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Börner K, Blood PD, Silverstein JC, Ruffalo M, Teichmann SA, Pryhuber G, Misra R, Purkerson J, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber G, Jain Y, Qaurooni D, Kong Y, Bueckle A, Herr BW. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587041. [PMID: 38826261 PMCID: PMC11142047 DOI: 10.1101/2024.03.27.587041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials. Experts from more than 20 consortia are collaborating to construct the HRA's Common Coordinate Framework (CCF), knowledge graphs, and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes, and biomarkers) and to use the HRA to understand changes that occur at each of these levels with aging, disease, and other perturbations. The 6th release of the HRA v2.0 covers 36 organs with 4,499 unique anatomical structures, 1,195 cell types, and 2,089 biomarkers (e.g., genes, proteins, lipids) linked to ontologies. In addition, three workflows were developed to map new experimental data into the HRA's CCF. This paper describes the HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interface (APIs), flexible hybrid cloud infrastructure, and demonstrates first atlas usage applications and previews.
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Affiliation(s)
- Katy Börner
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
- CIFAR MacMillan Multiscale Human program, CIFAR, Toronto, ON, Canada
| | - Philip D. Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan C. Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew Ruffalo
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sarah A. Teichmann
- CIFAR MacMillan Multiscale Human program, CIFAR, Toronto, ON, Canada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Ravi Misra
- University of Rochester Medical Center, Rochester, NY, USA
| | | | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
| | - John W. Hickey
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yashvardhan Jain
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Danial Qaurooni
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Yongxin Kong
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | | | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Bruce W. Herr
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
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Jain S, Eadon MT. Spatial transcriptomics in health and disease. Nat Rev Nephrol 2024:10.1038/s41581-024-00841-1. [PMID: 38719971 DOI: 10.1038/s41581-024-00841-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2024] [Indexed: 07/05/2024]
Abstract
The ability to localize hundreds of macromolecules to discrete locations, structures and cell types in a tissue is a powerful approach to understand the cellular and spatial organization of an organ. Spatially resolved transcriptomic technologies enable mapping of transcripts at single-cell or near single-cell resolution in a multiplex manner. The rapid development of spatial transcriptomic technologies has accelerated the pace of discovery in several fields, including nephrology. Its application to preclinical models and human samples has provided spatial information about new cell types discovered by single-cell sequencing and new insights into the cell-cell interactions within neighbourhoods, and has improved our understanding of the changes that occur in response to injury. Integration of spatial transcriptomic technologies with other omics methods, such as proteomics and spatial epigenetics, will further facilitate the generation of comprehensive molecular atlases, and provide insights into the dynamic relationships of molecular components in homeostasis and disease. This Review provides an overview of current and emerging spatial transcriptomic methods, their applications and remaining challenges for the field.
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Affiliation(s)
- Sanjay Jain
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| | - Michael T Eadon
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
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Nerger BA, Sinha S, Lee NN, Cheriyan M, Bertsch P, Johnson CP, Mahadevan L, Bonventre JV, Mooney DJ. 3D Hydrogel Encapsulation Regulates Nephrogenesis in Kidney Organoids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308325. [PMID: 38180232 PMCID: PMC10994733 DOI: 10.1002/adma.202308325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Stem cell-derived kidney organoids contain nephron segments that recapitulate morphological and functional aspects of the human kidney. However, directed differentiation protocols for kidney organoids are largely conducted using biochemical signals to control differentiation. Here, the hypothesis that mechanical signals regulate nephrogenesis is investigated in 3D culture by encapsulating kidney organoids within viscoelastic alginate hydrogels with varying rates of stress relaxation. Tubular nephron segments are significantly more convoluted in kidney organoids differentiated in encapsulating hydrogels when compared with those in suspension culture. Hydrogel viscoelasticity regulates the spatial distribution of nephron segments within the differentiating kidney organoids. Consistent with these observations, a particle-based computational model predicts that the extent of deformation of the hydrogel-organoid interface regulates the morphology of nephron segments. Elevated extracellular calcium levels in the culture medium, which can be impacted by the hydrogels, decrease the glomerulus-to-tubule ratio of nephron segments. These findings reveal that hydrogel encapsulation regulates nephron patterning and morphology and suggest that the mechanical microenvironment is an important design variable for kidney regenerative medicine.
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Affiliation(s)
- Bryan A. Nerger
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Sumit Sinha
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan N. Lee
- Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Maria Cheriyan
- Harvard College, Harvard University, Cambridge, MA 02138, USA
| | - Pascal Bertsch
- Radboud University Medical Center, Department of Dentistry – Regenerative Biomaterials, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | - Christopher P. Johnson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - L. Mahadevan
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph V. Bonventre
- Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David J. Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Su XT, Reyes JV, Lackey AE, Demirci H, Bachmann S, Maeoka Y, Cornelius RJ, McCormick JA, Yang CL, Jung HJ, Welling PA, Nelson JW, Ellison DH. Enriched Single-Nucleus RNA-Sequencing Reveals Unique Attributes of Distal Convoluted Tubule Cells. J Am Soc Nephrol 2024; 35:426-440. [PMID: 38238903 PMCID: PMC11000721 DOI: 10.1681/asn.0000000000000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/17/2023] [Indexed: 01/24/2024] Open
Abstract
SIGNIFICANCE STATEMENT High-resolution single-nucleus RNA-sequencing data indicate a clear separation between primary sites of calcium and magnesium handling within distal convoluted tubule (DCT). Both DCT1 and DCT2 express Slc12a3, but these subsegments serve distinctive functions, with more abundant magnesium-handling genes along DCT1 and more calcium-handling genes along DCT2. The data also provide insight into the plasticity of the distal nephron-collecting duct junction, formed from cells of separate embryonic origins. By focusing/changing gradients of gene expression, the DCT can morph into different physiological cell states on demand. BACKGROUND The distal convoluted tubule (DCT) comprises two subsegments, DCT1 and DCT2, with different functional and molecular characteristics. The functional and molecular distinction between these segments, however, has been controversial. METHODS To understand the heterogeneity within the DCT population with better clarity, we enriched for DCT nuclei by using a mouse line combining "Isolation of Nuclei Tagged in specific Cell Types" and sodium chloride cotransporter-driven inducible Cre recombinase. We sorted the fluorescently labeled DCT nuclei using Fluorescence-Activated Nucleus Sorting and performed single-nucleus transcriptomics. RESULTS Among 25,183 DCT cells, 75% were from DCT1 and 25% were from DCT2. In addition, there was a small population (<1%) enriched in proliferation-related genes, such as Top2a , Cenpp , and Mki67 . Although both DCT1 and DCT2 expressed sodium chloride cotransporter, magnesium transport genes were predominantly expressed along DCT1, whereas calcium, electrogenic sodium, and potassium transport genes were more abundant along DCT2. The transition between these two segments was gradual, with a transitional zone in which DCT1 and DCT2 cells were interspersed. The expression of the homeobox genes by DCT cells suggests that they develop along different trajectories. CONCLUSIONS Transcriptomic analysis of an enriched rare cell population using a genetically targeted approach clarifies the function and classification of distal cells. The DCT segment is short, can be separated into two subsegments that serve distinct functions, and is speculated to derive from different origins during development.
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Affiliation(s)
- Xiao-Tong Su
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Jeremiah V. Reyes
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Anne E. Lackey
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hasan Demirci
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Bachmann
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yujiro Maeoka
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Ryan J. Cornelius
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - James A. McCormick
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Chao-Ling Yang
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paul A. Welling
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan W. Nelson
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - David H. Ellison
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon
- Renal Section, VA Portland Healthcare System, Portland, Oregon
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Tabibzadeh N, Satlin LM, Jain S, Morizane R. Navigating the kidney organoid: insights into assessment and enhancement of nephron function. Am J Physiol Renal Physiol 2023; 325:F695-F706. [PMID: 37767571 PMCID: PMC10878724 DOI: 10.1152/ajprenal.00166.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Kidney organoids are three-dimensional structures generated from pluripotent stem cells (PSCs) that are capable of recapitulating the major structures of mammalian kidneys. As this technology is expected to be a promising tool for studying renal biology, drug discovery, and regenerative medicine, the functional capacity of kidney organoids has emerged as a critical question in the field. Kidney organoids produced using several protocols harbor key structures of native kidneys. Here, we review the current state, recent advances, and future challenges in the functional characterization of kidney organoids, strategies to accelerate and enhance kidney organoid functions, and access to PSC resources to advance organoid research. The strategies to construct physiologically relevant kidney organoids include the use of organ-on-a-chip technologies that integrate fluid circulation and improve organoid maturation. These approaches result in increased expression of the major tubular transporters and elements of mechanosensory signaling pathways suggestive of improved functionality. Nevertheless, continuous efforts remain crucial to create kidney tissue that more faithfully replicates physiological conditions for future applications in kidney regeneration medicine and their ethical use in patient care.NEW & NOTEWORTHY Kidney organoids are three-dimensional structures derived from stem cells, mimicking the major components of mammalian kidneys. Although they show great promise, their functional capacity has become a critical question. This review explores the advancements and challenges in evaluating and enhancing kidney organoid function, including the use of organ-on-chip technologies, multiomics data, and in vivo transplantation. Integrating these approaches to further enhance their physiological relevance will continue to advance disease modeling and regenerative medicine applications.
