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Vishy CE, Thomas C, Vincent T, Crawford DK, Goddeeris MM, Freedman BS. Genetics of cystogenesis in base-edited human organoids reveal therapeutic strategies for polycystic kidney disease. Cell Stem Cell 2024; 31:537-553.e5. [PMID: 38579684 DOI: 10.1016/j.stem.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
In polycystic kidney disease (PKD), microscopic tubules expand into macroscopic cysts. Among the world's most common genetic disorders, PKD is inherited via heterozygous loss-of-function mutations but is theorized to require additional loss of function. To test this, we establish human pluripotent stem cells in allelic series representing four common nonsense mutations, using CRISPR base editing. When differentiated into kidney organoids, homozygous mutants spontaneously form cysts, whereas heterozygous mutants (original or base corrected) express no phenotype. Using these, we identify eukaryotic ribosomal selective glycosides (ERSGs) as PKD therapeutics enabling ribosomal readthrough of these same nonsense mutations. Two different ERSGs not only prevent cyst initiation but also limit growth of pre-formed cysts by partially restoring polycystin expression. Furthermore, glycosides accumulate in cyst epithelia in organoids and mice. Our findings define the human polycystin threshold as a surmountable drug target for pharmacological or gene therapy interventions, with relevance for understanding disease mechanisms and future clinical trials.
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Affiliation(s)
- Courtney E Vishy
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Chardai Thomas
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Daniel K Crawford
- Eloxx Pharmaceuticals, Inc., 950 Winter Street, Waltham, MA 02451, USA
| | | | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA; Plurexa, 1209 6th Ave. N., Seattle, WA 98109, USA.
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2
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Alghadeer A, Hanson-Drury S, Patni AP, Ehnes DD, Zhao YT, Li Z, Phal A, Vincent T, Lim YC, O'Day D, Spurrell CH, Gogate AA, Zhang H, Devi A, Wang Y, Starita L, Doherty D, Glass IA, Shendure J, Freedman BS, Baker D, Regier MC, Mathieu J, Ruohola-Baker H. Single-cell census of human tooth development enables generation of human enamel. Dev Cell 2023; 58:2163-2180.e9. [PMID: 37582367 PMCID: PMC10629594 DOI: 10.1016/j.devcel.2023.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 05/05/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
Tooth enamel secreted by ameloblasts (AMs) is the hardest material in the human body, acting as a shield to protect the teeth. However, the enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here, we use single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) to establish a spatiotemporal single-cell census for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We identify key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in human ameloblast in vitro differentiation from induced pluripotent stem cells (iPSCs). We furthermore develop a disease model of amelogenesis imperfecta in a three-dimensional (3D) organoid system and show AM maturation to mineralized structure in vivo. These studies pave the way for future regenerative dentistry.
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Affiliation(s)
- Ammar Alghadeer
- Department of Biomedical Dental Sciences, Imam Abdulrahman bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia; Department of Oral Health Sciences University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Sesha Hanson-Drury
- Department of Oral Health Sciences University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Anjali P Patni
- Department of Oral Health Sciences University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Cancer Biology and Stem Cell Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Chennai 603203, India
| | - Devon D Ehnes
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Yan Ting Zhao
- Department of Oral Health Sciences University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Zicong Li
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Ashish Phal
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Thomas Vincent
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Yen C Lim
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Diana O'Day
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Cailyn H Spurrell
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Aishwarya A Gogate
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Seattle Children's Research Institute, Seattle, WA 98195, USA
| | - Hai Zhang
- Department of Restorative Dentistry, University of Washington, School of Dentistry, Seattle, WA 98195, USA
| | - Arikketh Devi
- Cancer Biology and Stem Cell Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Chennai 603203, India
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Lea Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dan Doherty
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98195, USA
| | - Ian A Glass
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin S Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle WA 98109
| | - David Baker
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mary C Regier
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biomedical Dental Sciences, Imam Abdulrahman bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia; Department of Oral Health Sciences University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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3
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Freedman BS, Dekel B. Engraftment of Kidney Organoids In Vivo. Curr Transplant Rep 2023; 10:29-39. [PMID: 37128257 PMCID: PMC10126570 DOI: 10.1007/s40472-023-00397-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Purpose of Review Kidney organoids are heterocellular structures grown in vitro that resemble nephrons. Organoids contain diverse cell types, including podocytes, proximal tubules, and distal tubules in contiguous segments, patterned along a proximal-to-distal axis. Human organoids are being explored for their potential as regenerative grafts, as an alternative to allograft transplants and hemodialysis. Earlier work, analyzing grafts of developing human kidney tissue and whole human embryonic kidney rudiments, serves as a baseline for organoid implantation experiments. Recent Findings When transplanted into immunodeficient mice beneath the kidney capsule, kidney organoid xenografts can form vascularized, glomerulus-like structures, which exhibit a degree of filtration function. However, the absence of an appropriate collecting duct outlet and the presence of abundant stromal-like cells limits the functionality of such grafts and raises safety concerns. Recently, ureteric-like organoids have also been generated, which extend projections that resemble collecting ducts. Summary Combining nephron-like and ureteric-like organoids, along with renal stromal cells, may provide a path towards more functional grafts.
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Affiliation(s)
- Benjamin S. Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Departments of Medicine, Pathology (Adjunct), and Bioengineering (Adjunct), University of Washington School of Medicine, Seattle, WA USA
- Plurexa LLC, Seattle, WA USA
| | - Benjamin Dekel
- Division of Pediatric Nephrology and the Pediatric Stem Cell Research Institute, Sagol Center for Regenerative Medicine, Sheba Medical Center, School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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4
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Taguchi K, Elias BC, Sugahara S, Sant S, Freedman BS, Waikar SS, Pozzi A, Zent R, Harris RC, Parikh SM, Brooks CR. Cyclin G1 induces maladaptive proximal tubule cell dedifferentiation and renal fibrosis through CDK5 activation. J Clin Invest 2022; 132:e158096. [PMID: 36453545 PMCID: PMC9711881 DOI: 10.1172/jci158096] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2022] Open
Abstract
Acute kidney injury (AKI) occurs in approximately 13% of hospitalized patients and predisposes patients to chronic kidney disease (CKD) through the AKI-to-CKD transition. Studies from our laboratory and others have demonstrated that maladaptive repair of proximal tubule cells (PTCs), including induction of dedifferentiation, G2/M cell cycle arrest, senescence, and profibrotic cytokine secretion, is a key process promoting AKI-to-CKD transition, kidney fibrosis, and CKD progression. The molecular mechanisms governing maladaptive repair and the relative contribution of dedifferentiation, G2/M arrest, and senescence to CKD remain to be resolved. We identified cyclin G1 (CG1) as a factor upregulated in chronically injured and maladaptively repaired PTCs. We demonstrated that global deletion of CG1 inhibits G2/M arrest and fibrosis. Pharmacological induction of G2/M arrest in CG1-knockout mice, however, did not fully reverse the antifibrotic phenotype. Knockout of CG1 did not alter dedifferentiation and proliferation in the adaptive repair response following AKI. Instead, CG1 specifically promoted the prolonged dedifferentiation of kidney tubule epithelial cells observed in CKD. Mechanistically, CG1 promotes dedifferentiation through activation of cyclin-dependent kinase 5 (CDK5). Deletion of CDK5 in kidney tubule cells did not prevent G2/M arrest but did inhibit dedifferentiation and fibrosis. Thus, CG1 and CDK5 represent a unique pathway that regulates maladaptive, but not adaptive, dedifferentiation, suggesting they could be therapeutic targets for CKD.
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Affiliation(s)
- Kensei Taguchi
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bertha C. Elias
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sho Sugahara
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Snehal Sant
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Benjamin S. Freedman
- Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, and Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Sushrut S. Waikar
- Section of Nephrology, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Hospital, Nashville, Tennessee, USA
| | - Roy Zent
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Hospital, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Raymond C. Harris
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Hospital, Nashville, Tennessee, USA
| | - Samir M. Parikh
- Division of Nephrology, Department of Internal Medicine, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Craig R. Brooks
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
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5
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Xu Y, Kuppe C, Perales-Patón J, Hayat S, Kranz J, Abdallah AT, Nagai J, Li Z, Peisker F, Saritas T, Halder M, Menzel S, Hoeft K, Kenter A, Kim H, van Roeyen CRC, Lehrke M, Moellmann J, Speer T, Buhl EM, Hoogenboezem R, Boor P, Jansen J, Knopp C, Kurth I, Smeets B, Bindels E, Reinders MEJ, Baan C, Gribnau J, Hoorn EJ, Steffens J, Huber TB, Costa I, Floege J, Schneider RK, Saez-Rodriguez J, Freedman BS, Kramann R. Adult human kidney organoids originate from CD24 + cells and represent an advanced model for adult polycystic kidney disease. Nat Genet 2022; 54:1690-1701. [PMID: 36303074 PMCID: PMC7613830 DOI: 10.1038/s41588-022-01202-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Adult kidney organoids have been described as strictly tubular epithelia and termed tubuloids. While the cellular origin of tubuloids has remained elusive, here we report that they originate from a distinct CD24+ epithelial subpopulation. Long-term-cultured CD24+ cell-derived tubuloids represent a functional human kidney tubule. We show that kidney tubuloids can be used to model the most common inherited kidney disease, namely autosomal dominant polycystic kidney disease (ADPKD), reconstituting the phenotypic hallmark of this disease with cyst formation. Single-cell RNA sequencing of CRISPR-Cas9 gene-edited PKD1- and PKD2-knockout tubuloids and human ADPKD and control tissue shows similarities in upregulation of disease-driving genes. Furthermore, in a proof of concept, we demonstrate that tolvaptan, the only approved drug for ADPKD, has a significant effect on cyst size in tubuloids but no effect on a pluripotent stem cell-derived model. Thus, tubuloids are derived from a tubular epithelial subpopulation and represent an advanced system for ADPKD disease modeling.
