We develop a continuum theory to describe the collective dynamics of deformable epithelial cells, distinguishing the force-generating active filaments in the cells from their shape. The theory demonstrates how active flows driven by active filaments can create nematic domains and topological defects in the cell shape field. We highlight the role of the filament flow-aligning parameter, ${\lambda }_{\mathit{Q}}$, a rheological quantity that determines the response of the filaments to velocity gradients in the active flows, and plays a significant, to date unappreciated, role in determining the pattern of extensional and compressional active flows. In a contractile cell layer, local flows are expected to align elongated cells perpendicular to the active filaments. However, with increasing ${\lambda }_{\mathit{Q}}$, long-range correlations in the active turbulent flow field lead to extended regions where this alignment is parallel, consistent with recent experiments on confluent Madin-Darby canine kidney (MDCK) cell layers. Further, we distinguish defects in the filament director field, which contribute to the active driving, and those in the shape director field, measured in experiments, which are advected by the active flows. By considering the shape-filament orientation, we explain the unexpected motion of $+1/2$ defects towards their head in contractile cell layers, consistent with recent experiments on epithelial layers examining stress around shape defects.

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• Mechanobiology
• Active nematics
• Cells
• Epithelial cells
• Living matter & active matter