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Affiliation(s)
- Nahid Tabibzadeh
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
| | - Lisa M Satlin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Ryuji Morizane
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
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6
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Chuang T, Bejar J, Yue Z, Slavinsky M, Marciano D, Drummond I, Oxburgh L. In Vivo Assessment of Laboratory-Grown Kidney Tissue Grafts. Bioengineering (Basel) 2023; 10:1261. [PMID: 38002385 PMCID: PMC10669198 DOI: 10.3390/bioengineering10111261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Directed differentiation of stem cells is an attractive approach to generate kidney tissue for regenerative therapies. Currently, the most informative platform to test the regenerative potential of this tissue is engraftment into kidneys of immunocompromised rodents. Stem cell-derived kidney tissue is vascularized following engraftment, but the connection between epithelial tubules that is critical for urine to pass from the graft to the host collecting system has not yet been demonstrated. We show that one significant obstacle to tubule fusion is the accumulation of fibrillar collagens at the interface between the graft and the host. As a screening strategy to identify factors that can prevent this collagen accumulation, we propose encapsulating laboratory-grown kidney tissue in fibrin hydrogels supplemented with candidate compounds such as recombinant proteins, small molecules, feeder cells, and gene therapy vectors to condition the local graft environment. We demonstrate that the AAV-DJ serotype is an efficient gene therapy vector for the subcapsular region and that it is specific for interstitial cells in this compartment. In addition to the histological evaluation of epithelial tubule fusion, we demonstrate the specificity of two urine biomarker assays that can be used to detect human-specific markers of the proximal nephron (CD59) and the distal nephron (uromodulin), and we demonstrate the deposition of human graft-derived urine into the mouse collecting system. Using the testing platform described in this report, it will be possible to systematically screen factors for their potential to promote epithelial fusion of graft and host tissue with a functional intravital read-out.
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Affiliation(s)
| | | | - Zhiwei Yue
- The Rogosin Institute, New York, NY 10021, USA
| | | | - Denise Marciano
- Division of Nephrology, Department of Internal Medicine, Department of Cell Biology, University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Iain Drummond
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
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7
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Ibi Y, Nishinakamura R. Kidney Bioengineering for Transplantation. Transplantation 2023; 107:1883-1894. [PMID: 36717963 DOI: 10.1097/tp.0000000000004526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The kidney is an important organ for maintenance of homeostasis in the human body. As renal failure progresses, renal replacement therapy becomes necessary. However, there is a chronic shortage of kidney donors, creating a major problem for transplantation. To solve this problem, many strategies for the generation of transplantable kidneys are under investigation. Since the first reports describing that nephron progenitors could be induced from human induced pluripotent stem cells, kidney organoids have been attracting attention as tools for studying human kidney development and diseases. Because the kidney is formed through the interactions of multiple renal progenitors, current studies are investigating ways to combine these progenitors derived from human induced pluripotent stem cells for the generation of transplantable kidney organoids. Other bioengineering strategies, such as decellularization and recellularization of scaffolds, 3-dimensional bioprinting, interspecies blastocyst complementation and progenitor replacement, and xenotransplantation, also have the potential to generate whole kidneys, although each of these strategies has its own challenges. Combinations of these approaches will lead to the generation of bioengineered kidneys that are transplantable into humans.
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Affiliation(s)
- Yutaro Ibi
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
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Kim S, Koppitch K, Parvez RK, Guo J, Achieng M, Schnell J, Lindström NO, McMahon AP. Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540880. [PMID: 37293066 PMCID: PMC10245679 DOI: 10.1101/2023.05.16.540880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.
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Han M, Moon S, Lee S, Kim K, An WJ, Ryu H, Kang E, Ahn JH, Sung HY, Park YS, Lee SE, Lee SH, Jeong KH, Ahn C, Kelly TN, Hsu JY, Feldman HI, Park SK, Oh KH. Novel Genetic Variants Associated with Chronic Kidney Disease Progression. J Am Soc Nephrol 2023; 34:857-875. [PMID: 36720675 PMCID: PMC10125649 DOI: 10.1681/asn.0000000000000066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 12/11/2022] [Indexed: 02/02/2023] Open
Abstract
SIGNIFICANCE STATEMENT eGFR slope has been used as a surrogate outcome for progression of CKD. However, genetic markers associated with eGFR slope among patients with CKD were unknown. We aimed to identify genetic susceptibility loci associated with eGFR slope. A two-phase genome-wide association study identified single nucleotide polymorphisms (SNPs) in TPPP and FAT1-LINC02374 , and 22 of them were used to derive polygenic risk scores that mark the decline of eGFR by disrupting binding of nearby transcription factors. This work is the first to identify the impact of TPPP and FAT1-LINC02374 on CKD progression, providing predictive markers for the decline of eGFR in patients with CKD. BACKGROUND The incidence of CKD is associated with genetic factors. However, genetic markers associated with the progression of CKD have not been fully elucidated. METHODS We conducted a genome-wide association study among 1738 patients with CKD, mainly from the KoreaN cohort study for Outcomes in patients With CKD. The outcome was eGFR slope. We performed a replication study for discovered single nucleotide polymorphisms (SNPs) with P <10 -6 in 2498 patients with CKD from the Chronic Renal Insufficiency Cohort study. Several expression quantitative trait loci (eQTL) studies, pathway enrichment analyses, exploration of epigenetic architecture, and predicting disruption of transcription factor (TF) binding sites explored potential biological implications of the loci. We developed and evaluated the effect of polygenic risk scores (PRS) on incident CKD outcomes. RESULTS SNPs in two novel loci, TPPP and FAT1-LINC02374 , were replicated (rs59402340 in TPPP , Pdiscovery =7.11×10 -7 , PCRIC =8.13×10 -4 , Pmeta =7.23×10 -8 ; rs28629773 in FAT1-LINC02374 , Pdiscovery =6.08×10 -7 , PCRIC =4.33×10 -2 , Pmeta =1.87×10 -7 ). The eQTL studies revealed that the replicated SNPs regulated the expression level of nearby genes associated with kidney function. Furthermore, these SNPs were near gene enhancer regions and predicted to disrupt the binding of TFs. PRS based on the independently significant top 22 SNPs were significantly associated with CKD outcomes. CONCLUSIONS This study demonstrates that SNP markers in the TPPP and FAT1-LINC02374 loci could be predictive markers for the decline of eGFR in patients with CKD.
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Affiliation(s)
- Miyeun Han
- Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Sungji Moon
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sangjun Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Korea
| | - Kyungsik Kim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Korea
| | - Woo Ju An
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eunjeong Kang
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Korea
| | - Jung-Hyuck Ahn
- Department of Biochemistry, Ewha Womans University College of Medicine, Seoul, Korea
| | - Hye Youn Sung
- Department of Biochemistry, Ewha Womans University College of Medicine, Seoul, Korea
| | - Yong Seek Park
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Seung Eun Lee
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Sang-Ho Lee
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Kyung Hwan Jeong
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Curie Ahn
- Department of Internal Medicine, National Medical Center, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tanika N. Kelly
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Jesse Y. Hsu
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sue K. Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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Jain S. Conundrums of choice of 'normal' kidney tissue for single cell studies. Curr Opin Nephrol Hypertens 2023; 32:249-256. [PMID: 36811638 PMCID: PMC10073328 DOI: 10.1097/mnh.0000000000000875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
PURPOSE OF REVIEW Defining molecular changes in key kidney cell types across lifespan and in disease states is essential to understand the pathogenetic basis of disease progression and targeted therapies. Various single cell approaches are being applied to define disease associated molecular signatures. Key considerations include the choice of reference tissue or 'normal' for comparison to diseased human specimens and a benchmark reference atlas. We provide an overview of select single cell technologies, key considerations for experimental design, quality control, choices and challenges associated with assay type and source for reference tissue. RECENT FINDINGS Several initiatives including Kidney Precision Medicine Project, Human Biomolecular Molecular Atlas Project, Genitourinary Disease Molecular Anatomy Project, ReBuilding a Kidney consortium, Human Cell Atlas and Chan Zuckerburg Initiative are generating single cell atlases of 'normal' or disease kidney. Different sources of kidney tissue are used as reference. Signatures of injury, resident pathology and procurement associated biological and technical artifacts have been identified in human kidney reference tissue. SUMMARY Committing to a particular reference or 'normal' tissue has significant implications in interpretation of data from disease samples or in ageing. Voluntarily donated kidney tissue from healthy individuals is generally unfeasible. Having reference datasets for different types of 'normal' tissue can aid in mitigating the confounds of choice of reference tissue and sampling biases.
