RNA-sequencing of iPSC-derived blood-brain barrier cell types across microenvironments

The blood-brain barrier (BBB) is lined by brain microvascular endothelial cells (BMECs) which regulate transport into and out of the brain. We used human induced pluripotent stem cell (iPSC)-derived cell types to model BBB function within 2D and 3D in vitro models. We compare gene expression between different iPSC-derived cell types, and specifically profile the response of iPSC-derived BMEC-like cells (iBMECs) to differentiation media volume, microenvironmental cues, and cytokines. 24 total samples were analyzed, across 5 cell types: (1) induced pluripotent stem cells (iPSCs), (2) iPSC-derived brain microvascular endothelial cell-like cells (iBMECs), (3) iPSC-derived pericyte-like cells (iPCs), (4) primary human dermal microvascular endothelial cells (HDMECs), and iPSC-derived endothelial cells (iECs). Differentiations of iBMECs were conducted across two source iPSCs (WTC and BC1), across media volumes (1 mL and 2 mL), across microenvironments (2D and 3D), and across cytokine exposures (with and without TNFa).