Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Level 7 Seminar Room 2, WEHI1

16 May 2017

Growing kidneys in a dish: using RNA-seq to verify the reproducibility of kidney organoid differentiation

Belinda Phipson

The ability to make three dimensional organoids from human pluripotent stem cells through directed differentiation opens up the possibilities of personalised drug testing, disease modelling and regeneration, as well as enhancing our knowledge of organ development. A recently published protocol by our collaborators defined the differentiation of human pluripotent stem cells into kidney organoids containing all the major components of the kidney. However, successfully using kidney organoids for drug screening or disease modelling will rely on the reproducibility and robustness of the differentiation protocol.

Here we investigate the reproducibility and robustness of kidney organoids generated from this protocol using RNA-seq data. We designed and performed extensive transcriptional profiling of kidney organoids taken from various time points across the differentiation protocol. We find massive transcriptional changes across the time course as the cells differentiate from stem cells to kidney organoids. This data corresponds to what is understood from kidney development in the mouse embryo. In addition, we specifically examined the sources of variability that arise during the step-wise differentiation process. We compared transcriptional profiles of day 18 organoids derived from distinct differentiations separated in time, as well as organoids grown concurrently from the same starting cells in separate vials. While transcriptional correlations were high between organoids, there were many genes showing a great deal of variability across organoids at a given time point in the differentiation protocol. Using random effects modelling to partition the variability from the different sources, in conjunction with the complete RNA-Seq time course, revealed that the relative maturity of the organoids was the major source of variation. Finally, I will present some initial results from related kidney single cell RNA-Seq projects.

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