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Affiliation(s)
- Sanjay Jain
- Departments of Medicine, Pathology and Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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11
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Treacy NJ, Clerkin S, Davis JL, Kennedy C, Miller AF, Saiani A, Wychowaniec JK, Brougham DF, Crean J. Growth and differentiation of human induced pluripotent stem cell (hiPSC)-derived kidney organoids using fully synthetic peptide hydrogels. Bioact Mater 2023; 21:142-156. [PMID: 36093324 PMCID: PMC9420433 DOI: 10.1016/j.bioactmat.2022.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived kidney organoids have prospective applications ranging from basic disease modelling to personalised medicine. However, there remains a necessity to refine the biophysical and biochemical parameters that govern kidney organoid formation. Differentiation within fully-controllable and physiologically relevant 3D growth environments will be critical to improving organoid reproducibility and maturation. Here, we matured hiPSC-derived kidney organoids within fully synthetic self-assembling peptide hydrogels (SAPHs) of variable stiffness (storage modulus, G'). The resulting organoids contained complex structures comparable to those differentiated within the animal-derived matrix, Matrigel. Single-cell RNA sequencing (scRNA-seq) was then used to compare organoids matured within SAPHs to those grown within Matrigel or at the air-liquid interface. A total of 13,179 cells were analysed, revealing 14 distinct clusters. Organoid compositional analysis revealed a larger proportion of nephron cell types within Transwell-derived organoids, while SAPH-derived organoids were enriched for stromal-associated cell populations. Notably, differentiation within a higher G' SAPH generated podocytes with more mature gene expression profiles. Additionally, maturation within a 3D microenvironment significantly reduced the derivation of off-target cell types, which are a known limitation of current kidney organoid protocols. This work demonstrates the utility of synthetic peptide-based hydrogels with a defined stiffness, as a minimally complex microenvironment for the selected differentiation of kidney organoids.
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Affiliation(s)
- Niall J Treacy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Shane Clerkin
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Jessica L Davis
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Ciarán Kennedy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Aline F Miller
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Alberto Saiani
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Jacek K Wychowaniec
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dermot F Brougham
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - John Crean
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
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12
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Zhang PL, Macknis JK. Immunohistochemical Panels to Evaluate Important Immunophenotypes of Human Mesonephros. Fetal Pediatr Pathol 2023; 42:1-17. [PMID: 35289709 DOI: 10.1080/15513815.2022.2045402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Background. The immunophenotypes and potential excretory function of human mesonephros are not well studied. Methods. Five mesonephros specimens of human embryos from the 6th to 10th weeks of gestation were stained with immunohistochemical markers. Results. PAX8 was universally expressed in all renal tubules, while α-methyacyl-CoA racemase (AMACAR) was positive in proximal tubules and GATA3 was positive in distal tubular mesonephric structures. At the 8th weeks of gestation, the mesonephric glomeruli were characterized by opened glomerular capillary loops with Periodic Acid Schiff (PAS)-positive glomerular basement membranes and GATA3-positive mesangial-like cells. By the 8th week, proximal tubules showed PAS-positive brush borders, indicating reabsorption capacity, and the proximal tubules also demonstrated positivity with kidney injury molecule-1 (KIM-1), representing tubular response to injury. Conclusion. Our overall findings show detailed phenotypes of the glomerular and tubular structures of the mesonephros and indicate that at the 8th week of gestation, the mesonephros may carry out temporary excretory function before metanephros becomes fully functional.
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Affiliation(s)
- Ping L Zhang
- Division of Anatomic Pathology, Beaumont Labs, Beaumont Health, Royal Oak, MI, USA
| | - Jacqueline K Macknis
- Division of Anatomic Pathology, Beaumont Labs, Beaumont Health, Royal Oak, MI, USA
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13
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Hall ML, Givens S, Santosh N, Iacovino M, Kyba M, Ogle BM. Laminin 411 mediates endothelial specification via multiple signaling axes that converge on β-catenin. Stem Cell Reports 2022; 17:569-583. [PMID: 35120622 PMCID: PMC9039757 DOI: 10.1016/j.stemcr.2022.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/24/2022] Open
Abstract
The extracellular matrix (ECM) provides essential cues to promote endothelial specification during tissue development in vivo; correspondingly, ECM is considered essential for endothelial differentiation outside of the body. However, systematic studies to assess the precise contribution of individual ECM proteins to endothelial differentiation have not been conducted. Further, the multi-component nature of differentiation protocols makes it challenging to study the underlying mechanisms by which the ECM contributes to cell fate. In this study, we determined that Laminin 411 alone increases endothelial differentiation of induced pluripotent stem cells over collagen I or Matrigel. The effect of ECM was shown to be independent of vascular endothelial growth factor (VEGF) binding capacity. We also show that ECM-guided endothelial differentiation is dependent on activation of focal adhesion kinase (FAK), integrin-linked kinase (ILK), Notch, and β-catenin pathways. Our results indicate that ECM contributes to endothelial differentiation through multiple avenues, which converge at the expression of active β-catenin.
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Affiliation(s)
- Mikayla L Hall
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sophie Givens
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Natasha Santosh
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Michelina Iacovino
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Lillehei Heart Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Brenda M Ogle
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Lillehei Heart Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Institute for Engineering in Medicine, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA.
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14
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Cereceda K, Jorquera R, Villarroel-Espíndola F. Advances in mass cytometry and its applicability to digital pathology in clinical-translational cancer research. ADVANCES IN LABORATORY MEDICINE 2022; 3:5-29. [PMID: 37359436 PMCID: PMC10197474 DOI: 10.1515/almed-2021-0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/16/2021] [Indexed: 06/28/2023]
Abstract
The development and subsequent adaptation of mass cytometry for the histological analysis of tissue sections has allowed the simultaneous spatial characterization of multiple components. This is useful to find the correlation between the genotypic and phenotypic profile of tumor cells and their environment in clinical-translational studies. In this revision, we provide an overview of the most relevant hallmarks in the development, implementation and application of multiplexed imaging in the study of cancer and other conditions. A special focus is placed on studies based on imaging mass cytometry (IMC) and multiplexed ion beam imaging (MIBI). The purpose of this review is to help our readers become familiar with the verification techniques employed on this tool and outline the multiple applications reported in the literature. This review will also provide guidance on the use of IMC or MIBI in any field of biomedical research.
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Affiliation(s)
- Karina Cereceda
- Laboratorio de Medicina Traslacional, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - Roddy Jorquera
- Laboratorio de Medicina Traslacional, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - Franz Villarroel-Espíndola
- Laboratorio de Medicina Traslacional, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
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15
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Chimerism and tolerance: past, present and future strategies to prolong renal allograft survival. Curr Opin Nephrol Hypertens 2021; 30:63-74. [PMID: 33186221 DOI: 10.1097/mnh.0000000000000666] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Immunological factors are a major cause of kidney allograft loss. Calcineurin inhibitors (CNIs) have improved short-term kidney allograft survival; however, they in turn contribute to long-term kidney allograft loss from chronic CNI nephrotoxicity. Tolerance induction in transplantation can avoid the long-term adverse effects of immunosuppressive medications. This review aims to critically discuss recent efforts in inducing transplantation tolerance. RECENT FINDINGS Tolerance induction mediated by chimerism has shown some promise in minimizing or even complete withdrawal of immunosuppressive treatments in kidney allograft recipients. There has been a number of approaches as varied as the number of centres conducting these trials. However, they can be grouped into those mediated by transient microchimerism and those facilitated by more stable macro or full donor chimerism. The success rates in terms of long-term drug-free graft survival has been limited in microchimerism-mediated tolerance induction approaches. Mixed macrochimerism of less than 50% donor may be unstable with mostly the recipient's native immune system overpowering the donor chimeric status.Tolerance induction leading to chimerism has been limited to living donor kidney transplantation and additional long-term outcomes are required. Furthermore, immune monitoring after tolerance induction has faced a limitation in studying due to a lack of sufficient study participants and appropriate study controls. SUMMARY Tolerance induction is one of several strategies used to prolong kidney allograft survival, but it has not been routinely utilized in clinical practice. However, future applications from the trials to clinical practice remain limited to living donor kidney transplantation. Once further data regarding tolerance inductions exist and practicality becomes widely accepted, tolerance induction may shift the paradigm in the field of kidney transplantation to achieve the best possible outcome of 'One Organ for Life'.
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16
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Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol 2021; 23:1117-1128. [PMID: 34750582 PMCID: PMC10079270 DOI: 10.1038/s41556-021-00788-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked parts of the HRA: (1) three-dimensional representations of anatomy that are linked to (2) tables that name and interlink major anatomical structures, cell types, plus biomarkers (ASCT+B). We discuss four examples that demonstrate the practical utility of the HRA.
