Project description:This dataset serves as comparison for PXD029718 using a different organoid differentiation protocol – as requested by reviewers. Kidney organoids are a promising model to study kidney disease, but use is constrained by limited knowledge of their functional protein expression profile. We aimed to define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increased deposition of extracellular matrix but decreased expression of glomerular proteins. Single cell transcriptome integration revealed that most proteome changes localized to podocytes, tubular and stromal cells. TNFα-treatment of organoids effected 320 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 320 proteins was significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression was increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing to human data, we provide crucial evidence of functional relevance of the kidney organoid model to human kidney disease.
Project description:To reveal the key pathways involved in kidney cystogenesis. We performed single nuclei gene expression and ATAC profiling using kidney organoids from ARPKD patients-iPSCs derived organoids.
Project description:Safety issues of human iPSC-derived kidney organoids as a regenerative therapy need to be evaluated. Therefore, we studied the immunogenicity of human iPSC-derived kidney organoids. We subcutaneously implanted kidney organoids in immune-deficient IL2Ry-/-RAG2-/- mice for 1 month and hereafter performed adoptive transfer of healthy allogeneic human PBMC. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of kidney organoid cells and immune cell profiles. We investigated whether innate and adaptive immune cells invade kidney organoids, evoke an immune response, and influence the kidney organoid differentiation and functional capacity. Understanding the immunogenicity of kidney organoids will advance studies in the applicability of kidney organoids for regenerative medicine. Furthermore, it can serve as an in-vivo transplantation model to study solid organ transplantation.
Project description:Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human ESCs and iPSCs reprogrammed from a family with HNF1B-asscociated DKMs. Mutant organoids contained enlarged malformed tubules and displayed deregulated cell turnover. This submission contains kidney tissue samples.