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Affiliation(s)
- Yaoxian Xu
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Javier Perales-Patón
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jennifer Kranz
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Urology and Pediatric Urology, RWTH Aachen University, Aachen, Germany
- Department of Urology and Kidney Transplantation, Martin-Luther-University, Halle, Germany
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research, RWTH Aachen University, Aachen, Germany
| | - James Nagai
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Zhijian Li
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Fabian Peisker
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Turgay Saritas
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Maurice Halder
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Sylvia Menzel
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Konrad Hoeft
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Annegien Kenter
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hyojin Kim
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Claudia R C van Roeyen
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Lehrke
- Department of Cardiology, RWTH Aachen University, Aachen, Germany
| | - Julia Moellmann
- Department of Cardiology, RWTH Aachen University, Aachen, Germany
| | - Thimoteus Speer
- Department of Nephrology, University Hospital Homburg, Homburg, Germany
| | - Eva M Buhl
- Institute of Pathology and Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter Boor
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Institute of Pathology and Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany
| | - Jitske Jansen
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Pathology, RIMLS, Radboudumc, Nijmegen, the Netherlands
| | - Cordula Knopp
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Bart Smeets
- Department of Pathology, RIMLS, Radboudumc, Nijmegen, the Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marlies E J Reinders
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carla Baan
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ewout J Hoorn
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Joachim Steffens
- Department of Urology, St Antonius Hospital, Eschweiler, Germany
| | - Tobias B Huber
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ivan Costa
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rebekka K Schneider
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Institute of Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology, Kidney Research Institute and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering (Adjunct), and Department of Laboratory Medicine & Pathology (Adjunct), University of Washington, Seattle, WA, USA
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany.
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany.
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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6
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Abstract
Kidney organoids derived from human pluripotent stem cells constitute a novel model of disease, development, and regenerative therapy. Organoids are human, experimentally accessible, high throughput, and enable reconstitution of tissue-scale biology in a petri dish. Although gene expression patterns in organoid cells have been analyzed extensively, less is known about the functionality of these structures. Here, we review assays of physiological function in human kidney organoids, including best practices for quality control, and future applications. Tubular structures in organoids accumulate specific molecules through active transport, including dextran and organic anions, and swell with fluid in response to cAMP stimulation. When engrafted into animal models in vivo, organoids form vascularized glomerulus-like structures capable of size-selective filtration. Organoids exhibit metabolic, endocrine, injury, and infection phenotypes, although their specificity is not yet fully clear. To properly interpret organoid physiology assays, it is important to incorporate appropriate negative and positive controls, statistical methods, data presentation, molecular mechanisms, and clinical data sets. Improvements in organoid perfusion, patterning, and maturation are needed to enable branching morphogenesis, urine production, and renal replacement. Reconstituting renal physiology with kidney organoids is a new field with potential to provide fresh insights into classical phenomena.
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Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, Department of Laboratory Medicine and Physiology (adjunct), and Department of Bioengineering (adjunct), University of Washington School of Medicine, Seattle, Washington
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7
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Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken SE, Ljubetič A, Edman N, Ueda G, Chow CM, Johnson M, Addetia A, Navarro MJ, Panpradist N, Gale M, Freedman BS, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Sci Transl Med 2022; 14:eabn1252. [PMID: 35412328 PMCID: PMC9258422 DOI: 10.1126/scitranslmed.abn1252] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.
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Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lydia B. Green
- Amgen Research, Biologic Discovery, Burnaby, V5A 1V7, BC, Canada
| | | | | | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Invizyne Technologies Inc., Monrovia, CA, 91016, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Laboratory Medicine, University of Wisconsin – Madison, Madison, WI, 53705, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department for Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, SI-1000, Slovenia
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, 98195, USA
- USA Medical Scientist Training Program, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Neolukin Therapeutics Inc., Seattle, WA, 98102, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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8
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Cruz NM, Reddy R, McFaline-Figueroa JL, Tran C, Fu H, Freedman BS. Modelling ciliopathy phenotypes in human tissues derived from pluripotent stem cells with genetically ablated cilia. Nat Biomed Eng 2022; 6:463-475. [PMID: 35478224 PMCID: PMC9228023 DOI: 10.1038/s41551-022-00880-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 03/08/2022] [Indexed: 11/08/2022]
Abstract
The functions of cilia-antenna-like organelles associated with a spectrum of disease states-are poorly understood, particularly in human cells. Here we show that human pluripotent stem cells (hPSCs) edited via CRISPR to knock out the kinesin-2 subunits KIF3A or KIF3B can be used to model ciliopathy phenotypes and to reveal ciliary functions at the tissue scale. KIF3A-/- and KIF3B-/- hPSCs lacked cilia, yet remained robustly self-renewing and pluripotent. Tissues and organoids derived from these hPSCs displayed phenotypes that recapitulated defective neurogenesis and nephrogenesis, polycystic kidney disease (PKD) and other features of the ciliopathy spectrum. We also show that human cilia mediate a critical switch in hedgehog signalling during organoid differentiation, and that they constitutively release extracellular vesicles containing signalling molecules associated with ciliopathy phenotypes. The capacity of KIF3A-/- and KIF3B-/- hPSCs to reveal endogenous mechanisms underlying complex ciliary phenotypes may facilitate the discovery of candidate therapeutics.
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Affiliation(s)
- Nelly M Cruz
- Division of Nephrology, University of Washington School of Medicine, Seattle, WA, USA
- Kidney Research Institute, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Raghava Reddy
- Division of Nephrology, University of Washington School of Medicine, Seattle, WA, USA
- Kidney Research Institute, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Christine Tran
- Division of Nephrology, University of Washington School of Medicine, Seattle, WA, USA
- Kidney Research Institute, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Hongxia Fu
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Bioengineering (Adjunct), University of Washington School of Medicine, Seattle, WA, USA
| | - Benjamin S Freedman
- Division of Nephrology, University of Washington School of Medicine, Seattle, WA, USA.
- Kidney Research Institute, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Bioengineering (Adjunct), University of Washington School of Medicine, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology (Adjunct), University of Washington School of Medicine, Seattle, WA, USA.
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9
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Helms L, Marchiano S, Stanaway IB, Hsiang TY, Juliar BA, Saini S, Zhao YT, Khanna A, Menon R, Alakwaa F, Mikacenic C, Morrell ED, Wurfel MM, Kretzler M, Harder JL, Murry CE, Himmelfarb J, Ruohola-Baker H, Bhatraju PK, Gale M, Freedman BS. Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations. JCI Insight 2021; 6:e154882. [PMID: 34767537 PMCID: PMC8783682 DOI: 10.1172/jci.insight.154882] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Kidneys are critical target organs of COVID-19, but susceptibility and responses to infection remain poorly understood. Here, we combine SARS-CoV-2 variants with genome-edited kidney organoids and clinical data to investigate tropism, mechanism, and therapeutics. SARS-CoV-2 specifically infects organoid proximal tubules among diverse cell types. Infections produce replicating virus, apoptosis, and disrupted cell morphology, features of which are revealed in the context of polycystic kidney disease. Cross-validation of gene expression patterns in organoids reflects proteomic signatures of COVID-19 in the urine of critically ill patients indicating interferon pathway upregulation. SARS-CoV-2 viral variants alpha, beta, gamma, kappa, and delta exhibit comparable levels of infection in organoids. Infection is ameliorated in ACE2-/- organoids and blocked via treatment with de novo-designed spike binder peptides. Collectively, these studies clarify the impact of kidney infection in COVID-19 as reflected in organoids and clinical populations, enabling assessment of viral fitness and emerging therapies.
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Affiliation(s)
- Louisa Helms
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
| | - Silvia Marchiano
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
| | - Ian B. Stanaway
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
| | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin A. Juliar
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
| | - Shally Saini
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
| | - Yan Ting Zhao
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
| | - Akshita Khanna
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Center for Cardiovascular Biology
| | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fadhl Alakwaa
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mikacenic
- Department of Medicine
- Translational Research, Benaroya Research Institute, Seattle, Washington, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eric D. Morrell
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark M. Wurfel
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer L. Harder
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles E. Murry
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
- Sana Biotechnology, Seattle, Washington, USA
| | | | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Pavan K. Bhatraju
- Department of Medicine
- Kidney Research Institute
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin S. Freedman
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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10
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Wang H, Brown PC, Chow EC, Ewart L, Ferguson SS, Fitzpatrick S, Freedman BS, Guo GL, Hedrich W, Heyward S, Hickman J, Isoherranen N, Li AP, Liu Q, Mumenthaler SM, Polli J, Proctor WR, Ribeiro A, Wang J, Wange RL, Huang S. 3D cell culture models: Drug pharmacokinetics, safety assessment, and regulatory consideration. Clin Transl Sci 2021; 14:1659-1680. [PMID: 33982436 PMCID: PMC8504835 DOI: 10.1111/cts.13066] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Nonclinical testing has served as a foundation for evaluating potential risks and effectiveness of investigational new drugs in humans. However, the current two-dimensional (2D) in vitro cell culture systems cannot accurately depict and simulate the rich environment and complex processes observed in vivo, whereas animal studies present significant drawbacks with inherited species-specific differences and low throughput for increased demands. To improve the nonclinical prediction of drug safety and efficacy, researchers continue to develop novel models to evaluate and promote the use of improved cell- and organ-based assays for more accurate representation of human susceptibility to drug response. Among others, the three-dimensional (3D) cell culture models present physiologically relevant cellular microenvironment and offer great promise for assessing drug disposition and pharmacokinetics (PKs) that influence drug safety and efficacy from an early stage of drug development. Currently, there are numerous different types of 3D culture systems, from simple spheroids to more complicated organoids and organs-on-chips, and from single-cell type static 3D models to cell co-culture 3D models equipped with microfluidic flow control as well as hybrid 3D systems that combine 2D culture with biomedical microelectromechanical systems. This article reviews the current application and challenges of 3D culture systems in drug PKs, safety, and efficacy assessment, and provides a focused discussion and regulatory perspectives on the liver-, intestine-, kidney-, and neuron-based 3D cellular models.