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Affiliation(s)
- Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen Browne
- Department of Health and Human Services, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Bruce W Herr
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Hrishikesh Paul
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Shin Lin
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Avinash Boppana
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Teri A Longacre
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - John Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yiing Lin
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - M Todd Valerius
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yongqun He
- Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Xin Sun
- Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Marda Jorgensen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Andrea J Radtke
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Clive Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Fiona Ginty
- Biology and Applied Physics, General Electric Research, Niskayuna, NY, USA
| | - Jonhan Ho
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel Sunshine
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca T Beuschel
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Rajeev Malhotra
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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17
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Shankland SJ, Wang Y, Shaw AS, Vaughan JC, Pippin JW, Wessely O. Podocyte Aging: Why and How Getting Old Matters. J Am Soc Nephrol 2021; 32:2697-2713. [PMID: 34716239 PMCID: PMC8806106 DOI: 10.1681/asn.2021050614] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/26/2021] [Indexed: 02/04/2023] Open
Abstract
The effects of healthy aging on the kidney, and how these effects intersect with superimposed diseases, are highly relevant in the context of the population's increasing longevity. Age-associated changes to podocytes, which are terminally differentiated glomerular epithelial cells, adversely affect kidney health. This review discusses the molecular and cellular mechanisms underlying podocyte aging, how these mechanisms might be augmented by disease in the aged kidney, and approaches to mitigate progressive damage to podocytes. Furthermore, we address how biologic pathways such as those associated with cellular growth confound aging in humans and rodents.
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Affiliation(s)
- Stuart J. Shankland
- Division of Nephrology, University of Washington, Seattle, Washington
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
| | - Yuliang Wang
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Andrey S. Shaw
- Department of Research Biology, Genentech, South San Francisco, California
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Jeffrey W. Pippin
- Division of Nephrology, University of Washington, Seattle, Washington
| | - Oliver Wessely
- Lerner Research Institute, Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, Ohio
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18
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Gupta AK, Ivancic DZ, Naved BA, Wertheim JA, Oxburgh L. An efficient method to generate kidney organoids at the air-liquid interface. J Biol Methods 2021; 8:e150. [PMID: 34258308 PMCID: PMC8270790 DOI: 10.14440/jbm.2021.357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/23/2022] Open
Abstract
The prevalence of kidney dysfunction continues to increase worldwide, driving the need to develop transplantable renal tissues. The kidney develops from four major renal progenitor populations: nephron epithelial, ureteric epithelial, interstitial and endothelial progenitors. Methods have been developed to generate kidney organoids but few or dispersed tubular clusters within the organoids hamper its use in regenerative applications. Here, we describe a detailed protocol of asynchronous mixing of kidney progenitors using organotypic culture conditions to generate kidney organoids tightly packed with tubular clusters and major renal structures including endothelial network and functional proximal tubules. This protocol provides guidance in the culture of human embryonic stem cells from a National Institute of Health-approved line and their directed differentiation into kidney organoids. Our 18-day protocol provides a rapid method to generate kidney organoids that facilitate the study of different nephrological events including in vitro tissue development, disease modeling and chemical screening. However, further studies are required to optimize the protocol to generate additional renal-specific cell types, interconnected nephron segments and physiologically functional renal tissues.
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Affiliation(s)
- Ashwani Kumar Gupta
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - David Z. Ivancic
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bilal A. Naved
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jason A. Wertheim
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Surgery, Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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19
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Balzer MS, Ma Z, Zhou J, Abedini A, Susztak K. How to Get Started with Single Cell RNA Sequencing Data Analysis. J Am Soc Nephrol 2021; 32:1279-1292. [PMID: 33722930 PMCID: PMC8259643 DOI: 10.1681/asn.2020121742] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the last 5 years, single cell methods have enabled the monitoring of gene and protein expression, genetic, and epigenetic changes in thousands of individual cells in a single experiment. With the improved measurement and the decreasing cost of the reactions and sequencing, the size of these datasets is increasing rapidly. The critical bottleneck remains the analysis of the wealth of information generated by single cell experiments. In this review, we give a simplified overview of the analysis pipelines, as they are typically used in the field today. We aim to enable researchers starting out in single cell analysis to gain an overview of challenges and the most commonly used analytical tools. In addition, we hope to empower others to gain an understanding of how typical readouts from single cell datasets are presented in the published literature.
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Affiliation(s)
- Michael S. Balzer
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ziyuan Ma
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jianfu Zhou
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Amin Abedini
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
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20
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Hickson LJ, Herrmann SM, McNicholas BA, Griffin MD. Progress toward the Clinical Application of Mesenchymal Stromal Cells and Other Disease-Modulating Regenerative Therapies: Examples from the Field of Nephrology. KIDNEY360 2021; 2:542-557. [PMID: 34316720 PMCID: PMC8312727 DOI: 10.34067/kid.0005692020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drawing from basic knowledge of stem-cell biology, embryonic development, wound healing, and aging, regenerative medicine seeks to develop therapeutic strategies that complement or replace conventional treatments by actively repairing diseased tissue or generating new organs and tissues. Among the various clinical-translational strategies within the field of regenerative medicine, several can be broadly described as promoting disease resolution indirectly through local or systemic interactions with a patient's cells, without permanently integrating or directly forming new primary tissue. In this review, we focus on such therapies, which we term disease-modulating regenerative therapies (DMRT), and on the extent to which they have been translated into the clinical arena in four distinct areas of nephrology: renovascular disease (RVD), sepsis-associated AKI (SA-AKI), diabetic kidney disease (DKD), and kidney transplantation (KTx). As we describe, the DMRT that has most consistently progressed to human clinical trials for these indications is mesenchymal stem/stromal cells (MSCs), which potently modulate ischemic, inflammatory, profibrotic, and immune-mediated tissue injury through diverse paracrine mechanisms. In KTx, several early-phase clinical trials have also tested the potential for ex vivo-expanded regulatory immune cell therapies to promote donor-specific tolerance and prevent or resolve allograft injury. Other promising DMRT, including adult stem/progenitor cells, stem cell-derived extracellular vesicles, and implantable hydrogels/biomaterials remain at varying preclinical stages of translation for these renal conditions. To date (2021), no DMRT has gained market approval for use in patients with RVD, SA-AKI, DKD, or KTx, and clinical trials demonstrating definitive, cost-effective patient benefits are needed. Nonetheless, exciting progress in understanding the disease-specific mechanisms of action of MSCs and other DMRT, coupled with increasing knowledge of the pathophysiologic basis for renal-tissue injury and the experience gained from pioneering early-phase clinical trials provide optimism that influential, regenerative treatments for diverse kidney diseases will emerge in the years ahead.
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Affiliation(s)
- LaTonya J. Hickson
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Jacksonville, Florida
| | - Sandra M. Herrmann
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Bairbre A. McNicholas
- Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, National University of Ireland Galway, Ireland,Nephrology Services, Galway University Hospitals, Saolta University Healthcare System, Galway, Ireland,Critical Care Services, Galway University Hospitals, Saolta University Healthcare System, Galway, Ireland
| | - Matthew D. Griffin
- Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, National University of Ireland Galway, Ireland,Nephrology Services, Galway University Hospitals, Saolta University Healthcare System, Galway, Ireland
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21
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Guo H, Deng N, Dou L, Ding H, Criswell T, Atala A, Furdui CM, Zhang Y. 3-D Human Renal Tubular Organoids Generated from Urine-Derived Stem Cells for Nephrotoxicity Screening. ACS Biomater Sci Eng 2020; 6:6701-6709. [PMID: 33320634 PMCID: PMC8118570 DOI: 10.1021/acsbiomaterials.0c01468] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of human cell-based systems to replace the use of rodents or the two-dimensional culture of cells for studying nephrotoxicity is urgently needed. Human urine-derived stem cells were differentiated into renal tubular epithelial cells in three-dimensional (3-D) culture after being induced by a kidney extracellular matrix. Levels of CYP2E1 and KIM-1 in 3-D organoids were significantly increased in response to acetone and cisplatin. This 3-D culture system provides an alternative tool for nephrotoxicity screening and research.
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Affiliation(s)
- Haibin Guo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States.,Reproductive Medicine, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, China
| | - Nan Deng
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States.,Department of Urology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China
| | - Lei Dou
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
| | - Huifen Ding
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
| | - Tracy Criswell
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, United States
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22
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Adelfio M, Szymkowiak S, Kaplan DL. Matrigel-Free Laminin-Entactin Matrix to Induce Human Renal Proximal Tubule Structure Formation In Vitro. ACS Biomater Sci Eng 2020; 6:6618-6625. [PMID: 33320630 DOI: 10.1021/acsbiomaterials.0c01385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A successful in vitro tissue model must recapitulate the native tissue features while also being reproducible. Currently, Matrigel is the principal biomaterial used to induce the formation of proximal convoluted tubules (PCTs) in vitro, because of its similar composition and structure with the kidney tubular basement membrane and the presence of critical growth factors. However, Matrigel is not well-defined, and batch-to-batch variability is a significant issue. Here, we define a Matrigel-free method, using a laminin-entactin (L-E) matrix to support the formation of proximal tubular-like structures in vitro using immortalized human renal epithelial cells (RPTEC/TERT1) cocultured with murine fibroblast stromal cells (FOXD1lacZ+). The matrix supports the presence of specific components of the tubular basement membrane (laminin, entactin/nidogen, and heparan sulfate proteoglycan) in addition to fibroblast growth factor 8a (FGF-8a). The matrix also induces tubulogenesis, leading to the formation of PCTs based on several key markers, including E-cadherin, aquaporin-1, and Na+/K+ ATPase. Moreover, these PCT structures displayed cell polarity and a well-defined lumen after 18 days in culture. This laminin-entactin (L-E) matrix constitutes a defined and consistent biomaterial that can be used in kidney tissue engineering for understanding in vitro proximal tubule development and for nephrotoxicity studies.
