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Chambers BE, Weaver NE, Lara CM, Nguyen TK, Wingert RA. (Zebra)fishing for nephrogenesis genes. Tissue Barriers 2024; 12:2219605. [PMID: 37254823 PMCID: PMC11042071 DOI: 10.1080/21688370.2023.2219605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/14/2023] [Indexed: 06/01/2023] Open
Abstract
Kidney disease is a devastating condition affecting millions of people worldwide, where over 100,000 patients in the United States alone remain waiting for a lifesaving organ transplant. Concomitant with a surge in personalized medicine, single-gene mutations, and polygenic risk alleles have been brought to the forefront as core causes of a spectrum of renal disorders. With the increasing prevalence of kidney disease, it is imperative to make substantial strides in the field of kidney genetics. Nephrons, the core functional units of the kidney, are epithelial tubules that act as gatekeepers of body homeostasis by absorbing and secreting ions, water, and small molecules to filter the blood. Each nephron contains a series of proximal and distal segments with explicit metabolic functions. The embryonic zebrafish provides an ideal platform to systematically dissect the genetic cues governing kidney development. Here, we review the use of zebrafish to discover nephrogenesis genes.
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Affiliation(s)
- Brooke E. Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Nicole E. Weaver
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Caroline M. Lara
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Rebecca A. Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
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2
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Davis SN, Grindel SH, Viola JM, Liu GY, Liu J, Qian G, Porter CM, Hughes AJ. Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568157. [PMID: 38045273 PMCID: PMC10690271 DOI: 10.1101/2023.11.21.568157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching 'life-cycle' to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo-Yap, retinoic acid (RA), and other pathways. We then find in human stem-cell derived nephron progenitor organoids that Wnt/β-catenin-induced differentiation is converted to a renewal signal when it temporally overlaps with YAP activation. Similar experiments using RA activation indicate a role in setting nephron progenitor exit from the naive state, the spatial extent of differentiation, and nephron segment bias. Together the data suggest that nephron progenitor interpretation of consistent Wnt/β-catenin differentiation signaling in the niche may be modified by rhythmic activity in ancillary pathways to set the pace of nephron formation. This would synchronize nephron formation with ureteric bud branching, which creates new sites for nephron condensation. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues.
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Affiliation(s)
- Sachin N Davis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Samuel H Grindel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - John M Viola
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Y Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Catherine M Porter
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
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Nguyen TK, Petrikas M, Chambers BE, Wingert RA. Principles of Zebrafish Nephron Segment Development. J Dev Biol 2023; 11:jdb11010014. [PMID: 36976103 PMCID: PMC10052950 DOI: 10.3390/jdb11010014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Nephrons are the functional units which comprise the kidney. Each nephron contains a number of physiologically unique populations of specialized epithelial cells that are organized into discrete domains known as segments. The principles of nephron segment development have been the subject of many studies in recent years. Understanding the mechanisms of nephrogenesis has enormous potential to expand our knowledge about the basis of congenital anomalies of the kidney and urinary tract (CAKUT), and to contribute to ongoing regenerative medicine efforts aimed at identifying renal repair mechanisms and generating replacement kidney tissue. The study of the zebrafish embryonic kidney, or pronephros, provides many opportunities to identify the genes and signaling pathways that control nephron segment development. Here, we describe recent advances of nephron segment patterning and differentiation in the zebrafish, with a focus on distal segment formation.
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Affiliation(s)
- Thanh Khoa Nguyen
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Madeline Petrikas
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brooke E Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
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4
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Drummond BE, Ercanbrack WS, Wingert RA. Modeling Podocyte Ontogeny and Podocytopathies with the Zebrafish. J Dev Biol 2023; 11:jdb11010009. [PMID: 36810461 PMCID: PMC9944608 DOI: 10.3390/jdb11010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Podocytes are exquisitely fashioned kidney cells that serve an essential role in the process of blood filtration. Congenital malformation or damage to podocytes has dire consequences and initiates a cascade of pathological changes leading to renal disease states known as podocytopathies. In addition, animal models have been integral to discovering the molecular pathways that direct the development of podocytes. In this review, we explore how researchers have used the zebrafish to illuminate new insights about the processes of podocyte ontogeny, model podocytopathies, and create opportunities to discover future therapies.
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The "3Ds" of Growing Kidney Organoids: Advances in Nephron Development, Disease Modeling, and Drug Screening. Cells 2023; 12:cells12040549. [PMID: 36831216 PMCID: PMC9954122 DOI: 10.3390/cells12040549] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
A kidney organoid is a three-dimensional (3D) cellular aggregate grown from stem cells in vitro that undergoes self-organization, recapitulating aspects of normal renal development to produce nephron structures that resemble the native kidney organ. These miniature kidney-like structures can also be derived from primary patient cells and thus provide simplified context to observe how mutations in kidney-disease-associated genes affect organogenesis and physiological function. In the past several years, advances in kidney organoid technologies have achieved the formation of renal organoids with enhanced numbers of specialized cell types, less heterogeneity, and more architectural complexity. Microfluidic bioreactor culture devices, single-cell transcriptomics, and bioinformatic analyses have accelerated the development of more sophisticated renal organoids and tailored them to become increasingly amenable to high-throughput experimentation. However, many significant challenges remain in realizing the use of kidney organoids for renal replacement therapies. This review presents an overview of the renal organoid field and selected highlights of recent cutting-edge kidney organoid research with a focus on embryonic development, modeling renal disease, and personalized drug screening.
