Journal article
Evaluation of variability in human kidney organoids
B Phipson, PX Er, AN Combes, TA Forbes, SE Howden, L Zappia, HJ Yen, KT Lawlor, LJ Hale, J Sun, E Wolvetang, M Takasato, A Oshlack, MH Little
Nature Methods | NATURE PORTFOLIO | Published : 2019
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..
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Awarded by National Institute of Diabetes and Digestive and Kidney Diseases
Funding Acknowledgements
We thank A. Christ and G. Baillie at the Institute for Molecular Bioscience, The University of Queensland, for sequencing services. We acknowledge A. Mallett and S. Alexander for assistance in ethics applications and patient recruitment. We thank D. Vukcevic and G.K. Smyth for valuable discussion regarding random effects modeling, and J. Maksimovic for initial analysis and mapping of the patient RNA-seq data. This study was funded by the National Institute of Diabetes and Digestive and Kidney Diseases (grant no. DK107344) and National Health and Medical Research Council of Australia (NHMRC) (grant nos. GNT1041277, GNT1100970, GNT1098654). The Murdoch Children's Research Institute is supported by the Victorian Government's Operational Infrastructure Support Program. M.H.L. is an NHMRC Senior Principal Research Fellow. A.O. is an NHMRC Career Development Fellow (grant no. GNT1126157). T.A.F. is an NHMRC Postgraduate Scholarship (grant no. GNT1114409) and Royal Australian College of Physicians Jacquot Award Recipient (grant no. APP1114409).