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Affiliation(s)
- M Adelfio
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - S Szymkowiak
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - D L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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23
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Eddy S, Mariani LH, Kretzler M. Integrated multi-omics approaches to improve classification of chronic kidney disease. Nat Rev Nephrol 2020; 16:657-668. [PMID: 32424281 DOI: 10.1038/s41581-020-0286-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/11/2022]
Abstract
Chronic kidney diseases (CKDs) are currently classified according to their clinical features, associated comorbidities and pattern of injury on biopsy. Even within a given classification, considerable variation exists in disease presentation, progression and response to therapy, highlighting heterogeneity in the underlying biological mechanisms. As a result, patients and clinicians experience uncertainty when considering optimal treatment approaches and risk projection. Technological advances now enable large-scale datasets, including DNA and RNA sequence data, proteomics and metabolomics data, to be captured from individuals and groups of patients along the genotype-phenotype continuum of CKD. The ability to combine these high-dimensional datasets, in which the number of variables exceeds the number of clinical outcome observations, using computational approaches such as machine learning, provides an opportunity to re-classify patients into molecularly defined subgroups that better reflect underlying disease mechanisms. Patients with CKD are uniquely poised to benefit from these integrative, multi-omics approaches since the kidney biopsy, blood and urine samples used to generate these different types of molecular data are frequently obtained during routine clinical care. The ultimate goal of developing an integrated molecular classification is to improve diagnostic classification, risk stratification and assignment of molecular, disease-specific therapies to improve the care of patients with CKD.
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Affiliation(s)
- Sean Eddy
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, USA.
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24
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Wang Y, Eng DG, Kaverina NV, Loretz CJ, Koirala A, Akilesh S, Pippin JW, Shankland SJ. Global transcriptomic changes occur in aged mouse podocytes. Kidney Int 2020; 98:1160-1173. [PMID: 32592814 PMCID: PMC7606654 DOI: 10.1016/j.kint.2020.05.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/28/2020] [Indexed: 01/15/2023]
Abstract
Glomerular podocytes undergo structural and functional changes with advanced age, that increase susceptibility of aging kidneys to worse outcomes following superimposed glomerular diseases. To delineate transcriptional changes in podocytes in aged mice, RNA-seq was performed on isolated populations of reporter-labeled (tdTomato) podocytes from multiple young (two to three months) and advanced aged mice (22 to 24 months, equivalent to 70 plus year old humans). Of the 2,494 differentially expressed genes, 1,219 were higher and 1,275 were lower in aged podocytes. Pathway enrichment showed that major biological processes increased in aged podocytes included immune responses, non-coding RNA metabolism, gene silencing and MAP kinase signaling. Conversely, aged podocytes showed downregulation of developmental, morphogenesis and metabolic processes. Canonical podocyte marker gene expression decreased in aged podocytes, with increases in apoptotic and senescence genes providing a mechanism for the progressive loss of podocytes seen with aging. In addition, we revealed aberrations in the podocyte autocrine signaling network, identified the top transcription factors perturbed in aged podocytes, and uncovered candidate gene modulations that might promote healthy aging in podocytes. The transcriptional signature of aging is distinct from other kidney diseases. Thus, our study provides insights into biomarker discovery and molecular targeting of the aging process itself within podocytes.
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Affiliation(s)
- Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Diana G Eng
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Natalya V Kaverina
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Carol J Loretz
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Abbal Koirala
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Stuart J Shankland
- Division of Nephrology, University of Washington, Seattle, Washington, USA.
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25
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Abstract
The field of tissue engineering has advanced over the past decade, but the largest impact on human health should be achieved with the transition of engineered solid organs to the clinic. The number of patients suffering from solid organ disease continues to increase, with over 100 000 patients on the U.S. national waitlist and approximately 730 000 deaths in the United States resulting from end-stage organ disease annually. While flat, tubular, and hollow nontubular engineered organs have already been implanted in patients, in vitro formation of a fully functional solid organ at a translatable scale has not yet been achieved. Thus, one major goal is to bioengineer complex, solid organs for transplantation, composed of patient-specific cells. Among the myriad of approaches attempted to engineer solid organs, 3D bioprinting offers unmatched potential. This review highlights the structural complexity which must be engineered at nano-, micro-, and mesostructural scales to enable organ function. We showcase key advances in bioprinting solid organs with complex vascular networks and functioning microstructures, advances in biomaterials science that have enabled this progress, the regulatory hurdles the field has yet to overcome, and cutting edge technologies that bring us closer to the promise of engineered solid organs.
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Affiliation(s)
- Adam M Jorgensen
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James J Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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26
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Ransick A, Lindström NO, Liu J, Zhu Q, Guo JJ, Alvarado GF, Kim AD, Black HG, Kim J, McMahon AP. Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Dev Cell 2020; 51:399-413.e7. [PMID: 31689386 DOI: 10.1016/j.devcel.2019.10.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/26/2019] [Accepted: 10/04/2019] [Indexed: 01/13/2023]
Abstract
Chronic kidney disease affects 10% of the population with notable differences in ethnic and sex-related susceptibility to kidney injury and disease. Kidney dysfunction leads to significant morbidity and mortality and chronic disease in other organ systems. A mouse-organ-centered understanding underlies rapid progress in human disease modeling and cellular approaches to repair damaged systems. To enhance an understanding of the mammalian kidney, we combined anatomy-guided single-cell RNA sequencing of the adult male and female mouse kidney with in situ expression studies and cell lineage tracing. These studies reveal cell diversity and marked sex differences, distinct organization and cell composition of nephrons dependent on the time of nephron specification, and lineage convergence, in which contiguous functionally related cell types are specified from nephron and collecting system progenitor populations. A searchable database, Kidney Cell Explorer (https://cello.shinyapps.io/kidneycellexplorer/), enables gene-cell relationships to be viewed in the anatomical framework of the kidney.
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Affiliation(s)
- Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Qin Zhu
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd, Philadelphia, PA 19104-6064, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Gregory F Alvarado
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Hannah G Black
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA.
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27
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Nishikawa M, Sakai Y, Yanagawa N. Design and strategy for manufacturing kidney organoids. Biodes Manuf 2020. [DOI: 10.1007/s42242-020-00060-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Foresto RD, Pestana JOM. Novel treatment options for chronic kidney disease complications. ACTA ACUST UNITED AC 2020; 66Suppl 1:s01-s02. [PMID: 31939528 DOI: 10.1590/1806-9282.66.s1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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29
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dos Santos ÍGD, de Oliveira Mendes TA, Silva GAB, Reis AMS, Monteiro-Vitorello CB, Schaker PDC, Herai RH, Fabotti ABC, Coutinho LL, Jorge EC. Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum. BMC Genomics 2019; 20:866. [PMID: 31730444 PMCID: PMC6858782 DOI: 10.1186/s12864-019-6240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development. RESULTS The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development. CONCLUSIONS The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.
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Affiliation(s)
- Íria Gabriela Dias dos Santos
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | | | - Gerluza Aparecida Borges Silva
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | - Amanda Maria Sena Reis
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | | | - Patricia Dayane Carvalho Schaker
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo Brazil
| | - Roberto Hirochi Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | | | - Luiz Lehmann Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo Brazil
| | - Erika Cristina Jorge
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
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30
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Abstract
The vertebrate kidney is comprised of functional units known as nephrons. Defects in nephron development or activity are a common feature of kidney disease. Current medical treatments are unable to ameliorate the dire consequences of nephron deficit or injury. Although there have been tremendous advancements in our understanding of nephron ontogeny and the response to damage, many significant knowledge gaps still remain. The zebrafish embryo kidney, or pronephros, is an ideal model for many renal development and regeneration studies because it is comprised of nephrons that share conserved features with the nephron units that comprise the mammalian metanephric kidney. In this chapter, we provide an overview about the benefits of using the zebrafish pronephros to study the mechanisms underlying nephrogenesis as well as epithelial repair and regeneration. We subsequently detail methods for the spatiotemporal assessment of gene and protein expression in zebrafish embryos that can be used to extend the understanding of nephron development and disease, and thereby create new opportunities to identify therapeutic strategies for regenerative medicine.
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31
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Chambers BE, Gerlach GF, Clark EG, Chen KH, Levesque AE, Leshchiner I, Goessling W, Wingert RA. Tfap2a is a novel gatekeeper of nephron differentiation during kidney development. Development 2019; 146:dev.172387. [PMID: 31160420 DOI: 10.1242/dev.172387] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
Abstract
Renal functional units known as nephrons undergo patterning events during development that create a segmental array of cellular compartments with discrete physiological identities. Here, from a forward genetic screen using zebrafish, we report the discovery that transcription factor AP-2 alpha (tfap2a) coordinates a gene regulatory network that activates the terminal differentiation program of distal segments in the pronephros. We found that tfap2a acts downstream of Iroquois homeobox 3b (irx3b), a distal lineage transcription factor, to operate a circuit consisting of tfap2b, irx1a and genes encoding solute transporters that dictate the specialized metabolic functions of distal nephron segments. Interestingly, this regulatory node is distinct from other checkpoints of differentiation, such as polarity establishment and ciliogenesis. Thus, our studies reveal insights into the genetic control of differentiation, where tfap2a is essential for regulating a suite of segment transporter traits at the final tier of zebrafish pronephros ontogeny. These findings have relevance for understanding renal birth defects, as well as efforts to recapitulate nephrogenesis in vivo to facilitate drug discovery and regenerative therapies.
