Kidney Organoid Modeling of WT1 Mutations Reveals Key Regulatory Paths Underlying Podocyte Development.

Wilms tumor-1(WT1) is a crucial transcription factor that regulates podocyte development. However, the epigenomic mechanism underlying the function of WT1 during podocyte development has yet to be fully elucidated. Here, single-cell chromatin accessibility and gene expression maps of foetal kidneys and kidney organoids are generated. Functional implications of WT1-targeted genes, which are crucial for the development of podocytes and the maintenance of their structure, including BMPER/PAX2/MAGI2 that regulates WNT signaling pathway, MYH9 that maintains actin filament organization and NPHS1 that modulates cell junction assembly are identified. To further illustrate the functional importance of WT1-mediated transcriptional regulation during podocyte development, cultured and implanted patient-derived kidney organoids derived from the Induced Pluripotent Stem Cell (iPSCs) of a patient with a heterozygous missense mutation in WT1 are generated. Results from single-cell RNA sequencing (scRNA-seq) and functional assays confirm that the WT1 mutation leads to delays in podocyte development and causes damage to cell structures, due to its failure to activate the targeting genes MAGI2, MYH9, and NPHS1. Notably, correcting the mutation in the patient iPSCs using CRISPR-Cas9 gene editing rescues the podocyte phenotype. Collectively, this work elucidates the WT1-related epigenomic landscape with respect to human podocyte development and identifies the disease-causing role of a WT1 mutation.

Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids.

Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.

Generating Kidney Organoids in Suspension from Induced Pluripotent Stem Cells.

Kidney organoids can be generated from induced pluripotent stem cells (iPSCs) through various approaches. These organoids hold great promise for disease modeling, drug screening, and potential therapeutic applications. This article presents a step-by-step procedure to create kidney organoids from iPSCs, starting from the posterior primitive streak (PS) to the intermediate mesoderm (IM). The approach relies on the APEL 2 medium, which is a defined, animal component-free medium. It is supplemented with a high concentration of WNT agonist (CHIR99021) for a duration of 4 days, followed by fibroblast growth factor 9 (FGF9)/heparin and a low concentration of CHIR99021 for an additional 3 days. During this process, emphasis is given to selecting the optimal cell density and CHIR99021 concentration at the start of iPSCs, as these factors are critical for successful kidney organoid generation. An important aspect of this protocol is the suspension culture in a low adherent plate, allowing the IM to gradually develop into nephron structures, encompassing glomerular, proximal tubular, and distal tubular structures, all presented in a visually comprehensible format. Overall, this detailed protocol offers an efficient and specific technique to produce kidney organoids from diverse iPSCs, ensuring successful and consistent results.

Establishment of the induced pluripotent stem cell line (NCKDi005-A) from a male patient with Alport syndrome carrying a homozygous frameshift mutation in the COL4A4 gene.

Alport syndrome is an inherited chronic kidney disease with genetic heterogeneity. There are three modes of inheritance: X-linked dominant inheritance, autosomal recessive inheritance, and autosomal dominant inheritance. Autosomal recessive inheritance accounts for about 14%-15% of all cases of Alport syndrome and is caused by the COL4A3 or COL4A4 gene mutation. In this study, the peripheral blood mononuclear cells (PBMCs) of a patient with a novel COL4A4 homozygous mutation were reprogrammed into an induced pluripotent stem cell (iPSC) line. The iPSC line can provide a cell model for studying the pathogenesis of the disease and drug screening.

Generation of the induced pluripotent stem cell line (NCKDi004-A) from a 17-year-old patient with Alport syndrome carrying a homozygous mutation in COL4A3 gene.

Alport syndrome is the second most common genetic renal disease which caused by mutations in COL4A3/COL4A4/COL4A5, according to different modes of inheritance. Recently, we identified a novel homozygous mutation in COL4A3 gene in a patient with Alport syndrome. The Peripheral Blood Mononuclear Cells (PBMCs) of the patient were obtained and a line of induced pluripotent stem cells (iPSCs) was successfully generated. The iPSC line will be useful for further study of the pathogenesis and drug screening for Alport syndrome.

Establishment of an induced pluripotent stem cell line (NCKDi003-A) from a patient with X-linked Dent disease (X-Dent) carrying the hemizygote mutation p. T277P (c. 829A > C) in the CLCN5 gene.

Dent disease (DD) is a rare X-linked proximal tubulopathy associated with low molecular weight proteinuria (LMWP), hypercalciuria, nephrolithiasis and phosphoruria, which may progress to chronic kidney disease (CKD). About 60% of cases are caused by the mutation in CLCN5 gene. Recently, we identified a mutation in the sequence of homodimer of CLCN5 gene in a patient with DD. The Peripheral Blood Mononuclear Cells (PBMCs) of the patient were obtained and a line of induced pluripotent stem cells (iPSCs) was successfully generated. The iPSC line will be useful for further study of the pathogenesis and drug screening for DD.

Generation of an induced pluripotent stem cell line (ZJUi007-A) from a 11-year-old patient of Fabry disease.

