A single-cell multiomic analysis of kidney organoid differentiation

Abstract

Kidney organoids differentiated from pluripotent stem cells are powerful models of kidney development and disease but are characterized by cell immaturity and off-target cell fates. Comparing the cell-specific gene regulatory landscape during organoid differentiation with human adult kidney can serve to benchmark progress in differentiation at the epigenome and transcriptome level for individual organoid cell types. Using single-cell multiome and histone modification analysis, we report more broadly open chromatin in organoid cell types compared to the human adult kidney. We infer enhancer dynamics by cis-coaccessibility analysis and validate an enhancer driving transcription of HNF1B by CRISPR interference both in cultured proximal tubule cells and also during organoid differentiation. Our approach provides an experimental framework to judge the cell-specific maturation state of human kidney organoids and shows that kidney organoids can be used to validate individual gene regulatory networks that regulate differentiation.

Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids

“…To elucidate transcription the top factors (TFs) regulating human PT, we analyzed single-cell multiome datasets that measured single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin with sequenc-ing generated from either human adult kidneys 39 or human kidney organoids. 40 The TFs with combined high gene expression and motif accessibility in the PT are listed (Figure 1, A and B, Supplemental Tables 1 and 2). HNF4A and HNF4G were the highest ranked TFs in both human adult kidneys and kidney organoids.…”

The chromatin landscape of healthy and injured cell types in the human kidney

“…In one study, reduced accessibility of glucocorticoid receptor binding sites was observed in the proximal tubule of diabetic humans 15 . Investigations have also examined chromatin accessibility in human Papillary RCC (pRCC), kidney organoid differentiation 5 , 17 , 18 , and in multiple murine models 19 , 20 . Each of these studies provides important insights into epigenetic expression regulation in the kidney.…”