Patient-derived organoids and neurospheres recapitulate salient features of primary tumor heterogeneity

The intra- and inter-tumoral heterogeneity of glioblastoma (GBM) represents a significant therapeutic challenge and barrier to the generation of reliable and accurate models for in vitro studies. Three-dimensional models, such as patient-derived neurospheres (PDN) and organoids (PDO), recapitulate complex cellular states. However, the direct comparison of models derived in parallel from the same primary tumor tissue has never been performed. The aim of this study was to determine the tumor cell composition of PDN and PDO models relative to matched primary GBM tissue.

Four GBM surgical samples were used to establish matched PDO and PDN models, which were genomically verified using single nucleotide polymorphism array. DNA methylation, histology, and transcriptome were examined for intra-tumoral heterogeneity correlating with the matched GBM tissue. PDN lines were used to investigate the tumor cell composition response to temozolomide chemotherapy over time, maximizing their utility.

We find that both patient-derived models recapitulate the genomic, epigenomic, and tumor cell heterogeneity of the primary tissue at similar capacity. Furthermore, single-nuclei RNA sequencing revealed a subset of organoids containing small numbers of non-malignant cells from neuron and immune cell lineages. Harnessing the intra-tumoral heterogeneity of PDN models, we reveal the impact of temozolomide chemotherapy on individual cell states, altering composition of tumors over time in response to treatment.

Our data confirms that both PDN and PDO patient-derived models recapitulate patient intra-tumoral heterogeneity providing a platform for tumor cell state refined therapeutic studies.