PBMCs were collected from a patient with a novel GLA gene mutation (c.140G > A) which contributed to Fabry disease. Subsequently, an induced pluripotent stem cell (iPSC) line was derived using an episomal reprogramming method that transfer the reprogramming plasmids expressing OCT3/4, SOX2, KLF4, LIN28 and L-MYC into the PBMCs. The expected mutation in the iPSC line was confirmed by Sanger sequencing, while the pluripotency status was validated by immunofluorescence assay and flow cytometry for pluripotency markers, as well as teratoma formation.

Generation of the induced pluripotent stem cell line (NCKDi002-A) from a 22-year-old patient with Focal Segmental Glomerular Sclerosis carrying a heterozygous mutation in WT1 gene.

Focal Segmental Glomerular Sclerosis (FSGS) is a glomerular disease which can be classified into primary, secondary, genetic, and unknown forms. WT1 mutation has been shown to be associated with this disorder. Recently, we identified a mutation in the Zinc finger C2H2 domain of WT1 gene in a patient with FSGS who also carried a family history of end-stage renal disease (ESRD). The Peripheral Blood Mononuclear Cells (PBMCs) of the patient were obtained and a line of induced pluripotent stem cells (iPSCs) was successfully generated. The iPSC line will be useful for further study of the pathogenesis and drug screening for FSGS.

Generation of induced pluripotent stem cell line (NCKDi001-A) from a 19-year-old patient with a novel COL4A5 gene mutation in Alport syndrome.

The clinical manifestations of Alport syndrome may vary depending on the involved organs such as the kidneys, cochlea and eyes. The pathogenic genes involved are those encoding different chains of type IV collagen. We collected PBMCs of a patient with a novel COL4A5 gene mutation(c.2687G > C). Subsequently, we used the electroporation system to transfer the reprogramming plasmids expressing OCT3/4, SOX2, KLF4, LIN28 and L-MYC into the PBMCs. We simultaneously carried out the tests on the iPSCs including Sanger sequencing for confirming the mutation site, immunofluorescence assay and flow cytometry for pluripotency markers as well as teratoma experiment for validating the pluripotency.

The clinical characteristics of Chinese patients with unilateral renal agenesis.

BACKGROUND: We aimed to investigate the clinical characteristics of Chinese patients with unilateral renal agenesis. METHODS: We enrolled patients with unilateral renal agenesis diagnosed radiologically at the Department of Nephrology from January 2008 to January 2016. Patients with a solitary kidney due to nephrectomy or renal atrophy due to secondary factors were excluded. Clinical data were recorded and analyzed. RESULTS: In this study, 118 Chinese patients with unilateral renal agenesis were recruited, and the gender ratio (male/female) was 1.11:1. A total of 14 (11.9%) patients had additional abnormalities, 15 (12.7%) had a family history, and 30 (25.4%) presented with renal insufficiency. Kidney length, serum creatinine level and estimated glomerular filtration rate were significantly different between patients with and without family history (P < 0.05, respectively). Gender showed a significant difference between patients with and without other abnormalities. Kidney length and the incidence of proteinuria, hematuria, hypertension, and hyperuricemia were significantly different between patients with and without renal insufficiency. Logistic regression analysis revealed that family history was associated with severe renal failure (OR = 7.11, 95% CI 1.52-33.25). CONCLUSION: Renal insufficiency is common in patients with unilateral renal agenesis. Patients with renal insufficiency have shorter kidney lengths and a higher incidence of proteinuria, hypertension, hematuria, and hyperuricemia. Family history is considered a risk factor for severe renal failure.

Identification of 8 Novel Mutations in Nephrogenesis-Related Genes in Chinese Han Patients with Unilateral Renal Agenesis.

BACKGROUND: Few genetic studies have focused on unilateral renal agenesis (URA), which is a disorder with insidious clinical manifestations and a tendency to result in renal failure. We aimed to detect pathogenic mutations in nephrogenesis-related genes, which were identified by a literature review conducted among a large cohort of Chinese Han patients with URA. METHODS: Totally, 86 unrelated URA patients were included. All URA patients were diagnosed by employing radiological methods. Patients with a solitary kidney owing to nephrectomy or renal atrophy due to secondary factors were excluded. Nine (10.5%) patients had a family history of abnormal nephrogenesis. Fifteen (17.4%) had other malformations in the urogenital system. All coding exons and adjacent intron regions of 25 genes were analyzed using next-generation sequencing and validated by Sanger sequencing and 100 ethnically matched healthy controls. RESULTS: Ten conserved mutations (9 missense mutations and 1 deletion mutation) were identified in SALL1, EYA1, RET, HNF1B, DSTYK, WNT4, and SIX5. All mutations were novel or rare (frequency <0.1%) in the public databases and absent from the 100 healthy controls. Nine patients carried mutations in candidate genes. Most of the patients carried one single heterozygous mutation, except for 2, who respectively carried compound heterozygous mutations and 2 single heterozygous mutations. In addition, 2 patients shared the same mutation in DSTYK. CONCLUSION: A total of 10.5% of our URA cases could be explained by mutations in our candidate genes. The mutations in nephrogenesis-related genes in the Chinese Han patients with URA had a decentralized distribution without any hotspot mutations.