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Affiliation(s)
- Hongbing Wang
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Paul C. Brown
- Center for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | - Edwin C.Y. Chow
- Office of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | | | - Stephen S. Ferguson
- Division of the National Toxicology ProgramNational Institute of Environmental Health SciencesResearch Triangle ParkNorth CarolinaUSA
| | - Suzanne Fitzpatrick
- Office of the Center DirectorCenter for Food Safety and Applied NutritionUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | - Benjamin S. Freedman
- Division of NephrologyDepartment of PathologyKidney Research Institute, and Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
- Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Grace L. Guo
- Department of Pharmacology and ToxicologyErnest Mario School of PharmacyRutgers UniversityPiscatawayNew JerseyUSA
| | - William Hedrich
- Pharmaceutical Candidate Optimization, Metabolism and PharmacokineticsBristol‐Myers Squibb CompanyPrincetonNew JerseyUSA
| | | | - James Hickman
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | - Nina Isoherranen
- Department of PharmaceuticsSchool of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Albert P. Li
- In Vitro ADMET LaboratoriesColumbiaMarylandUSA
- In Vitro ADMET LaboratoriesMaldenMassachusettsUSA
| | - Qi Liu
- Office of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | - Shannon M. Mumenthaler
- Lawrence J. Ellison Institute for Transformative MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - James Polli
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - William R. Proctor
- Predictive Toxicology, Safety AssessmentGenentech, IncSouth San FranciscoCaliforniaUSA
| | - Alexandre Ribeiro
- Office of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | - Jian‐Ying Wang
- Department of SurgeryCell Biology GroupUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Ronald L. Wange
- Center for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
| | - Shiew‐Mei Huang
- Office of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug Administration (FDA)Silver SpringMarylandUSA
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11
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Gopalan J, Omar MH, Roy A, Cruz NM, Falcone J, Jones KN, Forbush KA, Himmelfarb J, Freedman BS, Scott JD. Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis. eLife 2021; 10:e67828. [PMID: 34250905 PMCID: PMC8291974 DOI: 10.7554/elife.67828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/11/2021] [Indexed: 11/13/2022] Open
Abstract
Pathophysiological defects in water homeostasis can lead to renal failure. Likewise, common genetic disorders associated with abnormal cytoskeletal dynamics in the kidney collecting ducts and perturbed calcium and cAMP signaling in the ciliary compartment contribute to chronic kidney failure. We show that collecting ducts in mice lacking the A-Kinase anchoring protein AKAP220 exhibit enhanced development of primary cilia. Mechanistic studies reveal that AKAP220-associated protein phosphatase 1 (PP1) mediates this phenotype by promoting changes in the stability of histone deacetylase 6 (HDAC6) with concomitant defects in actin dynamics. This proceeds through a previously unrecognized adaptor function for PP1 as all ciliogenesis and cytoskeletal phenotypes are recapitulated in mIMCD3 knock-in cells expressing a phosphatase-targeting defective AKAP220-ΔPP1 mutant. Pharmacological blocking of local HDAC6 activity alters cilia development and reduces cystogenesis in kidney-on-chip and organoid models. These findings identify the AKAP220-PPI-HDAC6 pathway as a key effector in primary cilia development.
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Affiliation(s)
- Janani Gopalan
- Department of Pharmacology, University of WashingtonSeattleUnited States
| | - Mitchell H Omar
- Department of Pharmacology, University of WashingtonSeattleUnited States
| | - Ankita Roy
- Kidney Research Institute, Division of Nephrology, Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
- Institute for Stem Cell and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Nelly M Cruz
- Kidney Research Institute, Division of Nephrology, Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
- Institute for Stem Cell and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Jerome Falcone
- Department of Pharmacology, University of WashingtonSeattleUnited States
| | - Kiana N Jones
- Department of Pharmacology, University of WashingtonSeattleUnited States
| | | | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Benjamin S Freedman
- Kidney Research Institute, Division of Nephrology, Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
- Institute for Stem Cell and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - John D Scott
- Department of Pharmacology, University of WashingtonSeattleUnited States
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12
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Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. bioRxiv 2021:2021.07.07.451375. [PMID: 34268509 PMCID: PMC8282097 DOI: 10.1101/2021.07.07.451375] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Escape variants of SARS-CoV-2 are threatening to prolong the COVID-19 pandemic. To address this challenge, we developed multivalent protein-based minibinders as potential prophylactic and therapeutic agents. Homotrimers of single minibinders and fusions of three distinct minibinders were designed to geometrically match the SARS-CoV-2 spike (S) trimer architecture and were optimized by cell-free expression and found to exhibit virtually no measurable dissociation upon binding. Cryo-electron microscopy (cryoEM) showed that these trivalent minibinders engage all three receptor binding domains on a single S trimer. The top candidates neutralize SARS-CoV-2 variants of concern with IC 50 values in the low pM range, resist viral escape, and provide protection in highly vulnerable human ACE2-expressing transgenic mice, both prophylactically and therapeutically. Our integrated workflow promises to accelerate the design of mutationally resilient therapeutics for pandemic preparedness. ONE-SENTENCE SUMMARY We designed, developed, and characterized potent, trivalent miniprotein binders that provide prophylactic and therapeutic protection against emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | | | | | | | - Bastain Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Antje Krüger-Gericke
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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13
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Refaeli I, Hughes MR, Wong AKW, Bissonnette MLZ, Roskelley CD, Wayne Vogl A, Barbour SJ, Freedman BS, McNagny KM. Distinct Functional Requirements for Podocalyxin in Immature and Mature Podocytes Reveal Mechanisms of Human Kidney Disease. Sci Rep 2020; 10:9419. [PMID: 32523052 PMCID: PMC7286918 DOI: 10.1038/s41598-020-64907-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Dominant and recessive mutations in podocalyxin (PODXL) are associated with human kidney disease. Interestingly, some PODXL mutations manifest as anuria while others are associated with proteinuric kidney disease. PODXL heterozygosity is associated with adult-onset kidney disease and podocalyxin shedding into the urine is a common biomarker of a variety nephrotic syndromes. It is unknown, however, how various lesions in PODXL contribute to these disparate disease pathologies. Here we generated two mouse stains: one that deletes Podxl in developmentally mature podocytes (Podxl∆Pod) and a second that is heterozygous for podocalyxin in all tissues (Podxl+/-). We used histologic and ultrastructural analyses, as well as clinical chemistry assays to evaluate kidney development and function in these strains. In contrast to null knockout mice (Podxl-/-), which die shortly after birth from anuria and hypertension, Podxl∆Pod mice develop an acute congenital nephrotic syndrome characterized by focal segmental glomerulosclerosis (FSGS) and proteinuria. Podxl+/- mice, in contrast, have a normal lifespan, and fail to develop kidney disease under normal conditions. Intriguingly, although wild-type C57Bl/6 mice are resistant to puromycin aminonucleoside (PA)-induced nephrosis (PAN), Podxl+/- mice are highly sensitive and PA induces severe proteinuria and collapsing FSGS. In summary, we find that the developmental timepoint at which podocalyxin is ablated (immature vs. mature podocytes) has a profound effect on the urinary phenotype due to its critical roles in both the formation and the maintenance of podocyte ultrastructure. In addition, Podxl∆Pod and Podxl+/- mice offer powerful new mouse models to evaluate early biomarkers of proteinuric kidney disease and to test novel therapeutics.
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Affiliation(s)
- Ido Refaeli
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael R Hughes
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Alvin Ka-Wai Wong
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Mei Lin Z Bissonnette
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Calvin D Roskelley
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - A Wayne Vogl
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sean J Barbour
- Division of Nephrology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.,Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Kelly M McNagny
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. .,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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14
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Abstract
In February 2020, the European Molecular Biology Laboratory (EMBL) and the Institute for Bioengineering of Catalonia (IBEC) joined forces to unite researchers from all over the globe to discuss emerging topics in 'Engineering Multicellular Systems'. As we review here, key themes that arose throughout the meeting included the ethics of organoids in developmental biology, bottom-up versus top-down models, tissue organizing principles, and the future of improving these systems to better mimic the natural world.
