Gene expression profiles of CD8+ T cells cultured in extracellular matrices of different viscoelasticies

The efficacy of adoptive T cell therapy is highly dependent on the generation of T cell populations that are able to both provide immediate effector function and long-term protective immunity. Inspired by the emerging consensus that T cell phenotype and function are inherently linked to their tissue localization, we present an approach to generate functionally distinct T cell populations via the physical properties of their surrounding matrix. A collagen type I based extracellular matrix (ECM) was engineered to allow for independent tuning of matrix stiffness and viscoelasticity, two features that characterize the mechanical properties of tissues. To investigate how ECM viscoelasticity drives changes in the transcriptional landscape of T cells, scRNA-seq of CD8+ T cells cultured in fast relaxing and slow relaxing collagen matrices was performed CD8+ T cells were harvested from collagen gels, and live cells were enriched using a dead cell removal kit (Miltenyi #130-090-101). Single cell sequencing was performed using the Chromium Single Cell 3’ v3 platform (10x Genomics) on the NovaSeq S1.