Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease

Creators: Huang, Biao¹; Zeng, Zipeng¹; Kim, Sunghyun¹; Fausto, Connor C.¹; Koppitch, Kari¹; Li, Hui¹; Li, Zexu²; Chen, Xi¹; Guo, Jinjin¹; Zhang, Chennan C.¹; Ma, Tianyi¹; Medina, Pedro¹; Schreiber, Megan E.¹; Xia, Mateo W.¹; Vonk, Ariel C.¹; Xiang, Tianyuan¹; Patel, Tadrushi¹; Li, Yidan¹; Parvez, Riana K.¹; Der, Balint^{1, 3}; Chen, Jyun Hao¹; Liu, Zhenqing⁴; Thornton, Matthew E.¹; Grubbs, Brendan H.¹; Diao, Yarui⁵; Dou, Yali¹; Gnedeva, Ksenia¹; Ying, Qilong¹; Pastor-Soler, Nuria M.¹; Fei, Teng²; Hallows, Kenneth R.¹; Lindström, Nils O.¹; McMahon, Andrew P.¹; Li, Zhongwei¹

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

Abstract

Nephron progenitor cells (NPCs) self-renew and differentiate into nephrons, the functional units of the kidney. Here, manipulation of p38 and YAP activity allowed for long-term clonal expansion of primary mouse and human NPCs and induced NPCs (iNPCs) from human pluripotent stem cells (hPSCs). Molecular analyses demonstrated that cultured iNPCs closely resemble primary human NPCs. iNPCs generated nephron organoids with minimal off-target cell types and enhanced maturation of podocytes relative to published human kidney organoid protocols. Surprisingly, the NPC culture medium uncovered plasticity in human podocyte programs, enabling podocyte reprogramming to an NPC-like state. Scalability and ease of genome editing facilitated genome-wide CRISPR screening in NPC culture, uncovering genes associated with kidney development and disease. Further, NPC-directed modeling of autosomal-dominant polycystic kidney disease (ADPKD) identified a small-molecule inhibitor of cystogenesis. These findings highlight a broad application for the reported iNPC platform in the study of kidney development, disease, plasticity, and regeneration.

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Acknowledgement

We would like to thank the USC Flow Cytometry Facility, USC Optical Imaging Facility, Children’s Hospital Los Angeles Molecular Pathology Genomics Core, and USC Norris Medical Library Bioinformatics Service for data collection; Dr. Melissa L. Wilson (Department of Preventive Medicine, USC) 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, KSOM Dean’s Pilot Award, and NIH Director’s Award (DP2DK135739) to Zhongwei Li and NIH DK054364 and CZI seed network grant (CZIF2019-002430) 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. P.M. was supported by NIH T32 training grant (T32HD060549). M.W.X. was supported by USC Provost’s Undergrad Research Fellowship.

Funding

This work was supported by UKRO foundation funding, KSOM Dean’s Pilot Award, and NIH Director’s Award (DP2DK135739) to Zhongwei Li and NIH DK054364 and CZI seed network grant (CZIF2019-002430) 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. P.M. was supported by NIH T32 training grant (T32HD060549). M.W.X. was supported by USC Provost’s Undergrad Research Fellowship.

Contributions

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

Data Availability

Supplemental information can be found online at https://doi.org/10.1016/j.stem.2024.04.002.

Conflict of Interest

A.P.M. is a scientific advisor or consultant for Novartis, eGENESIS, Trestle Biotherapeutics, GentiBio, and IVIVA Medical. Zhongwei Li, B.H., Z.Z., A.P.M., K.R.H., and N.M.P.-S. have applied for intellectual property protection on the technologies discussed here.

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