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Affiliation(s)
- Kristina Haase
- EMBL Barcelona, Carrer/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Pathology (Adjunct), and Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
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15
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Barabino A, Flamier A, Hanna R, Héon E, Freedman BS, Bernier G. Deregulation of Neuro-Developmental Genes and Primary Cilium Cytoskeleton Anomalies in iPSC Retinal Sheets from Human Syndromic Ciliopathies. Stem Cell Reports 2020; 14:357-373. [PMID: 32160518 PMCID: PMC7066374 DOI: 10.1016/j.stemcr.2020.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 01/22/2023] Open
Abstract
Ciliopathies are heterogeneous genetic diseases affecting primary cilium structure and function. Meckel-Gruber (MKS) and Bardet-Biedl (BBS) syndromes are severe ciliopathies characterized by skeletal and neurodevelopment anomalies, including polydactyly, cognitive impairment, and retinal degeneration. We describe the generation and molecular characterization of human induced pluripotent stem cell (iPSC)-derived retinal sheets (RSs) from controls, and MKS (TMEM67) and BBS (BBS10) cases. MKS and BBS RSs displayed significant common alterations in the expression of hundreds of developmental genes and members of the WNT and BMP pathways. Induction of crystallin molecular chaperones was prominent in MKS and BBS RSs suggesting a stress response to misfolded proteins. Unique to MKS photoreceptors was the presence of supernumerary centrioles and cilia, and aggregation of ciliary proteins. Unique to BBS photoreceptors was the accumulation of DNA damage and activation of the mitotic spindle checkpoint. This study reveals how combining cell reprogramming, organogenesis, and next-generation sequencing enables the elucidation of mechanisms involved in human ciliopathies.
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Affiliation(s)
- Andrea Barabino
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. Assomption, Montreal, QC H1T 2M4, Canada
| | - Anthony Flamier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. Assomption, Montreal, QC H1T 2M4, Canada
| | - Roy Hanna
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. Assomption, Montreal, QC H1T 2M4, Canada
| | - Elise Héon
- Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, Program of Genetics and Genome Biology, 555 University av., Toronto, ON M5G 1X8, Canada
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology, Kidney Research Institute, and Institute of Stem Cell and Regenerative Medicine, and Department of Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA.
| | - Gilbert Bernier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. Assomption, Montreal, QC H1T 2M4, Canada; Department of Neurosciences, University of Montreal, Montreal, QC H3C 3J7, Canada; Department of Ophthalmology, University of Montreal, Montreal, QC H3C 3J7, Canada.
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16
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Liu E, Radmanesh B, Chung BH, Donnan MD, Yi D, Dadi A, Smith KD, Himmelfarb J, Li M, Freedman BS, Lin J. Profiling APOL1 Nephropathy Risk Variants in Genome-Edited Kidney Organoids with Single-Cell Transcriptomics. Kidney360 2020; 1:203-215. [PMID: 32656538 PMCID: PMC7351353 DOI: 10.34067/kid.0000422019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND DNA variants in APOL1 associate with kidney disease, but the pathophysiologic mechanisms remain incompletely understood. Model organisms lack the APOL1 gene, limiting the degree to which disease states can be recapitulated. Here we present single-cell RNA sequencing (scRNA-seq) of genome-edited human kidney organoids as a platform for profiling effects of APOL1 risk variants in diverse nephron cell types. METHODS We performed footprint-free CRISPR-Cas9 genome editing of human induced pluripotent stem cells (iPSCs) to knock in APOL1 high-risk G1 variants at the native genomic locus. iPSCs were differentiated into kidney organoids, treated with vehicle, IFN-γ, or the combination of IFN-γ and tunicamycin, and analyzed with scRNA-seq to profile cell-specific changes in differential gene expression patterns, compared with isogenic G0 controls. RESULTS Both G0 and G1 iPSCs differentiated into kidney organoids containing nephron-like structures with glomerular epithelial cells, proximal tubules, distal tubules, and endothelial cells. Organoids expressed detectable APOL1 only after exposure to IFN-γ. scRNA-seq revealed cell type-specific differences in G1 organoid response to APOL1 induction. Additional stress of tunicamycin exposure led to increased glomerular epithelial cell dedifferentiation in G1 organoids. CONCLUSIONS Single-cell transcriptomic profiling of human genome-edited kidney organoids expressing APOL1 risk variants provides a novel platform for studying the pathophysiology of APOL1-mediated kidney disease.
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Affiliation(s)
- Esther Liu
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Behram Radmanesh
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Byungha H. Chung
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Michael D. Donnan
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Dan Yi
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Amal Dadi
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kelly D. Smith
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Benjamin S. Freedman
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jennie Lin
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Section of Nephrology, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
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17
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Nam SA, Seo E, Kim JW, Kim HW, Kim HL, Kim K, Kim TM, Ju JH, Gomez IG, Uchimura K, Humphreys BD, Yang CW, Lee JY, Kim J, Cho DW, Freedman BS, Kim YK. Correction to: Graft immaturity and safety concerns in transplanted human kidney organoids. Exp Mol Med 2020; 52:180. [PMID: 31956266 PMCID: PMC8115108 DOI: 10.1038/s12276-019-0366-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Sun Ah Nam
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunjeong Seo
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Won Kim
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyung Wook Kim
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Internal Medicine, College of Medicine, The Catholic University of Korea, St. Vincent's Hospital, Suwon, Korea
| | - Hong Lim Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyuryung Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea and Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tae-Min Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea and Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ji Hyeon Ju
- Catholic iPSC Research Center, and Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ivan G Gomez
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Kohei Uchimura
- Division of Nephrology, Department of Medicine, and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chul Woo Yang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae Yeon Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, South Korea
| | - Jin Kim
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Woo Cho
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, South Korea.
| | - Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| | - Yong Kyun Kim
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Department of Internal Medicine, College of Medicine, The Catholic University of Korea, St. Vincent's Hospital, Suwon, Korea.
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18
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Kaverina NV, Eng DG, Freedman BS, Kutz JN, Chozinski TJ, Vaughan JC, Miner JH, Pippin JW, Shankland SJ. Dual lineage tracing shows that glomerular parietal epithelial cells can transdifferentiate toward the adult podocyte fate. Kidney Int 2019; 96:597-611. [PMID: 31200942 PMCID: PMC7008116 DOI: 10.1016/j.kint.2019.03.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Podocytes are differentiated post-mitotic cells that cannot replace themselves after injury. Glomerular parietal epithelial cells are proposed to be podocyte progenitors. To test whether a subset of parietal epithelial cells transdifferentiate to a podocyte fate, dual reporter PEC-rtTA|LC1|tdTomato|Nphs1-FLPo|FRT-EGFP mice, named PEC-PODO, were generated. Doxycycline administration permanently labeled parietal epithelial cells with tdTomato reporter (red), and upon doxycycline removal, the parietal epithelial cells (PECs) cannot label further. Despite the presence or absence of doxycycline, podocytes cannot label with tdTomato, but are constitutively labeled with an enhanced green fluorescent protein (EGFP) reporter (green). Only activation of the Nphs1-FLPo transgene by labeled parietal epithelial cells can generate a yellow color. At day 28 of experimental focal segmental glomerulosclerosis, podocyte density was 20% lower in 20% of glomeruli. At day 56 of experimental focal segmental glomerulosclerosis, podocyte density was 18% lower in 17% of glomeruli. TdTomato+ parietal epithelial cells were restricted to Bowman's capsule in healthy mice. However, by days 28 and 56 of experimental disease, two-thirds of tdTomato+ parietal epithelial cells within glomerular tufts were yellow in color. These cells co-expressed the podocyte markers podocin, nephrin, p57 and VEGF164, but not markers of endothelial (ERG) or mesangial (Perlecan) cells. Expansion microscopy showed primary, secondary and minor processes in tdTomato+EGFP+ cells in glomerular tufts. Thus, our studies provide strong evidence that parietal epithelial cells serve as a source of new podocytes in adult mice.
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Affiliation(s)
- Natalya V Kaverina
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Diana G Eng
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | | | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, Washington, USA
| | - Tyler J Chozinski
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA; Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Jeffrey H Miner
- Division of Nephrology, Washington University School of Medicine, St Louis, Missouri, 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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19
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Abstract
It is now possible to direct the differentiation of human pluripotent stem cells into three-dimensional nephron-like structures called kidney organoids. Organoids contain proximal and distal tubules as well as podocytes, in addition to a variety of other lineages such as endothelial cells. Organoid technology has great potential for kidney regeneration and has already been proven to be suitable for modeling kidney disease. However, the methodologies that are used for the generation of kidney organoids require expertise and can be daunting for the inexperienced. Here, we describe in detail a well-established and relatively simple method for the generation of human kidney organoids. We include notes on technical and design considerations for these experiments, and highlight key advantages and limitations of the system.
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Affiliation(s)
- Nelly M Cruz
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA, United States; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, United States; Department of Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA, United States; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, United States; Department of Pathology, University of Washington School of Medicine, Seattle, WA, United States.
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20
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Freedman BS. Producing Purer Podocytes. J Am Soc Nephrol 2019; 30:183-184. [PMID: 30635374 DOI: 10.1681/asn.2018101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, .,Kidney Research Institute, .,and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, and .,Department of Pathology, University of Washington School of Medicine, Seattle, Washington
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21
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Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight 2019; 4:122697. [PMID: 30626756 PMCID: PMC6485369 DOI: 10.1172/jci.insight.122697] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Podocyte injury is central to many forms of kidney disease, but transcriptional signatures reflecting podocyte injury and compensation mechanisms are challenging to analyze in vivo. Human kidney organoids derived from pluripotent stem cells (PSCs), a potentially new model for disease and regeneration, present an opportunity to explore the transcriptional plasticity of podocytes. Here, transcriptional profiling of more than 12,000 single cells from human PSC-derived kidney organoid cultures was used to identify robust and reproducible cell lineage gene expression signatures shared with developing human kidneys based on trajectory analysis. Surprisingly, the gene expression signature characteristic of developing glomerular epithelial cells was also observed in glomerular tissue from a kidney disease cohort. This signature correlated with proteinuria and inverse eGFR, and it was confirmed in an independent podocytopathy cohort. Three genes in particular were further characterized as potentially novel components of the glomerular disease signature. We conclude that cells in human PSC-derived kidney organoids reliably recapitulate the developmental transcriptional program of podocytes and other cell lineages in the human kidney and that transcriptional profiles seen in developing podocytes are reactivated in glomerular disease. Our findings demonstrate an approach to identifying potentially novel molecular programs involved in the pathogenesis of glomerulopathies.
