Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids

Creators: Huang, Biao¹; Zeng, Zipeng¹; Li, Hui¹; Li, Zexu²; Chen, Xi¹; Guo, Jinjin¹; Zhang, Chennan C.¹; Schreiber, Megan E.¹; Vonk, Ariel C.¹; Xiang, Tianyuan¹; Patel, Tadrushi¹; Li, Yidan¹; Parvez, Riana K.¹; Der, Balint¹; Chen, Jyun Hao¹; Liu, Zhenqing³; Thornton, Matthew E.¹; Grubbs, Brendan H.¹; Diao, Yarui⁴; Dou, Yali¹; Gnedeva, Ksenia¹; Lindström, Nils O.¹; Ying, Qilong¹; Pastor-Soler, Nuria M.¹; Fei, Teng²; Hallows, Kenneth R.¹; McMahon, Andrew P.¹; Li, Zhongwei^{1, 5}

1. University of Southern California
2. Northeastern University
3. Beckman Research Institute of City of Hope
4. Duke University
5. Lead contact

Abstract

Nephron progenitor cells (NPCs) self-renew and differentiate into nephrons, the functional units of the kidney. Here we report manipulation of p38 and YAP activity creates a synthetic niche that allows the long-term clonal expansion of primary mouse and human NPCs, and induced NPCs (iNPCs) from human pluripotent stem cells. Cultured iNPCs resemble closely primary human NPCs, generating nephron organoids with abundant distal convoluted tubule cells, which are not observed in published kidney organoids. The synthetic niche reprograms differentiated nephron cells into NPC state, recapitulating the plasticity of developing nephron in vivo. Scalability and ease of genome-editing in the cultured NPCs allow for genome-wide CRISPR screening, identi-fying novel genes associated with kidney development and disease. A rapid, efficient, and scala-ble organoid model for polycystic kidney disease was derived directly from genome-edited NPCs, and validated in drug screen. These technological platforms have broad applications to kidney development, disease, plasticity, and regeneration.

Copyright and License

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

Acknowledgement

We would like to thank Jeffrey Boyd and Bernadette Masinsin of the USC Flow Cytometry Facility for FACS, Seth Ruffins of the USC Optical Imaging Facility for help with microscopy, Dejerianne Ostrow and David Ruble of the Children’s Hospital Los Angeles Molecular Pathology Genomics Core for RNA-seq, Yibu Chen of the USC Norris Medical Library Bioinformatics Service for help with the RNA-seq computational analysis, Dr. Melissa L. Wilson (Department of Preventive Medicine, University of Southern California) and Family Planning Associates for coordinating fetal tissue collection, and Cristy Lytal for help with editing the manuscript. This work was supported by UKRO foundation funding, a KSOM Dean’s Pilot Award and an NIH Director’s New Innovator Award (DP2DK135739) to Z.L., and NIH DK054364 to A.P.M. Z.Z. was supported by a USC Stem Cell Challenge Award. M.E.S. was supported by a CIRM Bridges Award.

Funding

This work was supported by UKRO foundation funding, a KSOM Dean’s Pilot Award and an NIH Director’s New Innovator Award (DP2DK135739) to Z.L., and NIH DK054364 to A.P.M. Z.Z. was supported by a USC Stem Cell Challenge Award. M.E.S. was supported by a CIRM Bridges Award.

Contributions

Conceptualization, B.H. and Z.L.; methodology, investigation and validation, B.H., Z.Z., H.L., X.C., J.G., C.C.Z., M.E.S., A.C.V., T.X., T.P., Y.L., R.K.P., B.D., and J.H.C.; software and formal analysis, B.H., Z.Z., Z.L., and T.F.; resources, M.E.T., B.H.G., Y.D., Y.D., Q.Y., K.G., N.O.L., and A.P.M.; writing – original draft, B.H. and Z.Z.; writing – review and editing, T.F., N.M.P.S., K.R.H., A.P.M. and Z.L.

Conflict of Interest

A.P.M. is a scientific advisor or consultant for Novartis, eGENESIS, Trestle Biotherapeutics and IVIVA Medical. All other authors declare no competing interests.

Supplemental Material

Supplemental Information[supplements/542343_file02.pdf]
Video S1[supplements/542343_file03.mp4]
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Table S14[supplements/542343_file17.pdf]

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