De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout of Bbs1.

Freke, G.; Martins, T.; Davies, R.; Beyer, T.; Seda, M.; Peskett, E.; Haq, N.; Prasai, A.; Otto, G.; Jeyabalan Srikaran, J.; Hernandez, V.; Diwan, G.; Russell, R. B.; Ueffing, M.; Huranova, M.; Boldt, K.; Beales, P. L.; Jenkins, D.

doi:10.1101/2023.10.02.560442

bioRxiv · 10.1101/2023.10.02.560442

De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout of Bbs1.

Freke, G.·Martins, T.·Davies, R.·Beyer, T.·Seda, M.·Peskett, E.·Haq, N.·Prasai, A.·Otto, G.·Jeyabalan Srikaran, J.·Hernandez, V.·Diwan, G.·Russell, R. B.·Ueffing, M.·Huranova, M.·Boldt, K.·Beales, P. L.·Jenkins, D.

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Abstract

Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue specific, and gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane trafficking and intraflagellar transport (IFT) adaptor protein complex formed by 8 BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically-defined clones. Our results suggest that BBS1 is required for suppression of mesenchymal cell identities as IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, and BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively this work suggests that the dynamic stability of the BBSome is essential for suppression of mesenchymal cell identities as epithelial cells differentiate.

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Freke, G., Martins, T., Davies, R., Beyer, T., Seda, M., Peskett, E., Haq, N., Prasai, A., Otto, G., Jeyabalan Srikaran, J., Hernandez, V., Diwan, G., Russell, R. B., Ueffing, M., Huranova, M., Boldt, K., Beales, P. L., Jenkins, D.. 2023-10-03. De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout of Bbs1.. https://doi.org/10.1101/2023.10.02.560442

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