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Affiliation(s)
- Brooke E Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gary F Gerlach
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Eleanor G Clark
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Karen H Chen
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Anna E Levesque
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ignaty Leshchiner
- Brigham and Women's Hospital, Genetics and Gastroenterology Division, Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02215, USA
| | - Wolfram Goessling
- Brigham and Women's Hospital, Genetics and Gastroenterology Division, Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02215, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN 46556, USA
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32
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Chevalier RL. Evolution, kidney development, and chronic kidney disease. Semin Cell Dev Biol 2019; 91:119-131. [PMID: 29857053 PMCID: PMC6281795 DOI: 10.1016/j.semcdb.2018.05.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/29/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
There is a global epidemic of chronic kidney disease (CKD) characterized by a progressive loss of nephrons, ascribed in large part to a rising incidence of hypertension, metabolic syndrome, and type 2 diabetes mellitus. There is a ten-fold variation in nephron number at birth in the general population, and a 50% overall decrease in nephron number in the last decades of life. The vicious cycle of nephron loss stimulating hypertrophy by remaining nephrons and resulting in glomerulosclerosis has been regarded as maladaptive, and only partially responsive to angiotensin inhibition. Advances over the past century in kidney physiology, genetics, and development have elucidated many aspects of nephron formation, structure and function. Parallel advances have been achieved in evolutionary biology, with the emergence of evolutionary medicine, a discipline that promises to provide new insight into the treatment of chronic disease. This review provides a framework for understanding the origins of contemporary developmental nephrology, and recent progress in evolutionary biology. The establishment of evolutionary developmental biology (evo-devo), ecological developmental biology (eco-devo), and developmental origins of health and disease (DOHaD) followed the discovery of the hox gene family, the recognition of the contribution of cumulative environmental stressors to the changing phenotype over the life cycle, and mechanisms of epigenetic regulation. The maturation of evolutionary medicine has contributed to new investigative approaches to cardiovascular disease, cancer, and infectious disease, and promises the same for CKD. By incorporating these principles, developmental nephrology is ideally positioned to answer important questions regarding the fate of nephrons from embryo through senescence.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, The University of Virginia, P.O. Box 800386, Charlottesville, VA, United States.
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33
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Singh N, Avigan ZM, Kliegel JA, Shuch BM, Montgomery RR, Moeckel GW, Cantley LG. Development of a 2-dimensional atlas of the human kidney with imaging mass cytometry. JCI Insight 2019; 4:129477. [PMID: 31217358 DOI: 10.1172/jci.insight.129477] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022] Open
Abstract
An incomplete understanding of the biology of the human kidney, including the relative abundances of and interactions between intrinsic and immune cells, has long constrained the development of therapies for kidney disease. The small amount of tissue obtained by renal biopsy has previously limited the ability to use patient samples for discovery purposes. Imaging mass cytometry (IMC) is an ideal technology for quantitative interrogation of scarce samples, permitting concurrent analysis of more than 40 markers on a single tissue section. Using a validated panel of metal-conjugated antibodies designed to confer unique signatures on the structural and infiltrating cells comprising the human kidney, we performed simultaneous multiplexed imaging with IMC in 23 channels on 16 histopathologically normal human samples. We devised a machine-learning pipeline (Kidney-MAPPS) to perform single-cell segmentation, phenotyping, and quantification, thus creating a spatially preserved quantitative atlas of the normal human kidney. These data define selected baseline renal cell types, respective numbers, organization, and variability. We demonstrate the utility of IMC coupled to Kidney-MAPPS to qualitatively and quantitatively distinguish individual cell types and reveal expected as well as potentially novel abnormalities in diseased versus normal tissue. Our studies define a critical baseline data set for future quantitative analysis of human kidney disease.
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Affiliation(s)
- Nikhil Singh
- Section of Nephrology, Department of Internal Medicine
| | | | | | | | | | - Gilbert W Moeckel
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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34
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Chambers BE, Wingert RA. Mechanisms of Nephrogenesis Revealed by Zebrafish Chemical Screen: Prostaglandin Signaling Modulates Nephron Progenitor Fate. Nephron Clin Pract 2019; 143:68-76. [PMID: 31216548 DOI: 10.1159/000501037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
Nephron development involves the creation of discrete segment populations that are specialized to fulfill unique physiological roles. As such, renal function is reliant on the proper execution of segment patterning programs. Despite the central importance of nephron segmentation, the genetic mechanisms that regulate this process are far from understood, in large part due to the experimental complexities and cost of interrogating these events in the mammalian metanephros. For this reason, forward genetics utilizing phenotypic screening in the zebrafish pronephros provides an avenue to gain novel insights about the mechanisms of nephron segmentation in the vertebrate kidney. Discoveries from zebrafish can highlight possible conserved pathways and provide a useful starting point for reverse genetic analyses with other animal models or in vitro approaches. In this review, we discuss the results of a novel chemical screen using the zebrafish to identify segmentation regulators. Through this screen, we identified for the first time that prostaglandin signaling can modulate nephron segmentation, and that it is normally requisite during development to mitigate segment fate choice in the embryonic kidney. We briefly discuss how these discoveries relate to current knowledge about nephron segmentation. Finally, we explore the possible implications of these findings for understanding renal ontogeny and disease, and how this knowledge may be useful for ongoing research initiatives that are aimed at deciphering how to build or rebuild the human kidney.
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Affiliation(s)
- Brooke E Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, USA,
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35
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Wragg NM, Burke L, Wilson SL. A critical review of current progress in 3D kidney biomanufacturing: advances, challenges, and recommendations. RENAL REPLACEMENT THERAPY 2019. [DOI: 10.1186/s41100-019-0218-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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36
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Gupta AK, Coburn JM, Davis-Knowlton J, Kimmerling E, Kaplan DL, Oxburgh L. Scaffolding kidney organoids on silk. J Tissue Eng Regen Med 2019; 13:812-822. [PMID: 30793851 DOI: 10.1002/term.2830] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/10/2019] [Accepted: 02/21/2019] [Indexed: 12/26/2022]
Abstract
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.
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Affiliation(s)
- Ashwani Kumar Gupta
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
| | | | - Jessica Davis-Knowlton
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine.,Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts
| | - Erica Kimmerling
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, Massachusetts
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, Massachusetts
| | - Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
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Abstract
Regeneration of a functional kidney from pluripotent stem cells (PSCs) is challenging because of its complex structure. Kidneys are derived from embryonic metanephros, which are composed of three progenitor cells: nephron progenitors, ureteric bud, and stromal progenitors. Nephron progenitors and ureteric bud have been induced successfully from PSCs as a result of the understanding of their detailed developmental process through cell-lineage tracing analysis. Moreover, these induced progenitors can be used to reconstruct the three-dimensional (3D) structure of kidneys in vitro, including glomeruli with podocytes, renal tubules, and the branching ureters. Induction of the remaining renal progenitors (that is, stromal progenitors from PSCs and the further maturation of reconstructed kidneys) needs to be studied extensively to regenerate functional and sophisticated kidneys from PSCs. In addition to the proper induction of renal progenitors, new bioengineering methods such as decellularization and 3D bioprinting and the recent advancements in the regeneration of kidneys in other species are promising leads for regenerating the complex spatial arrangement of kidneys, including the vascular network and urinary excretion pathway in humans.
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Affiliation(s)
- Sho Hasegawa
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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38
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Daniel E, Cleaver O. Vascularizing organogenesis: Lessons from developmental biology and implications for regenerative medicine. Curr Top Dev Biol 2019; 132:177-220. [PMID: 30797509 DOI: 10.1016/bs.ctdb.2018.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Organogenesis requires tightly coordinated and patterned growth of numerous cell types to form a fully mature and vascularized organ. Endothelial cells (ECs) that line blood vessels develop alongside the growing organ, but only recently has their role in directing epithelial and stromal growth been appreciated. Endothelial, epithelial, and stromal cells in embryonic organs actively communicate with one another throughout development to ensure that the organ forms appropriately. What signals tell blood vessel progenitors where to go? How are tissues influenced by the vasculature that pervades it? In this chapter, we review the ways in which crosstalk between ECs and epithelial or stromal cells during development leads to a fully patterned pancreas, lung, or kidney. ECs in all of these organs are necessary for proper epithelial and stromal growth, but how they direct this process is organ- and time-specific, highlighting the concept of dynamic EC heterogeneity. We end with a discussion on how understanding cell-cell crosstalk during development can be applied therapeutically through the generation of transplantable miniature organ-like tissues called "organoids." We will discuss the current state of organoid technology and highlight the major challenges in forming a properly patterned vascular network that will be critical in transforming them into a viable therapeutic option.