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Affiliation(s)
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, and
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, and
| | - Noel L Wys
- Department of Internal Medicine, Division of Nephrology, and
| | | | | | - Viji Nair
- Department of Internal Medicine, Division of Nephrology, and
| | - Cristina Cebrian
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Markus Bitzer
- Department of Internal Medicine, Division of Nephrology, and
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, New York, USA.,Lewis-Sigler Institute for Integrative Genomics and.,Department of Computer Science, Princeton University, Princeton, New Jersey, USA
| | | | - Roger C Wiggins
- Department of Internal Medicine, Division of Nephrology, and
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology.,Kidney Research Institute.,Institute for Stem Cell and Regenerative Medicine, and.,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, and.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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22
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Abstract
CONTEXT Human kidney organoids are complex structures resembling nephron arrays, which can be derived in a variety of ways. Whether all of these differentiation protocols produce qualitatively similar organoid cell types is not yet clear. Subject of Review: A comparative analysis of 2 organoid differentiation protocols is recently reported in Cell Stem Cell [Wu et al.: Cell Stem Cell 2018;pii:S1934-5909(18)30491-0], using single cell RNA sequencing (scRNA-seq) as an analytical tool. This demonstrates that the 2 protocols have much in common, and that neither produces kidney cells in a pure or comprehensive manner. Ureteric lineages appear to be absent, and organoids are contaminated with non-kidney cell types, including neurons and muscle cells. Based on the scRNA-seq datasets, a new differentiation protocol is devised to reduce non-kidney cell types, without adversely affecting organoid epithelial cells. Second Opinion: Together with published analyses of a third differentiation protocol, these findings suggest more commonalities than differences between kidney organoid platforms, and identify critical strategies for functional improvement of these cellular structures.
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Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, and Department of Pathology, University of Washington School of Medicine, Seattle, Washington, USA,
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23
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Hamatani H, Eng DG, Kaverina NV, Gross KW, Freedman BS, Pippin JW, Shankland SJ. Lineage tracing aged mouse kidneys shows lower number of cells of renin lineage and reduced responsiveness to RAAS inhibition. Am J Physiol Renal Physiol 2018; 315:F97-F109. [PMID: 29412700 PMCID: PMC6087792 DOI: 10.1152/ajprenal.00570.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 11/22/2022] Open
Abstract
Blocking the renin-angiotensin-aldosterone system (RAAS) remains a mainstay of therapy in hypertension and glomerular diseases. With the population aging, our understanding of renin-producing cells in kidneys with advanced age is more critical than ever. Accordingly, we administered tamoxifen to Ren1cCreERxRs-tdTomato-R mice to permanently fate map cells of renin lineage (CoRL). The number of Td-tomato-labeled CoRL decreased significantly in aged mice (24 mo of age) compared with young mice (3.5 mo of age), as did renin mRNA levels. To determine whether aged CoRL responded less to RAAS blockade, enalapril and losartan were administered over 25 days following uninephrectomy in young and aged mice. The number of CoRL increased in young mice in response to enalapril and losartan. However, this was significantly lower in aged mice compared with young mice due to limited proliferation, but not recruitment. Gene expression analysis of laser-captured CoRL showed a substantial increase in mRNA levels for proapoptotic and prosenescence genes, and an increase in a major prosenescence protein on immunostaining. These results show that CoRL are lower in aged mice and do not respond to RAAS inhibition to the same extent as young mice.
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Affiliation(s)
- Hiroko Hamatani
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
| | - Diana G Eng
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
| | - Natalya V Kaverina
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
| | - Kenneth W Gross
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute , Buffalo, New York
| | - Benjamin S Freedman
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
| | - Stuart J Shankland
- Division of Nephrology, University of Washington School of Medicine , Seattle, Washington
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24
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Abstract
CRISPR is a nuclease guidance system that enables rapid and efficient gene editing of specific DNA sequences within genomes. We review applications of CRISPR for the study and treatment of kidney disease. CRISPR enables functional experiments in cell lines and model organisms to validate candidate genes arising from genetic studies. CRISPR has furthermore been used to establish the first models of genetic disease in human kidney organoids derived from pluripotent stem cells. These gene-edited organoids are providing new insight into the cellular mechanisms of polycystic kidney disease and nephrotic syndrome. CRISPR-engineered cell therapies are currently in clinical trials for cancers and immunologic syndromes, an approach that may be applicable to inflammatory conditions such as lupus nephritis. Use of CRISPR in large domestic species such as pigs raises the possibility of farming kidneys for transplantation to alleviate the shortage of donor organs. However, significant challenges remain, including how to effectively deliver CRISPR to kidneys and how to control gene editing events within the genome. Thorough testing of CRISPR in preclinical models will be critical to the safe and efficacious translation of this powerful young technology into therapies.
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Affiliation(s)
- Nelly M Cruz
- Division of Nephrology, University of Washington School of Medicine, Seattle WA; Kidney Research Institute, University of Washington School of Medicine, Seattle WA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA; Department of Medicine, University of Washington School of Medicine, Seattle WA
| | - Benjamin S Freedman
- Division of Nephrology, University of Washington School of Medicine, Seattle WA; Kidney Research Institute, University of Washington School of Medicine, Seattle WA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA; Department of Medicine, University of Washington School of Medicine, Seattle WA.
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25
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Czerniecki SM, Cruz NM, Harder JL, Menon R, Annis J, Otto EA, Gulieva RE, Islas LV, Kim YK, Tran LM, Martins TJ, Pippin JW, Fu H, Kretzler M, Shankland SJ, Himmelfarb J, Moon RT, Paragas N, Freedman BS. High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping. Cell Stem Cell 2018; 22:929-940.e4. [PMID: 29779890 PMCID: PMC5984728 DOI: 10.1016/j.stem.2018.04.022] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 02/05/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022]
Abstract
Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-throughput screening (HTS), but the complexity of organoid cultures poses a significant challenge for miniaturization and automation. Here, we present a fully automated, HTS-compatible platform for enhanced differentiation and phenotyping of human kidney organoids. The entire 21-day protocol, from plating to differentiation to analysis, can be performed automatically by liquid-handling robots, or alternatively by manual pipetting. High-content imaging analysis reveals both dose-dependent and threshold effects during organoid differentiation. Immunofluorescence and single-cell RNA sequencing identify previously undetected parietal, interstitial, and partially differentiated compartments within organoids and define conditions that greatly expand the vascular endothelium. Chemical modulation of toxicity and disease phenotypes can be quantified for safety and efficacy prediction. Screening in gene-edited organoids in this system reveals an unexpected role for myosin in polycystic kidney disease. Organoids in HTS formats thus establish an attractive platform for multidimensional phenotypic screening.
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Affiliation(s)
- Stefan M Czerniecki
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Nelly M Cruz
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - James Annis
- Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ramila E Gulieva
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Laura V Islas
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Yong Kyun Kim
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Linh M Tran
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Hematology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Timothy J Martins
- Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jeffrey W Pippin
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Hongxia Fu
- Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Hematology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Stuart J Shankland
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jonathan Himmelfarb
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Randall T Moon
- Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Pharmacology, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Neal Paragas
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine and Quellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA.
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26
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Jing P, Liu Y, Keeler EG, Cruz NM, Freedman BS, Lin LY. Optical tweezers system for live stem cell organization at the single-cell level. Biomed Opt Express 2018; 9:771-779. [PMID: 29552411 PMCID: PMC5854077 DOI: 10.1364/boe.9.000771] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 05/04/2023]
Abstract
Cell manipulation is one of the most impactful applications for optical tweezers, and derived from this promise, we demonstrate a new optical tweezers system for the study of cell adhesion and organization. This method utilizes photonic-crystal-enhanced optical tweezers to manipulate cells with low laser intensities. By doing so, it enables effective cell patterning and culturing within the conditions necessary for successful differentiation and colony formation of human pluripotent stem cells. To this end, the biocompatibility of plasma-treated parylene-C for cell culturing was studied, and a thorough characterization of cellular interactive forces was performed using this system. Furthermore, this study also demonstrates construction of patterned cell arrays at arbitrary positions with micrometer-scale precision.
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Affiliation(s)
- Peifeng Jing
- Department of Electrical Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
| | - Yannan Liu
- Department of Electrical Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
| | - Ethan G Keeler
- Department of Electrical Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
| | - Nelly M Cruz
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, 850 Republican St., Seattle, WA 98109, USA
| | - Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, 850 Republican St., Seattle, WA 98109, USA
| | - Lih Y Lin
- Department of Electrical Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
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27
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Cruz NM, Song X, Czerniecki SM, Gulieva RE, Churchill AJ, Kim YK, Winston K, Tran LM, Diaz MA, Fu H, Finn LS, Pei Y, Himmelfarb J, Freedman BS. Organoid cystogenesis reveals a critical role of microenvironment in human polycystic kidney disease. Nat Mater 2017; 16:1112-1119. [PMID: 28967916 PMCID: PMC5936694 DOI: 10.1038/nmat4994] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/29/2017] [Indexed: 05/23/2023]
Abstract
Polycystic kidney disease (PKD) is a life-threatening disorder, commonly caused by defects in polycystin-1 (PC1) or polycystin-2 (PC2), in which tubular epithelia form fluid-filled cysts. A major barrier to understanding PKD is the absence of human cellular models that accurately and efficiently recapitulate cystogenesis. Previously, we have generated a genetic model of PKD using human pluripotent stem cells and derived kidney organoids. Here we show that systematic substitution of physical components can dramatically increase or decrease cyst formation, unveiling a critical role for microenvironment in PKD. Removal of adherent cues increases cystogenesis 10-fold, producing cysts phenotypically resembling PKD that expand massively to 1-centimetre diameters. Removal of stroma enables outgrowth of PKD cell lines, which exhibit defects in PC1 expression and collagen compaction. Cyclic adenosine monophosphate (cAMP), when added, induces cysts in both PKD organoids and controls. These biomaterials establish a highly efficient model of PKD cystogenesis that directly implicates the microenvironment at the earliest stages of the disease.