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Prahl LS, Viola JM, Liu J, Hughes AJ. The developing murine kidney actively negotiates geometric packing conflicts to avoid defects. Dev Cell 2023; 58:110-120.e5. [PMID: 36693318 PMCID: PMC9924533 DOI: 10.1016/j.devcel.2022.12.008] [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: 04/15/2022] [Revised: 10/17/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
The physiological functions of several organs rely on branched epithelial tubule networks bearing specialized structures for secretion, gas exchange, or filtration. Little is known about conflicts in development between building enough tubules for adequate function and geometric constraints imposed by organ size. We show that the mouse embryonic kidney epithelium negotiates a physical packing conflict between increasing tubule tip numbers through branching and limited organ surface area. Through imaging of whole kidney explants, combined with computational and soft material modeling of tubule families, we identify six possible geometric packing phases, including two defective ones. Experiments in explants show that a radially oriented tension on tubule families is necessary and sufficient for them to switch to a vertical packing arrangement that increases surface tip density while avoiding defects. These results reveal developmental contingencies in response to physical limitations and create a framework for classifying congenital kidney defects.
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Affiliation(s)
- Louis S Prahl
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John M Viola
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell & Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Röck R, Rizzo L, Lienkamp SS. Kidney Development: Recent Insights from Technological Advances. Physiology (Bethesda) 2022; 37:0. [PMID: 35253460 DOI: 10.1152/physiol.00041.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The kidney is a complex organ, and how it forms is a fascinating process. New technologies, such as single-cell transcriptomics, and enhanced imaging modalities are offering new approaches to understand the complex and intertwined processes during embryonic kidney development.
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Affiliation(s)
- Ruth Röck
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland
| | - Ludovica Rizzo
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland.,PhD program "Molecular and Translational Biomedicine," Life Science Zurich Graduate School, Zurich, Switzerland
| | - Soeren S Lienkamp
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland
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Nunez-Nescolarde AB, Nikolic-Paterson DJ, Combes AN. Human Kidney Organoids and Tubuloids as Models of Complex Kidney Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:738-749. [PMID: 35181335 DOI: 10.1016/j.ajpath.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
Abstract
Kidney organoids derived from pluripotent stem cells and epithelial organoids derived from adult tissue (tubuloids) have been used to study various kidney disorders with a strong genetic component, such as polycystic kidney disease, Wilms tumor, and congenital nephrotic syndrome. However, complex disorders without clear genetic associations, such as acute kidney injury and many forms of chronic kidney disease, are only just beginning to be investigated using these in vitro approaches. Although organoids are a reductionist model, they contain clinically relevant cell populations that may help to elucidate human-specific pathogenic mechanisms. Thus, organoids may complement animal disease models to accelerate the translation of laboratory proof-of-concept research into clinical practice. This review discusses whether kidney organoids and tubuloids are suitable models for the study of complex human kidney disease and highlights their advantages and limitations compared with monolayer cell culture and animal models.
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Affiliation(s)
- Ana B Nunez-Nescolarde
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David J Nikolic-Paterson
- Department of Nephrology, Monash Health and Monash University Centre for Inflammatory Diseases, Monash Medical Centre, Clayton, Victoria, Australia.
| | - Alexander N Combes
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Bejoy J, Qian ES, Woodard LE. Tissue Culture Models of AKI: From Tubule Cells to Human Kidney Organoids. J Am Soc Nephrol 2022; 33:487-501. [PMID: 35031569 PMCID: PMC8975068 DOI: 10.1681/asn.2021050693] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
AKI affects approximately 13.3 million people around the world each year, causing CKD and/or mortality. The mammalian kidney cannot generate new nephrons after postnatal renal damage and regenerative therapies for AKI are not available. Human kidney tissue culture systems can complement animal models of AKI and/or address some of their limitations. Donor-derived somatic cells, such as renal tubule epithelial cells or cell lines (RPTEC/hTERT, ciPTEC, HK-2, Nki-2, and CIHP-1), have been used for decades to permit drug toxicity screening and studies into potential AKI mechanisms. However, tubule cell lines do not fully recapitulate tubular epithelial cell properties in situ when grown under classic tissue culture conditions. Improving tissue culture models of AKI would increase our understanding of the mechanisms, leading to new therapeutics. Human pluripotent stem cells (hPSCs) can be differentiated into kidney organoids and various renal cell types. Injury to human kidney organoids results in renal cell-type crosstalk and upregulation of kidney injury biomarkers that are difficult to induce in primary tubule cell cultures. However, current protocols produce kidney organoids that are not mature and contain off-target cell types. Promising bioengineering techniques, such as bioprinting and "kidney-on-a-chip" methods, as applied to kidney nephrotoxicity modeling advantages and limitations are discussed. This review explores the mechanisms and detection of AKI in tissue culture, with an emphasis on bioengineered approaches such as human kidney organoid models.
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Affiliation(s)
- Julie Bejoy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eddie S. Qian
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lauren E. Woodard
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
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Affiliation(s)
- Jake Cornwall-Scoones
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Magdalena Zernicka-Goetz
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA, 91125, USA; Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Cambridge, CB2 3EG, UK.
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