Gene expression profiling via RNA sequencing of patient brain tumors cultured in 3D bioengineered cultures

Using pediatric ependymoma and adult glioblastoma (GBM) as examples, it was shown that the 3D brain ECM-containing microenvironment with a balance of cell-cell and cell-matrix interactions supports distinctive phenotypes, which are associated with tumor type-specific and ECM-dependent patterns in the tumor cells’ transcriptomic profiles. 3D model’s culture conditions affect tumor tissue’s gene expression profiles, and suggest that these genetic changes underlie the phenotypic outcomes of tumor growth in the different microenvironments. In particular, 3D tissue models with brain-ECM containing hydrogels (i.e. derived from fetal or adult brain sources) differed from those with non-brain derived ECM hydrogels (i.e. unsupplemented collagen I) for both ependymoma and GBM. Examination of patient anaplastic ependymoma across three experimental categories: media type (FBS versus serum free), time point in culture (0.5, 1.5 and 4 months), and ECM (fetal brain ECM enriched collagen I- FECM, adult brain ECM enriched collagen I-AECM or plain collagen I- CLG1) and patient GBM across the three ECM conditions. n=1 for each experimental category (and n=2 for GBM samples) were sequenced.