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Affiliation(s)
- Nelly M. Cruz
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Xuewen Song
- Division of Nephrology, University Health Network, ON, M5G2N2, Canada
- University of Toronto, Toronto, ON, M5G2N2, Canada
| | - Stefan M. Czerniecki
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Ramila E. Gulieva
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Angela J. Churchill
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Yong Kyun Kim
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Kosuke Winston
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Linh M. Tran
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Marco A. Diaz
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Hongxia Fu
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Division of Hematology, Department of Medicine and Seattle WA 98109, USA
- Department of Bioengineering, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Laura S. Finn
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98105, USA
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - York Pei
- Division of Nephrology, University Health Network, ON, M5G2N2, Canada
- University of Toronto, Toronto, ON, M5G2N2, Canada
| | - Jonathan Himmelfarb
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
| | - Benjamin S. Freedman
- Division of Nephrology, University of Washington School of Medicine, Seattle WA 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
- Department of Medicine, University of Washington School of Medicine, Seattle WA 98109, USA
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28
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Abstract
CONTEXT The clinical need for organ replacement therapies has inspired the idea of growing human organs in animal hosts. The injection of human pluripotent stem cells into animal blastocysts provides a possible strategy to accomplish this goal. Subject of Review: A recent study [Wu et al. Cell 2017;168:473-486.e415] tests the feasibility of this approach by creating chimeric embryos between humans and large domestic animals, including pigs and cattle. The study further examines the potential of combining CRISPR-Cas9 gene editing with blastocyst complementation to grow fully foreign organs in chimeric hosts. Second Opinion: Here, we consider what this report and related studies reveal about the likelihood of human-animal chimeras reaching the clinic and translating into therapies. A careful look suggests hope for eventual success in this area but also underscores important challenges that will require dedicated effort to resolve.
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29
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Kim YK, Refaeli I, Brooks CR, Jing P, Gulieva RE, Hughes MR, Cruz NM, Liu Y, Churchill AJ, Wang Y, Fu H, Pippin JW, Lin LY, Shankland SJ, Vogl AW, McNagny KM, Freedman BS. Gene-Edited Human Kidney Organoids Reveal Mechanisms of Disease in Podocyte Development. Stem Cells 2017; 35:2366-2378. [PMID: 28905451 DOI: 10.1002/stem.2707] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/04/2017] [Indexed: 11/07/2022]
Abstract
A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. hPSC-podocytes in vitro progressively establish junction-rich basal membranes (nephrin+ podocin+ ZO-1+ ) and microvillus-rich apical membranes (podocalyxin+ ), similar to CLS podocytes in vivo. Ultrastructural, biophysical, and transcriptomic analysis of podocalyxin-knockout hPSCs and derived podocytes, generated using CRISPR/Cas9, reveals defects in the assembly of microvilli and lateral spaces between developing podocytes, resulting in failed junctional migration. These defects are phenocopied in CLS glomeruli of podocalyxin-deficient mice, which cannot produce urine, thereby demonstrating that podocalyxin has a conserved and essential role in mammalian podocyte maturation. Defining the maturity of hPSC-podocytes and their capacity to reveal and recapitulate pathophysiological mechanisms establishes a powerful framework for studying human kidney disease and regeneration. Stem Cells 2017;35:2366-2378.
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Affiliation(s)
- Yong Kyun Kim
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Ido Refaeli
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig R Brooks
- Division of Nephrology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peifeng Jing
- Department of Electrical Engineering, University of Washington, Seattle, Washington, USA
| | - Ramila E Gulieva
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael R Hughes
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nelly M Cruz
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Yannan Liu
- Department of Electrical Engineering, University of Washington, Seattle, Washington, USA
| | - Angela J Churchill
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
| | - Hongxia Fu
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Division of Hematology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Bioengineering, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jeffrey W Pippin
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Lih Y Lin
- Department of Electrical Engineering, University of Washington, Seattle, Washington, USA
| | - Stuart J Shankland
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - A Wayne Vogl
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kelly M McNagny
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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30
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Tögel F, Valerius MT, Freedman BS, Iatrino R, Grinstein M, Bonventre JV. Repair after nephron ablation reveals limitations of neonatal neonephrogenesis. JCI Insight 2017; 2:e88848. [PMID: 28138555 DOI: 10.1172/jci.insight.88848] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The neonatal mouse kidney retains nephron progenitor cells in a nephrogenic zone for 3 days after birth. We evaluated whether de novo nephrogenesis can be induced postnatally beyond 3 days. Given the long-term implications of nephron number for kidney health, it would be useful to enhance nephrogenesis in the neonate. We induced nephron reduction by cryoinjury with or without contralateral nephrectomy during the neonatal period or after 1 week of age. There was no detectable compensatory de novo nephrogenesis, as determined by glomerular counting and lineage tracing. Contralateral nephrectomy resulted in additional adaptive healing, with little or no fibrosis, but did not also stimulate de novo nephrogenesis. In contrast, injury initiated at 1 week of age led to healing with fibrosis. Thus, despite the presence of progenitor cells and ongoing nephron maturation in the newborn mouse kidney, de novo nephrogenesis is not inducible by acute nephron reduction. This indicates that additional nephron progenitors cannot be recruited after birth despite partial renal ablation providing a reparative stimulus and suggests that nephron number in the mouse is predetermined at birth.
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Affiliation(s)
- Florian Tögel
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - M Todd Valerius
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Benjamin S Freedman
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Rossella Iatrino
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Mor Grinstein
- Center for Regenerative Medicine and Department of Orthopaedic Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Joseph V Bonventre
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
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31
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Pang P, Abbott M, Chang SL, Abdi M, Chauhan N, Mistri M, Ghofrani J, Fucci QA, Walker C, Leonardi C, Grady S, Halim A, Hoffman R, Lu T, Cao H, Tullius SG, Malek S, Kumar S, Steele G, Kibel A, Freedman BS, Waikar SS, Siedlecki AM. Human vascular progenitor cells derived from renal arteries are endothelial-like and assist in the repair of injured renal capillary networks. Kidney Int 2017; 91:129-143. [PMID: 27692806 PMCID: PMC5179298 DOI: 10.1016/j.kint.2016.07.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/21/2022]
Abstract
Vascular progenitor cells show promise for the treatment of microvasculature endothelial injury. We investigated the function of renal artery progenitor cells derived from radical nephrectomy patients, in animal models of acute ischemic and hyperperfusion injuries. Present in human adventitia, CD34positive/CD105negative cells were clonal and expressed transcription factors Sox2/Oct4 as well as surface markers CXCR4 (CD184)/KDR(CD309) consistent with endothelial progenitor cells. Termed renal artery-derived vascular progenitor cells (RAPC), injected cells were associated with decreased serum creatinine after ischemia/reperfusion, reduced albuminuria after hyperperfusion, and improved blood flow in both models. A small population of RAPC integrated with the renal microvasculature following either experimental injury. At a cellular level, RAPC promoted local endothelial migration in co-culture. Profiling of RAPC microRNA identified high levels of miRNA 218; also found at high levels in exosomes isolated from RAPC conditioned media after cell contact for 24 hours. After hydrogen peroxide-induced endothelial injury, RAPC exosomes harbored Robo-1 transcript; a gene known to be regulated by mir218. Such exosomes enhanced endothelial cell migration in culture in the absence of RAPC. Thus, our work shows the feasibility of pre-emptive pro-angiogenic progenitor cell procurement from a targeted patient population and potential therapeutic use in the form of autologous cell transplantation.
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Affiliation(s)
- Paul Pang
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Molly Abbott
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven L Chang
- Urology Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Malyun Abdi
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nikita Chauhan
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Murti Mistri
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua Ghofrani
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Quynh-Anh Fucci
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Colleen Walker
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Corey Leonardi
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel Grady
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Arvin Halim
- Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryan Hoffman
- Internal Medicine, Touro College of Osteopathic Medicine, New York, NY, USA
| | - Tzongshi Lu
- Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Huixia Cao
- Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stefan G Tullius
- Transplant Surgery Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sayeed Malek
- Transplant Surgery Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjaya Kumar
- Transplant Surgery Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Graeme Steele
- Urology Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam Kibel
- Urology Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Sushrut S Waikar
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew M Siedlecki
- Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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32
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Freedman BS, Zeidel ML, Steinman TI. TECHNOLOGY AND THE FUTURE OF KIDNEY CARE. Nephrol News Issues 2016; 30:24-28. [PMID: 30645802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The coming decades will see enormous changes in how kidney disease is diagnosed and treated. We can only predict a small proportion of the discoveries that will catalyze these changes. It is exhilarating to imagine how such discoveries might soon translate into improved medical care for millions of people.
