7358
KeywordsCell Communication, Cell Movement, Endothelial Cells, Humans, Neoplasms
Abstract

<p>Collective, coordinated cellular motions underpin key processes in all multicellular organisms, yet it has been difficult to simultaneously express the 'rules' behind these motions in clear, interpretable forms that effectively capture high-dimensional cell-cell interaction dynamics in a manner that is intuitive to the researcher. Here we apply deep attention networks to analyze several canonical living tissues systems and present the underlying collective migration rules for each tissue type using only cell migration trajectory data. We use these networks to learn the behaviors of key tissue types with distinct collective behaviors-epithelial, endothelial, and metastatic breast cancer cells-and show how the results complement traditional biophysical approaches. In particular, we present attention maps indicating the relative influence of neighboring cells to the learned turning decisions of a 'focal cell'-the primary cell of interest in a collective setting. Colloquially, we refer to this learned relative influence as 'attention', as it serves as a proxy for the physical parameters modifying the focal cell's future motion as a function of each neighbor cell. These attention networks reveal distinct patterns of influence and attention unique to each model tissue. Endothelial cells exhibit tightly focused attention on their immediate forward-most neighbors, while cells in more expansile epithelial tissues are more broadly influenced by neighbors in a relatively large forward sector. Attention maps of ensembles of more mesenchymal, metastatic cells reveal completely symmetric attention patterns, indicating the lack of any particular coordination or direction of interest. Moreover, we show how attention networks are capable of detecting and learning how these rules change based on biophysical context, such as location within the tissue and cellular crowding. That these results require only cellular trajectories and no modeling assumptions highlights the potential of attention networks for providing further biological insights into complex cellular systems.</p>

DOI10.1371/journal.pcbi.1009293
Alternate JournalPLoS Comput Biol
PubMed ID35476698
PubMed Central IDPMC9106212
Grant ListR35 GM133574 / GM / NIGMS NIH HHS / United States