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Affiliation(s)
- Edward Daniel
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Ondine Cleaver
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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39
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Fine LG. Are Current Strategies for Building a Human Kidney Misguided? Speculative Alternatives. J Am Soc Nephrol 2018; 29:2780-2782. [PMID: 30377234 DOI: 10.1681/asn.2018080822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Leon G Fine
- Program in the History of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
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40
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Lindström NO, De Sena Brandine G, Ransick A, McMahon AP. Single-Cell RNA Sequencing of the Adult Mouse Kidney: From Molecular Cataloging of Cell Types to Disease-Associated Predictions. Am J Kidney Dis 2018; 73:140-142. [PMID: 30241960 DOI: 10.1053/j.ajkd.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/22/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Guilherme De Sena Brandine
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA.
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41
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Su J, Satchell SC, Shah RN, Wertheim JA. Kidney decellularized extracellular matrix hydrogels: Rheological characterization and human glomerular endothelial cell response to encapsulation. J Biomed Mater Res A 2018; 106:2448-2462. [PMID: 29664217 PMCID: PMC6376869 DOI: 10.1002/jbm.a.36439] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/23/2018] [Accepted: 04/05/2018] [Indexed: 01/15/2023]
Abstract
Hydrogels, highly-hydrated crosslinked polymer networks, closely mimic the microenvironment of native extracellular matrix (ECM) and thus present as ideal platforms for three-dimensional cell culture. Hydrogels derived from tissue- and organ-specific decellularized ECM (dECM) may retain bioactive signaling cues from the native tissue or organ that could in turn modulate cell-material interactions and response. In this study, we demonstrate that porcine kidney dECM can be processed to form hydrogels suitable for cell culture and encapsulation studies. Scanning electron micrographs of hydrogels demonstrated a fibrous ultrastructure with interconnected pores, and rheological analysis revealed rapid gelation times with shear moduli dependent upon the protein concentration of the hydrogels. Conditionally-immortalized human glomerular endothelial cells (GEnCs) cultured on top of or encapsulated within hydrogels exhibited high cell viability and proliferation over a one-week culture period. However, gene expression analysis of GEnCs encapsulated within kidney dECM hydrogels revealed significantly lower expression of several relevant genes of interest compared to those encapsulated within hydrogels composed of only purified collagen I. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A:2448-2462, 2018.
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Affiliation(s)
- Jimmy Su
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL, USA
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Simon C. Satchell
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - Ramille N. Shah
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL, USA
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Materials Science & Engineering, Northwestern University, Evanston, IL, USA
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jason A. Wertheim
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL, USA
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Department of Surgery, Jesse Brown VA Medical Center, Chicago, IL, USA
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Abstract
The nephron is a multifunctional filtration device equipped with an array of sophisticated sensors. For appropriate physiological function in the human and mouse, nephrons must be stereotypically arrayed in large numbers, and this essential structural property that defines the kidney is determined during its fetal development. This review explores the process of nephron determination in the fetal kidney, providing an overview of the foundational literature in the field as well as exploring new developments in this dynamic research area. Mechanisms that ensure that a large number of nephrons can be formed from a small initial number of progenitor cells are central to this process, and the question of how the nephron progenitor cell population balances epithelial differentiation with renewal in the progenitor state is a subject of particular interest. Key growth factor signaling pathways and transcription factor networks are discussed.
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Affiliation(s)
- Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine 04074, USA;
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43
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Norton JM, Ketchum CJ, Rankin TL, Star RA. Rebuilding the Pipeline of Investigators in Nephrology Research in the United States. Clin J Am Soc Nephrol 2018; 13:1285-1287. [PMID: 30018051 PMCID: PMC6086709 DOI: 10.2215/cjn.03360318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jenna M Norton
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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Zambon JP, Ko IK, Abolbashari M, Huling J, Clouse C, Kim TH, Smith C, Atala A, Yoo JJ. Comparative analysis of two porcine kidney decellularization methods for maintenance of functional vascular architectures. Acta Biomater 2018; 75:226-234. [PMID: 29883813 DOI: 10.1016/j.actbio.2018.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/30/2018] [Accepted: 06/03/2018] [Indexed: 10/14/2022]
Abstract
Kidney transplantation is currently the only definitive solution for the treatment of end-stage renal disease (ESRD), however transplantation is severely limited by the shortage of available donor kidneys. Recent progress in whole organ engineering based on decellularization/recellularization techniques has enabled pre-clinical in vivo studies using small animal models; however, these in vivo studies have been limited to short-term assessments. We previously developed a decellularization system that effectively removes cellular components from porcine kidneys. While functional re-endothelialization on the porcine whole kidney scaffold was able to improve vascular patency, as compared to the kidney scaffold only, the duration of patency lasted only a few hours. In this study, we hypothesized that significant damage in the microvasculatures within the kidney scaffold resulted in the cessation of blood flow, and that thorough investigation is necessary to accurately evaluate the vascular integrity of the kidney scaffolds. Two decellularization protocols [sodium dodecyl sulfate (SDS) with DNase (SDS + DNase) or Triton X-100 with SDS (TRX + SDS)] were used to evaluate and optimize the levels of vascular integrity within the kidney scaffold. Results from vascular analysis studies using vascular corrosion casting and angiograms demonstrated that the TRX + SDS method was able to better maintain intact and functional microvascular architectures such as glomeruli within the acellular matrices than that by the SDS + DNase treatment. Importantly, in vitro blood perfusion of the re-endothelialized kidney construct revealed improved vascular function of the scaffold by TRX + SDS treatment compared with the SDS + DNase. Our results suggest that the optimized TRX + SDS decellularization method preserves kidney-specific microvasculatures and may contribute to long-term vascular patency following implantation. STATEMENT OF SIGNIFICANCE Kidney transplantation is the only curative therapy for patients with end-stage renal disease (ESRD). However, in the United States, the supply of donor kidneys meets less than one-fifth of the demand; and those patients that receive a donor kidney need life-long immunosuppressive therapy to avoid organ rejection. In the last two decades, regenerative medicine and tissue engineering have emerged as an attractive alternative to overcome these limitations. In 2013, Song et al. published the first experimental orthotopic transplantation of a bioengineering kidney in rodents. In this study, they demonstrated evidences of kidney tissue regeneration and partial function restoration. Despite these initial promising results, there are still many challenges to achieve long-term blood perfusion without graft thrombosis. In this paper, we demonstrated that perfusion of detergents through the renal artery of porcine kidneys damages the glomeruli microarchitecture as well as peritubular capillaries. Modifying dynamic parameters such as flow rate, detergent concentration, and decellularization time, we were able to establish an optimized decellularization protocol with no evidences of disruption of glomeruli microarchitecture. As a proof of concept, we recellularized the kidney scaffolds with endothelial cells and in vitro perfused whole porcine blood successfully for 24 h with no evidences of thrombosis.
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Becherucci F, Mazzinghi B, Allinovi M, Angelotti ML, Romagnani P. Regenerating the kidney using human pluripotent stem cells and renal progenitors. Expert Opin Biol Ther 2018; 18:795-806. [PMID: 29939787 DOI: 10.1080/14712598.2018.1492546] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Chronic kidney disease is a major health-care problem worldwide and its cost is becoming no longer affordable. Indeed, restoring damaged renal structures or building a new kidney represents an ambitious and ideal alternative to renal replacement therapy. Streams of research have explored the possible application of pluripotent stem cells (SCs) (embryonic SCs and induced pluripotent SCs) in different strategies aimed at regenerate functioning nephrons and at understanding the mechanisms of kidney regeneration. AREAS COVERED In this review, we will focus on the main potential applications of human pluripotent SCs to kidney regeneration, including those leading to rebuilding new kidneys or part of them (organoids, scaffolds, biological microdevices) as well as those aimed at understanding the pathophysiological mechanisms of renal disease and regenerative processes (modeling of kidney disease, genome editing). Moreover, we will discuss the role of endogenous renal progenitors cells in order to understand and promote kidney regeneration, as an attractive alternative to pluripotent SCs. EXPERT OPINION Opportunities and pitfalls of all these strategies will be underlined, finally leading to the conclusion that a deeper knowledge of the biology of pluripotent SCs is mandatory, in order to allow us to hypothesize their clinical application.
