Evaluation of variability in human kidney organoids
The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although individual organoids within a differentiation batch showed strong transcriptional correlation, we noted significant variation between experimental batches, particularly in genes associated with temporal maturation. Single-cell profiling revealed shifts in nephron patterning and proportions of component cells. Distinct induced pluripotent stem cell clones showed congruent transcriptional programs, with interexperimental and interclonal variation also strongly associated with nephron patterning. Epithelial cells isolated from organoids aligned with total organoids at the same day of differentiation, again implicating relative maturation as a confounder. This understanding of experimental variation facilitated an optimized analysis of organoid-based disease modeling, thereby increasing the utility of kidney organoids for personalized medicine and functional genomics.
Citation
@article{phipson2018,
author = {Phipson, Belinda and X Er, Pei and N Combes, Alexander and A
Forbes, Thomas and E Howden, Sara and Zappia, Luke and Yen, Hsan-Jan
and T Lawlor, Kynan and J Hale, Lorna and Sun, Jane and Wolvetang,
Ernst and Takasato, Minoru and Oshlack, Alicia and H Little,
Melissa},
title = {Evaluation of Variability in Human Kidney Organoids},
journal = {Nature methods},
volume = {16},
number = {1},
pages = {79-87},
date = {2018-12-01},
url = {https://lazappi.id.au/publications/2018-phipson-variability},
doi = {10.1038/s41592-018-0253-2},
issn = {1548-7091, 1548-7105},
langid = {en},
abstract = {The utility of human pluripotent stem cell–derived kidney
organoids relies implicitly on the robustness and transferability of
the protocol. Here we analyze the sources of transcriptional
variation in a specific kidney organoid protocol. Although
individual organoids within a differentiation batch showed strong
transcriptional correlation, we noted significant variation between
experimental batches, particularly in genes associated with temporal
maturation. Single-cell profiling revealed shifts in nephron
patterning and proportions of component cells. Distinct induced
pluripotent stem cell clones showed congruent transcriptional
programs, with interexperimental and interclonal variation also
strongly associated with nephron patterning. Epithelial cells
isolated from organoids aligned with total organoids at the same day
of differentiation, again implicating relative maturation as a
confounder. This understanding of experimental variation facilitated
an optimized analysis of organoid-based disease modeling, thereby
increasing the utility of kidney organoids for personalized medicine
and functional genomics.}
}