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33
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Morizane R, Lam AQ, Freedman BS, Kishi S, Valerius MT, Bonventre JV. Nephron organoids derived from human pluripotent stem cells model kidney development and injury. Nat Biotechnol 2016; 33:1193-200. [PMID: 26458176 PMCID: PMC4747858 DOI: 10.1038/nbt.3392] [Citation(s) in RCA: 571] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/06/2015] [Indexed: 12/23/2022]
Abstract
Kidney cells and tissues derived from human pluripotent stem cells (hPSCs) would enable organ regeneration, disease modeling, and drug screening in vitro. We established an efficient, chemically defined protocol for differentiating hPSCs into multipotent nephron progenitor cells (NPCs) that can form nephron-like structures. By recapitulating metanephric kidney development in vitro, we generate SIX2+SALL1+WT1+PAX2+ NPCs with 90% efficiency within 9 days of differentiation. The NPCs possess the developmental potential of their in vivo counterparts and form PAX8+LHX1+ renal vesicles that self-pattern into nephron structures. In both 2D and 3D culture, NPCs form kidney organoids containing epithelial nephron-like structures expressing markers of podocytes, proximal tubules, loops of Henle, and distal tubules in an organized, continuous arrangement that resembles the nephron in vivo. We also show that this organoid culture system can be used to study mechanisms of human kidney development and toxicity.
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Abstract
Induced pluripotent stem cells (iPSCs) are somatic cells that have been transcriptionally reprogrammed to an embryonic stem cell (ESC)-like state. iPSCs are a renewable source of diverse somatic cell types and tissues matching the original patient, including nephron-like kidney organoids. iPSCs have been derived representing several kidney disorders, such as ADPKD, ARPKD, Alport syndrome, and lupus nephritis, with the goals of generating replacement tissue and ‘disease in a dish’ laboratory models. Cellular defects in iPSCs and derived kidney organoids provide functional, personalized biomarkers, which can be correlated with genetic and clinical information. In proof of principle, disease-specific phenotypes have been described in iPSCs and ESCs with mutations linked to polycystic kidney disease or focal segmental glomerulosclerosis. In addition, these cells can be used to model nephrotoxic chemical injury. Recent advances in directed differentiation and CRISPR genome editing enable more specific iPSC models and present new possibilities for diagnostics, disease modeling, therapeutic screens, and tissue regeneration using human cells. This review outlines growth opportunities and design strategies for this rapidly expanding and evolving field.
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Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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35
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Freedman BS, Brooks CR, Lam AQ, Fu H, Morizane R, Agrawal V, Saad AF, Li MK, Hughes MR, Werff RV, Peters DT, Lu J, Baccei A, Siedlecki AM, Valerius MT, Musunuru K, McNagny KM, Steinman TI, Zhou J, Lerou PH, Bonventre JV. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat Commun 2015; 6:8715. [PMID: 26493500 PMCID: PMC4620584 DOI: 10.1038/ncomms9715] [Citation(s) in RCA: 479] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022] Open
Abstract
Human-pluripotent-stem-cell-derived kidney cells (hPSC-KCs) have important potential for disease modelling and regeneration. Whether the hPSC-KCs can reconstitute tissue-specific phenotypes is currently unknown. Here we show that hPSC-KCs self-organize into kidney organoids that functionally recapitulate tissue-specific epithelial physiology, including disease phenotypes after genome editing. In three-dimensional cultures, epiblast-stage hPSCs form spheroids surrounding hollow, amniotic-like cavities. GSK3β inhibition differentiates spheroids into segmented, nephron-like kidney organoids containing cell populations with characteristics of proximal tubules, podocytes and endothelium. Tubules accumulate dextran and methotrexate transport cargoes, and express kidney injury molecule-1 after nephrotoxic chemical injury. CRISPR/Cas9 knockout of podocalyxin causes junctional organization defects in podocyte-like cells. Knockout of the polycystic kidney disease genes PKD1 or PKD2 induces cyst formation from kidney tubules. All of these functional phenotypes are distinct from effects in epiblast spheroids, indicating that they are tissue specific. Our findings establish a reproducible, versatile three-dimensional framework for human epithelial disease modelling and regenerative medicine applications. Generating organized kidney tissues from human pluripotent stem cell is a major challenge. Here, Freedman et al. describe a differentiation system forming spheroids and tubular structures, characteristic of these kidney structures, and using CRISPR/Cas9, delete PKD1/2, to model polycystic kidney disease.
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Affiliation(s)
- Benjamin S Freedman
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Division of Nephrology, Department of Medicine, University of Washington School of Medicine, 850 Republican Street, Room S565, Seattle, Washington 98109, USA.,Kidney Research Institute, Department of Medicine, University of Washington, 325 Ninth Avenue, Box 359606, Seattle, Washington 98104, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Craig R Brooks
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Albert Q Lam
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Hongxia Fu
- Department of Biological Chemistry and Pharmacology, Boston Children's Hospital, Center for Life Sciences, Harvard Medical School, Room 3103, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Ryuji Morizane
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Vishesh Agrawal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 823, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Abdelaziz F Saad
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Michelle K Li
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Sherman Fairchild Biochemistry Building 160, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Michael R Hughes
- The Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Ryan Vander Werff
- The Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Derek T Peters
- Department of Stem Cell and Regenerative Biology, Harvard University, Sherman Fairchild Biochemistry Building 160, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.,Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Junjie Lu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 823, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna Baccei
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 823, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrew M Siedlecki
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - M Todd Valerius
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Kiran Musunuru
- Department of Stem Cell and Regenerative Biology, Harvard University, Sherman Fairchild Biochemistry Building 160, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.,Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kelly M McNagny
- The Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Theodore I Steinman
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue DA517, Boston, Massachusetts 02115, USA
| | - Jing Zhou
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Paul H Lerou
- Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 823, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph V Bonventre
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Suite 550, 4 Blackfan Circle, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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36
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Freedman BS, Steinman TI. iPS cell technology: Future impact on renal care. Nephrol News Issues 2015; 29:18-21. [PMID: 26454909 PMCID: PMC4918073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
iPS cells from patients with kidney disease are a new tool with the potential to impact the future of renal care. They can be used in the laboratory to model the pathophysiology of human kidney disease, and have the potential to establish a new area of immunocompatible, on-demand renal transplantation. Critical challenges remain before the full potential of these cells can be accurately assessed. We need to understand whether the derived cell types are mature and can replace kidney function(s). To what extent can iPS cells model kidney disease in the simplified environment of cell culture? Ultimately, successful integration of these cells as autograft therapies will require demonstration of safety and efficacy equal or superior to the existing gold standards of kidney allograft transplantation and dialysis. Specific educational and infrastructural changes will be necessary if these specialized technologies are to be adopted as an accepted modalities in clinical medicine. Given these barriers, the first fruit of these labors is likely to be improved understanding of pathophysiological pathways in human IPS cell disease models, followed by drug discovery and testing. These experiments will lead naturally to improvements in differentiation and experiments in animal models testing function. The time course to achieve the desired goals remains unknown, but the ultimate hope is that new, more effective and less expensive modalities for renal replacement therapy will occur in the foreseeable future. A new standard of care for patients is anticipated that addresses limitations of currently available treatments.
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37
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Lam AQ, Freedman BS, Morizane R, Lerou PH, Valerius MT, Bonventre JV. Rapid and efficient differentiation of human pluripotent stem cells into intermediate mesoderm that forms tubules expressing kidney proximal tubular markers. J Am Soc Nephrol 2013; 25:1211-25. [PMID: 24357672 DOI: 10.1681/asn.2013080831] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) can generate a diversity of cell types, but few methods have been developed to derive cells of the kidney lineage. Here, we report a highly efficient system for differentiating human embryonic stem cells and induced pluripotent stem cells (referred to collectively as hPSCs) into cells expressing markers of the intermediate mesoderm (IM) that subsequently form tubule-like structures. Treatment of hPSCs with the glycogen synthase kinase-3β inhibitor CHIR99021 induced BRACHYURY(+)MIXL1(+) mesendoderm differentiation with nearly 100% efficiency. In the absence of additional exogenous factors, CHIR99021-induced mesendodermal cells preferentially differentiated into cells expressing markers of lateral plate mesoderm with minimal IM differentiation. However, the sequential treatment of hPSCs with CHIR99021 followed by fibroblast growth factor-2 and retinoic acid generated PAX2(+)LHX1(+) cells with 70%-80% efficiency after 3 days of differentiation. Upon growth factor withdrawal, these PAX2(+)LHX1(+) cells gave rise to apically ciliated tubular structures that coexpressed the proximal tubule markers Lotus tetragonolobus lectin, N-cadherin, and kidney-specific protein and partially integrated into embryonic kidney explant cultures. With the addition of FGF9 and activin, PAX2(+)LHX1(+) cells specifically differentiated into cells expressing SIX2, SALL1, and WT1, markers of cap mesenchyme nephron progenitor cells. Our findings demonstrate the effective role of fibroblast growth factor signaling in inducing IM differentiation in hPSCs and establish the most rapid and efficient system whereby hPSCs can be differentiated into cells with features characteristic of kidney lineage cells.
