Identifying Kidney Cell Phenotype Factors Using Single Cell RNA Sequencing

Key Personnel

Junhyong Kim (PI)
University of Pennsylvania

James Eberwine (PI)
University of Pennsylvania

  • Susanna Nazarian
    University of Pennsylvania

Project Description

The goal of the Penn project is to develop molecular biology and informatics tools to identify key regulatory factors that determine kidney cell phenotypes. Single cell resolution transcriptome data can reveal cryptic cell types as well as help identify regulatory systems related to cell phenotypes. We hypothesize that cell phenotype determining genes are often at low to moderate abundance in a cell, making them difficult to approach using current methods. The Penn group will develop novel molecular biology techniques to enrich single cell transcriptomes for low abundance genes. We will also develop informatics tools that will help identify targets for trans-differentiation experiments, leveraging single cell level measurements.


  1. In Vivo Developmental Trajectories of Human Podocyte Inform In Vitro Differentiation of Pluripotent Stem Cell-Derived Podocytes.

    Tran, Tracy; Lindstrom, Nils O.; Ransick, Andrew; De Sena Brandine, Guilherme; Guo, Qiuyu; Kim, Albert D.; Der, Balint; Peti-Peterdi, Janos; Smith, Andrew D.; Thornton, Matthew; Grubbs, Brendan; McMahon, Jill A.; McMahon, Andrew P. Dev Cell. 50(1):102–116.e6. July 2019.

    The renal corpuscle of the kidney comprises a glomerular vasculature embraced by podocytes and supported by mesangial myofibroblasts, which ensure plasma filtration at the podocyte-generated slit diaphragm. With a spectrum of podocyte-expressed gene mutations causing chronic disease, an enhanced understanding of podocyte development and function to create relevant in vitro podocyte models is a clinical imperative. To characterize podocyte development, scRNA-seq was performed on human fetal kidneys, identifying distinct transcriptional signatures accompanying the differentiation of functional podocytes from progenitors. Interestingly, organoid-generated podocytes exhibited highly similar, progressive transcriptional profiles despite an absence of the vasculature, although abnormal gene expression was pinpointed in late podocytes. On transplantation into mice, organoid-derived podocytes recruited the host vasculature and partially corrected transcriptional profiles. Thus, human podocyte development is mostly intrinsically regulated and vascular interactions refine maturation. These studies support the application of organoid-derived podocytes to model disease and to restore or replace normal kidney functions.

  2. Polycystin 2 regulates mitochondrial Ca(2+) signaling, bioenergetics, and dynamics through mitofusin 2.

    Kuo, Ivana Y.; Brill, Allison L.; Lemos, Fernanda O.; Jiang, Jason Y.; Falcone, Jeffrey L.; Kimmerling, Erica P.; Cai, Yiqiang; Dong, Ke; Kaplan, David L.; Wallace, Darren P.; Hofer, Aldebaran M.; Ehrlich, Barbara E. Sci Signal. 12(580). May 2019.

    Mitochondria and the endoplasmic reticulum (ER) have an intimate functional relationship due to tethering proteins that bring their membranes in close (~30 nm) apposition. One function of this interorganellar junction is to increase the efficiency of Ca(2+) transfer into mitochondria, thus stimulating mitochondrial respiration. Here, we showed that the ER cation-permeant channel polycystin 2 (PC2) functions to reduce mitochondria-ER contacts. In cell culture models, PC2 knockdown led to a 50% increase in mitofusin 2 (MFN2) expression, an outer mitochondrial membrane GTPase. Live-cell super-resolution and electron microscopy analyses revealed enhanced MFN2-dependent tethering between the ER and mitochondria in PC2 knockdown cells. PC2 knockdown also led to increased

  3. Scaffolding kidney organoids on silk.

    Gupta, Ashwani Kumar; Coburn, Jeannine M.; Davis-Knowlton, Jessica; Kimmerling, Erica; Kaplan, David L.; Oxburgh, Leif. J Tissue Eng Regen Med. 13(5):812–822. May 2019.

    End stage kidney disease affects hundreds of thousands of patients in the United States. The therapy of choice is kidney replacement, but availability of organs is limited, and alternative sources of tissue are needed. Generation of new kidney tissue in the laboratory has been made possible through pluripotent cell reprogramming and directed differentiation. In current procedures, aggregates of cells known as organoids are grown either submerged or at the air-liquid interface. These studies have demonstrated that kidney tissue can be generated from pluripotent stem cells, but they also identify limitations. The first is that perfusion of cell aggregates is limited, restricting the size to which they can be grown. The second is that aggregates lack the structural integrity required for convenient engraftment and suturing or adhesion to regions of kidney injury. In this study, we evaluated the capacity of silk to serve as a support for the growth and differentiation of kidney tissue from primary cells and from human induced pluripotent stem cells. We find that cells can differentiate to epithelia characteristic of the developing kidney on this material and that these structures are maintained following engraftment under the capsule of the adult kidney. Blood vessel investment can be promoted by the addition of vascular endothelial growth factor to the scaffold, but the proliferation of stromal cells within the graft presents a challenge, which will require some readjustment of cell growth and differentiation conditions. In summary, we find that silk can be used to support growth of stem cell derived kidney tissue.

  4. Renal reabsorption in 3D vascularized proximal tubule models

    Lin, Neil Y. C.; Homan, Kimberly A.; Robinson, Sanlin S.; Kolesky, David B.; Duarte, Nathan; Moisan, Annie; Lewis, Jennifer A. Proceedings of the National Academy of Sciences. 116(12):5399–5404. 2019.

