Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models

In this study, genome-wide gene expression profiles of primary hepatocytes and liver sinusoidal endothelial cells (LSECs) were measured at day 12 for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA). The culture systems analyzed include the commonly used collagen sandwich and monolayers of hepatocytes, as well as 3-dimensional (3D) engineered liver models that contain hepatocytes and LSECs (3DHL) and hepatocytes, LSECs, and Kupffer cells (3DHLK). Our results highlight the up-regulation of several hepatocyte specific functions in hepatocytes and a novel interplay between Ppara signaling and bile acid biosynthesis in LSECs. We measured gene expression in hepatocytes, LSECs, and Kupffer cells from the 3DHL and 3DHLK models at day 12 to better understand LSEC function in in vitro liver cultures. For additional comparisons, we collected gene expression from hepatocytes in a collagen sandwich (CS) and hepatocyte monolayer (HM) as well as Kupffer cells at day 3 prior to their inclusion in the 3D liver model. We obtained Affymetrix microarray data for 23 samples, considering three cell-types and across four culture systems. Each cell-type culture system was performed in triplicate, except Kupffer cells at day 12 was performed in duplicate.