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Affiliation(s)
- Albert Q Lam
- Renal Division, Department of Medicine, and Harvard Stem Cell Institute, Cambridge, Massachusetts; and
| | - Benjamin S Freedman
- Renal Division, Department of Medicine, and Harvard Stem Cell Institute, Cambridge, Massachusetts; and
| | - Ryuji Morizane
- Renal Division, Department of Medicine, and Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Paul H Lerou
- Harvard Stem Cell Institute, Cambridge, Massachusetts; and Department of Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - M Todd Valerius
- Renal Division, Department of Medicine, and Harvard Stem Cell Institute, Cambridge, Massachusetts; and
| | - Joseph V Bonventre
- Renal Division, Department of Medicine, and Harvard Stem Cell Institute, Cambridge, Massachusetts; and
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38
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Freedman BS, Lam AQ, Sundsbak JL, Iatrino R, Su X, Koon SJ, Wu M, Daheron L, Harris PC, Zhou J, Bonventre JV. Reduced ciliary polycystin-2 in induced pluripotent stem cells from polycystic kidney disease patients with PKD1 mutations. J Am Soc Nephrol 2013; 24:1571-86. [PMID: 24009235 DOI: 10.1681/asn.2012111089] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Heterozygous mutations in PKD1 or PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively, cause autosomal dominant PKD (ADPKD), whereas mutations in PKHD1, which encodes fibrocystin/polyductin (FPC), cause autosomal recessive PKD (ARPKD). However, the relationship between these proteins and the pathogenesis of PKD remains unclear. To model PKD in human cells, we established induced pluripotent stem (iPS) cell lines from fibroblasts of three ADPKD and two ARPKD patients. Genetic sequencing revealed unique heterozygous mutations in PKD1 of the parental ADPKD fibroblasts but no pathogenic mutations in PKD2. Undifferentiated PKD iPS cells, control iPS cells, and embryonic stem cells elaborated primary cilia and expressed PC1, PC2, and FPC at similar levels, and PKD and control iPS cells exhibited comparable rates of proliferation, apoptosis, and ciliogenesis. However, ADPKD iPS cells as well as somatic epithelial cells and hepatoblasts/biliary precursors differentiated from these cells expressed lower levels of PC2 at the cilium. Additional sequencing confirmed the retention of PKD1 heterozygous mutations in iPS cell lines from two patients but identified possible loss of heterozygosity in iPS cell lines from one patient. Furthermore, ectopic expression of wild-type PC1 in ADPKD iPS-derived hepatoblasts rescued ciliary PC2 protein expression levels, and overexpression of PC1 but not a carboxy-terminal truncation mutant increased ciliary PC2 expression levels in mouse kidney cells. Taken together, these results suggest that PC1 regulates ciliary PC2 protein expression levels and support the use of PKD iPS cells for investigating disease pathophysiology.
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Affiliation(s)
- Benjamin S Freedman
- Renal Division and Harvard Center for Polycystic Kidney Disease Research, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Abstract
Histone H1 binds to linker DNA between nucleosomes, but the dynamics and biological ramifications of this interaction remain poorly understood. We performed single-molecule experiments using magnetic tweezers to determine the effects of H1 on naked DNA in buffer or during chromatin assembly in Xenopus egg extracts. In buffer, nanomolar concentrations of H1 induce bending and looping of naked DNA at stretching forces below 0.6 pN, effects that can be reversed with 2.7-pN force or in 200 mM monovalent salt concentrations. Consecutive tens-of-nanometer bending events suggest that H1 binds to naked DNA in buffer at high stoichiometries. In egg extracts, single DNA molecules assemble into nucleosomes and undergo rapid compaction. Histone H1 at endogenous physiological concentrations increases the DNA compaction rate during chromatin assembly under 2-pN force and decreases it during disassembly under 5-pN force. In egg cytoplasm, histone H1 protects sperm nuclei undergoing genome-wide decondensation and chromatin assembly from becoming abnormally stretched or fragmented due to astral microtubule pulling forces. These results reveal functional ramifications of H1 binding to DNA at the single-molecule level and suggest an important physiological role for H1 in compacting DNA under force and during chromatin assembly.
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Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
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40
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Fu H, Freedman BS, Lim CT, Heald R, Yan J. Atomic force microscope imaging of chromatin assembled in Xenopus laevis egg extract. Chromosoma 2011; 120:245-54. [PMID: 21369955 DOI: 10.1007/s00412-010-0307-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 01/11/2023]
Abstract
Gaps persist in our understanding of chromatin lower- and higher-order structures. Xenopus egg extracts provide a way to study essential chromatin components which are difficult to manipulate in living cells, but nanoscale imaging of chromatin assembled in extracts poses a challenge. We describe a method for preparing chromatin assembled in extracts for atomic force microscopy (AFM) utilizing restriction enzyme digestion followed by transferring to a mica surface. Using this method, we find that buffer dilution of the chromatin assembly extract or incubation of chromatin in solutions of low ionic strength results in loosely compacted chromatin fibers that are prone to unraveling into naked DNA. We also describe a method for direct AFM imaging of chromatin which does not utilize restriction enzymes and reveals higher-order fibers of varying widths. Due to the capability of controlling chromatin assembly conditions, we believe these methods have broad potential for studying physiologically relevant chromatin structures.
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Affiliation(s)
- Hongxia Fu
- Mechanobiology Institute, National University of Singapore
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41
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Abstract
Background Linker histone H1 has been studied in vivo and using reconstituted chromatin, but there have been few systematic studies of the effects of the cellular environment on its function. Due to the presence of many other chromatin factors and specific chaperones such as RanBP7/importin beta that regulate histone H1, linker histones likely function differently in vivo than in purified systems. Methodology/Principal Findings We have directly compared H1 binding to sperm nuclei in buffer versus Xenopus egg extract cytoplasm, and monitored the effects of adding nuclear import chaperones. In buffer, RanBP7 decondenses sperm nuclei, while H1 binds tightly to the chromatin and rescues RanBP7-mediated decondensation. H1 binding is reduced in cytoplasm, and H1 exhibits rapid FRAP dynamics in cytoplasm but not in buffer. RanBP7 decreases H1 binding to chromatin in both buffer and extract but does not significantly affect H1 dynamics in either condition. Importin beta has a lesser effect than RanBP7 on sperm chromatin decondensation and H1 binding, while a combination of RanBP7/importin beta is no more effective than RanBP7 alone. In extracts supplemented with RanBP7, H1 localizes to chromosomal foci, which increase after DNA damage. Unlike somatic H1, the embryonic linker histone H1M binds equally well to chromatin in cytoplasm compared to buffer. Amino-globular and carboxyl terminal domains of H1M bind chromatin comparably to the full-length protein in buffer, but are inhibited ∼10-fold in cytoplasm. High levels of H1 or its truncations distort mitotic chromosomes and block their segregation during anaphase. Conclusion/Significance RanBP7 can decondense sperm nuclei and decrease H1 binding, but the rapid dynamics of H1 on chromatin depend on other cytoplasmic factors. Cytoplasm greatly impairs the activity of individual H1 domains, and only the full-length protein can condense chromatin properly. Our findings begin to bridge the gap between purified and in vivo chromatin systems.
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Affiliation(s)
- Benjamin S. Freedman
- Molecular and Cell Biology Department, University of California, Berkeley, California, United States of America
| | - Kelly E. Miller
- Molecular and Cell Biology Department, University of California, Berkeley, California, United States of America
| | - Rebecca Heald
- Molecular and Cell Biology Department, University of California, Berkeley, California, United States of America
- * E-mail:
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Freedman BS, Heald R. Functional comparison of H1 histones in Xenopus reveals isoform-specific regulation by Cdk1 and RanGTP. Curr Biol 2010; 20:1048-52. [PMID: 20471264 DOI: 10.1016/j.cub.2010.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/06/2010] [Accepted: 04/12/2010] [Indexed: 12/20/2022]
Abstract
H1 "linker" histones bind dynamically to nucleosomes and promote their compaction into chromatin fibers. Developmental H1 isoforms are evolutionarily conserved, but their function, regulation, and posttranslational modifications are poorly understood. In Xenopus egg extracts, the embryonic linker histone H1M does not affect nuclear assembly or replication but is required for proper chromosome architecture during mitosis. We report here that somatic H1 isoforms, which are more positively charged and feature multiple Cdk1 phosphorylation sites, cannot substitute for H1M at endogenous concentrations, instead causing chromatin compaction during interphase and dissociating from chromosomes at the onset of mitosis. Mitotic Cdk1 phosphorylation is not responsible for this dissociation and instead functions to enhance H1 binding in egg extracts and embryos. Nuclear import receptors RanBP7 and importin beta bind tightly to somatic H1 but not H1M, and addition of a constitutively active Ran mutant abolishes this interaction and enhances the ability of somatic H1 to rescue mitotic chromosome architecture. Our results reveal distinct regulatory mechanisms among linker histone isoforms and a specific role for H1M to compact chromosomes during egg meiotic arrest and early embryonic divisions.
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Affiliation(s)
- Benjamin S Freedman
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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Abstract
During cell division, condensation and resolution of chromosome arms and the assembly of a functional kinetochore at the centromere of each sister chromatid are essential steps for accurate segregation of the genome by the mitotic spindle, yet the contribution of individual chromatin proteins to these processes is poorly understood. We have investigated the role of embryonic linker histone H1 during mitosis in Xenopus laevis egg extracts. Immunodepletion of histone H1 caused the assembly of aberrant elongated chromosomes that extended off the metaphase plate and outside the perimeter of the spindle. Although functional kinetochores assembled, aligned, and exhibited poleward movement, long and tangled chromosome arms could not be segregated in anaphase. Histone H1 depletion did not significantly affect the recruitment of known structural or functional chromosomal components such as condensins or chromokinesins, suggesting that the loss of H1 affects chromosome architecture directly. Thus, our results indicate that linker histone H1 plays an important role in the structure and function of vertebrate chromosomes in mitosis.
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Affiliation(s)
- Thomas J Maresca
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Britton WJ, Blessing WW, Freedman BS. Student evaluation of the Sydney university medical course. Med J Aust 1973; 1:179-84. [PMID: 4694273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Young JA, Freedman BS. Renal tubular transport of amino acids. Clin Chem 1971; 17:245-66. [PMID: 4930400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Affiliation(s)
| | - JA Young
- Physiology Department, University of Sydney
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