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

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, identify-ing novel genes associated with kidney development and disease. A rapid, efficient, and scalable 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.

Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis

“…Together with the Hippo GSEA data ( Note S3 , Fig. S3E ) these data suggest that YAP activity is likely higher in nephron progenitors in post-branching niches – Yap signaling is required for nephron progenitor renewal 19,20,84 .…”

“…5A,B ). TRULI has recently been found to recruit YAP to the nucleus of iPSC-derived nephron progenitors and extend their long-term renewal in 2D culture, while retaining their nephron differentiation potential 84 . We verified that TRULI increases YAP nuclear recruitment and target gene expression ( CTGF , CYR61 ) in our day 10 nephron progenitors by immunofluorescence and qPCR respectively ( Fig.…”

“…S3E), and due to the known role of YAP in nephron progenitor decision-making. Namely, increased YAP signaling in vivo and in vitro appears to drive nephron progenitor renewal at the expense of differentiation, and vice versa (despite some conflicting observations) 19,20,22,[81][82][83][84] . According to our GeoMx analysis, Wnt/β-catenin activity is likely higher in nephron progenitors in pre-/mid-branching niches, while Hippo signaling transcripts were enriched in mid-branching niches.…”

“…Other genes with potential life-cycle dependence include the TGFβ superfamily members or associated genes Bmp7 (involved in nephron progenitor proliferation 24 and priming 23 ) and Tgfbi (a secreted collagenassociated protein thought to interact with the ECM 51,71 ); and the Yap-dependent genes Traf1 and Capn6 (thought to be involved in microtubule and actin cytoskeletal organization) 19,135 . Yap signaling is required for nephron progenitor renewal 19,20,82 . Note S5.…”