    Current kidney-on-chip models lack the 3D geometry, complexity, and functionality vital for recapitulating in vivo renal tissue. We report the fabrication and perfusion of 3D vascularized proximal tubules embedded within an engineered ECM that exhibit active reabsorption of solutes via tubular–vascular exchange. Using this model, we quantified albumin and glucose reabsorption over time. We also studied hyperglycemic effects in the absence and presence of a glucose transport inhibitor. Our 3D kidney tissue provides a platform for in vitro studies of kidney function, disease modeling, and pharmacology.Three-dimensional renal tissues that emulate the cellular composition, geometry, and function of native kidney tissue would enable fundamental studies of filtration and reabsorption. Here, we have created 3D vascularized proximal tubule models composed of adjacent conduits that are lined with confluent epithelium and endothelium, embedded in a permeable ECM, and independently addressed using a closed-loop perfusion system to investigate renal reabsorption. Our 3D kidney tissue allows for coculture of proximal tubule epithelium and vascular endothelium that exhibits active reabsorption via tubular–vascular exchange of solutes akin to native kidney tissue. Using this model, both albumin uptake and glucose reabsorption are quantified as a function of time. Epithelium–endothelium cross-talk is further studied by exposing proximal tubule cells to hyperglycemic conditions and monitoring endothelial cell dysfunction. This diseased state can be rescued by administering a glucose transport inhibitor. Our 3D kidney tissue provides a platform for in vitro studies of kidney function, disease modeling, and pharmacology.

  5. Flow-enhanced vascularization and maturation of kidney organoids in vitro

    Homan, Kimberly A.; Gupta, Navin; Kroll, Katharina T.; Kolesky, David B.; Skylar-Scott, Mark; Miyoshi, Tomoya; Mau, Donald; Valerius, M. Todd; Ferrante, Thomas; Bonventre, Joseph V.; Lewis, Jennifer A.; Morizane, Ryuji. Nature Methods. February 2019.

    Kidney organoids derived from human pluripotent stem cells have glomerular- and tubular-like compartments that are largely avascular and immature in static culture. Here we report an in vitro method for culturing kidney organoids under flow on millifluidic chips, which expands their endogenous pool of endothelial progenitor cells and generates vascular networks with perfusable lumens surrounded by mural cells. We found that vascularized kidney organoids cultured under flow had more mature podocyte and tubular compartments with enhanced cellular polarity and adult gene expression compared with that in static controls. Glomerular vascular development progressed through intermediate stages akin to those involved in the embryonic mammalian kidney’s formation of capillary loops abutting foot processes. The association of vessels with these compartments was reduced after disruption of the endogenous VEGF gradient. The ability to induce substantial vascularization and morphological maturation of kidney organoids in vitro under flow opens new avenues for studies of kidney development, disease, and regeneration.

  6. Conserved and Divergent Features of Human and Mouse Kidney Organogenesis.

    Lindström, NO; McMahon, JA; Guo, J; Tran, T; Guo, Q; Rutledge, E; Parvez, RK; Saribekyan, G; Schuler, RE; Liao, C; Kim, AD; Abdelhalim, A; Ruffins, SW; Thornton, ME; Basking, L; Grubbs, B; Kesselman, C; McMahon, AP. J Am Soc Nephrol. February 2018.

    Human kidney function is underpinned by approximately 1,000,000 nephrons, although the number varies substantially, and low nephron number is linked to disease. Human kidney development initiates around 4 weeks of gestation and ends around 34-37 weeks of gestation. Over this period, a reiterative inductive process establishes the nephron complement. Studies have provided insightful anatomic descriptions of human kidney development, but the limited histologic views are not readily accessible to a broad audience. In this first paper in a series providing comprehensive insight into human kidney formation, we examined human kidney development in 135 anonymously donated human kidney specimens. We documented kidney development at a macroscopic and cellular level through histologic analysis, RNA in situ hybridization, immunofluorescence studies, and transcriptional profiling, contrasting human development (4-23 weeks) with mouse development at selected stages (embryonic day 15.5 and postnatal day 2). The high-resolution histologic interactive atlas of human kidney organogenesis generated can be viewed at the GUDMAP database ( together with three-dimensional reconstructions of key components of the data herein. At the anatomic level, human and mouse kidney development differ in timing, scale, and global features such as lobe formation and progenitor niche organization. The data also highlight differences in molecular and cellular features, including the expression and cellular distribution of anchor gene markers used to identify key cell types in mouse kidney studies. These data will facilitate and inform in vitro efforts to generate human kidney structures and comparative functional analyses across mammalian species.

  7. Gene-Edited Human Kidney Organoids Reveal Mechanisms of Disease in Podocyte Development

    Kim, YK; Refaeli, I; Brooks, CR; Jing, P; Gulieva, RE; Hughes, MR; Cruz, NM; Liu, Y; Churchill, AJ; Wang, Y; Fu, H; Pippin, JW; Lin, LY; Shankland, SJ; Vogl, AW; McNagny, KM; Freedman, BS. Stem Cells. 35(12):2366–2378. December 2017.

    A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. hPSC-podocytes in vitro progressively establish junction-rich basal membranes (nephrin+ podocin+ ZO-1+ ) and microvillus-rich apical membranes (podocalyxin+ ), similar to CLS podocytes in vivo. Ultrastructural, biophysical, and transcriptomic analysis of podocalyxin-knockout hPSCs and derived podocytes, generated using CRISPR/Cas9, reveals defects in the assembly of microvilli and lateral spaces between developing podocytes, resulting in failed junctional migration. These defects are phenocopied in CLS glomeruli of podocalyxin-deficient mice, which cannot produce urine, thereby demonstrating that podocalyxin has a conserved and essential role in mammalian podocyte maturation. Defining the maturity of hPSC-podocytes and their capacity to reveal and recapitulate pathophysiological mechanisms establishes a powerful framework for studying human kidney disease and regeneration. Stem Cells 2017;35:2366-2378