Introduction: Molecular heterogeneity of bladder cancer (BC) is affecting response to treatment. To test treatment response, several patient derived models have been established that may vary in their suitability to test targets. We have previously established patient derived organoids (PDO) from BC patients and found a highly conserved genomic landscape. In this analysis, we aim to investigate the cellular composition and pathway activities of this patient derived model.
Methods: We generated PDOs from more than 35 BC specimens. Based on the marker expression, we selected 5 pairs of BC and subsequent PDO to include different molecular subtypes (e.g. luminal-, basal-like). Single-cell suspensions were directed to scRNA-seq technology from 10x Genomics. For the analysis, unsupervised clustering, gene expression, as well as pathway analysis were used to compare the cell type composition and pathway activity.
Results: Overall, we observed a high degree of heterogeneity of cell type composition between BCs, between PDOs, as well as between BCs to subsequent PDOs.
Unsupervised clustering separated cancerous- as well as non-cancerous cells in BCs and PDOs in individual clusters. In most BC, both luminal-like and basal-like cells were detected. In the subsequent PDOs however, luminal-like cells were present with a higher proportion compared to basal-like cells. This was true for different luminal-like subcategories (lum-pap and lum-nonspecified).
While immune cells (e.g. B-cells, CD4+ and CD8+ T-cells) were present in both BC and PDO samples, stromal cells (e.g. smooth muscle and endothelial cells) were absent in PDOs. Consequently, immune- and cancer cell related pathways such as interferon_gamma_response or FGFR3_signature were active in both BC and PDO. Contrarily, pathways related to stroma interactions such as angiogenesis or epithelial_mesenchymal_transition were less active in PDOs.
Conclusions: Single-cell transcriptomic profiling of parental BCs and subsequent PDOs revealed a high degree of heterogeneity in both the tumor and organoid cellular composition. Our data show preservation of immune cells in PDOs and thus suggest that organoids may even allow to investigate cellular interactions between cancer and immune cells. On the other hand, since stromal cells were mainly lost in PDOs, other models may be needed to investigate angiogenesis or epithelial mesenchymal transition.
Source of Funding: SNSF Grant Nr. 310030
Novartis Grant #19C200
grant #2017-510 of the Strategic Focal Area “Personalized Health and Related Technologies (PHRT)” of the ETH Domain