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Affiliation(s)
- Francesca Becherucci
- a Nephrology and Dialysis Unit , Meyer Children's University Hospital , Florence , Italy
| | - Benedetta Mazzinghi
- a Nephrology and Dialysis Unit , Meyer Children's University Hospital , Florence , Italy
| | - Marco Allinovi
- b Department of Biomedical Experimental and Clinical Sciences "Mario Serio" , University of Florence , Florence , Italy
| | - Maria Lucia Angelotti
- b Department of Biomedical Experimental and Clinical Sciences "Mario Serio" , University of Florence , Florence , Italy
| | - Paola Romagnani
- a Nephrology and Dialysis Unit , Meyer Children's University Hospital , Florence , Italy.,b Department of Biomedical Experimental and Clinical Sciences "Mario Serio" , University of Florence , Florence , Italy
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An optimal serum-free defined condition for in vitro culture of kidney organoids. Biochem Biophys Res Commun 2018; 501:996-1002. [DOI: 10.1016/j.bbrc.2018.05.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022]
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47
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Herrera GA, Teng J, Zeng C, Xu H, Liang M, Alexander JS, Liu B, Boyer C, Turbat-Herrera EA. Phenotypic plasticity of mesenchymal stem cells is crucial for mesangial repair in a model of immunoglobulin light chain-associated mesangial damage. Ultrastruct Pathol 2018; 42:262-288. [PMID: 29668344 DOI: 10.1080/01913123.2018.1449772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mesangiopathies produced by glomerulopathic monoclonal immunoglobulin light chains (GLCs) acting on the glomerular mesangium produce two characteristic lesions: AL-amyloidosis (AL-Am) and light chain deposition disease (LCDD). In both cases, the pathology is centered in the mesangium, where initial and progressive damage occurs. In AL-Am the mesangial matrix is destroyed and replaced by amyloid fibrils and in LCDD, the mesangial matrix is increased and remodeled. The collagen IV rich matrix is replaced by tenascin. In both conditions, mesangial cells (MCs) become apoptotic as a direct effect of the GLCs. MCs were incubated in-vitro with GLCs and animal kidneys were perfused ex-vivo via the renal artery with GLCs, producing expected lesions, and then mesenchymal stem cells (MSCs) were added to both platforms. Each of the two platforms provided unique information that when put together created a comprehensive evaluation of the processes involved. A "cocktail" with growth and differentiating factors was used to study its effect on mesangial repair. MSCs displayed remarkable phenotypic plasticity during the repair process. The first role of the MSCs after migrating to the affected areas was to dispose of the amyloid fibrils (in AL-Am), the altered mesangial matrix (in LCDD) and apoptotic MCs/debris. To accomplish this task, MSCs transformed into facultative macrophages acquiring an abundance of lysosomes and endocytotic capabilities required to engage in phagocytic functions. Once the mesangial cleaning was completed, MSCs transformed into functional MCs restoring the mesangium to normal. "Cocktail" made the repair process more efficient.
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Affiliation(s)
- Guillermo A Herrera
- a Departments of Pathology and Translational Pathobiology and Cell Biology and Anatomy , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Jiamin Teng
- b Department of Pathology and Translational Pathobiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Chun Zeng
- b Department of Pathology and Translational Pathobiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Hongzhi Xu
- b Department of Pathology and Translational Pathobiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Man Liang
- b Department of Pathology and Translational Pathobiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - J Steven Alexander
- c Department of Molecular and Cellular Physiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Bing Liu
- b Department of Pathology and Translational Pathobiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Chris Boyer
- c Department of Molecular and Cellular Physiology , Louisiana State Health Sciences Center , Shreveport , LA , USA
| | - Elba A Turbat-Herrera
- d Departments of Pathology and Translational Pathobiology , Medicine, and Cell Biology and Anatomy, Louisiana State Health Sciences Center , Shreveport , LA , USA
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48
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Daniel E, Azizoglu DB, Ryan AR, Walji TA, Chaney CP, Sutton GI, Carroll TJ, Marciano DK, Cleaver O. Spatiotemporal heterogeneity and patterning of developing renal blood vessels. Angiogenesis 2018; 21:617-634. [PMID: 29627966 DOI: 10.1007/s10456-018-9612-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/03/2018] [Indexed: 01/01/2023]
Abstract
The kidney vasculature facilitates the excretion of wastes, the dissemination of hormones, and the regulation of blood chemistry. To carry out these diverse functions, the vasculature is regionalized within the kidney and along the nephron. However, when and how endothelial regionalization occurs remains unknown. Here, we examine the developing kidney vasculature to assess its 3-dimensional structure and transcriptional heterogeneity. First, we observe that endothelial cells (ECs) grow coordinately with the kidney bud as early as E10.5, and begin to show signs of specification by E13.5 when the first arteries can be identified. We then focus on how ECs pattern and remodel with respect to the developing nephron and collecting duct epithelia. ECs circumscribe nephron progenitor populations at the distal tips of the ureteric bud (UB) tree and form stereotyped cruciform structures around each tip. Beginning at the renal vesicle (RV) stage, ECs form a continuous plexus around developing nephrons. The endothelial plexus envelops and elaborates with the maturing nephron, becoming preferentially enriched along the early distal tubule. Lastly, we perform transcriptional and immunofluorescent screens to characterize spatiotemporal heterogeneity in the kidney vasculature and identify novel regionally enriched genes. A better understanding of development of the kidney vasculature will help instruct engineering of properly vascularized ex vivo kidneys and evaluate diseased kidneys.
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Affiliation(s)
- Edward Daniel
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - D Berfin Azizoglu
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Anne R Ryan
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Tezin A Walji
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Christopher P Chaney
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Gabrielle I Sutton
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Thomas J Carroll
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA
| | - Denise K Marciano
- Department of Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NA8.300, Dallas, TX, 75390-9148, USA.
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49
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Lindström NO, Guo J, Kim AD, Tran T, Guo Q, De Sena Brandine G, Ransick A, Parvez RK, Thornton ME, Baskin L, Grubbs B, McMahon JA, Smith AD, McMahon AP. Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney. J Am Soc Nephrol 2018; 29:806-824. [PMID: 29449449 DOI: 10.0.6.145/asn.2017080890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 05/24/2023] Open
Abstract
Cellular interactions among nephron, interstitial, and collecting duct progenitors drive mammalian kidney development. In mice, Six2+ nephron progenitor cells (NPCs) and Foxd1+ interstitial progenitor cells (IPCs) form largely distinct lineage compartments at the onset of metanephric kidney development. Here, we used the method for analyzing RNA following intracellular sorting (MARIS) approach, single-cell transcriptional profiling, in situ hybridization, and immunolabeling to characterize the presumptive NPC and IPC compartments of the developing human kidney. As in mice, each progenitor population adopts a stereotypical arrangement in the human nephron-forming niche: NPCs capped outgrowing ureteric branch tips, whereas IPCs were sandwiched between the NPCs and the renal capsule. Unlike mouse NPCs, human NPCs displayed a transcriptional profile that overlapped substantially with the IPC transcriptional profile, and key IPC determinants, including FOXD1, were readily detected within SIX2+ NPCs. Comparative gene expression profiling in human and mouse Six2/SIX2+ NPCs showed broad agreement between the species but also identified species-biased expression of some genes. Notably, some human NPC-enriched genes, including DAPL1 and COL9A2, are linked to human renal disease. We further explored the cellular diversity of mesenchymal cell types in the human nephrogenic niche through single-cell transcriptional profiling. Data analysis stratified NPCs into two main subpopulations and identified a third group of differentiating cells. These findings were confirmed by section in situ hybridization with novel human NPC markers predicted through the single-cell studies. This study provides a benchmark for the mesenchymal progenitors in the human nephrogenic niche and highlights species-variability in kidney developmental programs.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | | | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Laurence Baskin
- Department of Urology and Pediatrics, University of California San Francisco, San Francisco, California
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, and
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine,
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50
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Lindström NO, Guo J, Kim AD, Tran T, Guo Q, De Sena Brandine G, Ransick A, Parvez RK, Thornton ME, Baskin L, Grubbs B, McMahon JA, Smith AD, McMahon AP. Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney. J Am Soc Nephrol 2018; 29:806-824. [PMID: 29449449 DOI: 10.1681/asn.2017080890] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 01/12/2023] Open
Abstract
Cellular interactions among nephron, interstitial, and collecting duct progenitors drive mammalian kidney development. In mice, Six2+ nephron progenitor cells (NPCs) and Foxd1+ interstitial progenitor cells (IPCs) form largely distinct lineage compartments at the onset of metanephric kidney development. Here, we used the method for analyzing RNA following intracellular sorting (MARIS) approach, single-cell transcriptional profiling, in situ hybridization, and immunolabeling to characterize the presumptive NPC and IPC compartments of the developing human kidney. As in mice, each progenitor population adopts a stereotypical arrangement in the human nephron-forming niche: NPCs capped outgrowing ureteric branch tips, whereas IPCs were sandwiched between the NPCs and the renal capsule. Unlike mouse NPCs, human NPCs displayed a transcriptional profile that overlapped substantially with the IPC transcriptional profile, and key IPC determinants, including FOXD1, were readily detected within SIX2+ NPCs. Comparative gene expression profiling in human and mouse Six2/SIX2+ NPCs showed broad agreement between the species but also identified species-biased expression of some genes. Notably, some human NPC-enriched genes, including DAPL1 and COL9A2, are linked to human renal disease. We further explored the cellular diversity of mesenchymal cell types in the human nephrogenic niche through single-cell transcriptional profiling. Data analysis stratified NPCs into two main subpopulations and identified a third group of differentiating cells. These findings were confirmed by section in situ hybridization with novel human NPC markers predicted through the single-cell studies. This study provides a benchmark for the mesenchymal progenitors in the human nephrogenic niche and highlights species-variability in kidney developmental programs.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | | | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Laurence Baskin
- Department of Urology and Pediatrics, University of California San Francisco, San Francisco, California
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, and
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine,
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