1
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He YO, Barisoni L, Rosenberg AZ, Robinson P, Diehl AD, Chen Y, Phuong JP, Hansen J, Herr BW, Börner K, Schaub J, Bonevich N, Arnous G, Boddapati S, Zheng J, Alakwaa F, Sarder P, Duncan WD, Liang C, Valerius MT, Jain S, Iyengar R, Himmelfarb J, Kretzler M. Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine. bioRxiv 2024:2024.04.01.587658. [PMID: 38617362 PMCID: PMC11014593 DOI: 10.1101/2024.04.01.587658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO), and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e.g., HPO, CL, and Uberon) and represents 259 kidney-related biomarkers. We also developed a precision medicine metadata ontology (PMMO) to integrate 50 variables from KPMP and CZ CellxGene data resources and applied PMMO for integrative kidney data analysis. The gene expression profiles of kidney gene biomarkers were specifically analyzed under healthy control or AKI/CKD disease statuses. This work demonstrates how ontology-based approaches support multi-domain data and knowledge integration in precision medicine.
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2
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Galichon P, Lannoy M, Li L, Serre J, Vandermeersch S, Legouis D, Valerius MT, Hadchouel J, Bonventre JV. Energy depletion by cell proliferation sensitizes the kidney epithelial cells to injury. Am J Physiol Renal Physiol 2024; 326:F326-F337. [PMID: 38205542 DOI: 10.1152/ajprenal.00023.2023] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 01/12/2024] Open
Abstract
Acute kidney injury activates both proliferative and antiproliferative pathways, the consequences of which are not fully elucidated. If an initial proliferation of the renal epithelium is necessary for the successful repair, the persistence of proliferation markers is associated with the occurrence of chronic kidney disease. We hypothesized that proliferation in stress conditions impacts cell viability and renal outcomes. We found that proliferation is associated with cell death after various stresses in kidney cells. In vitro, the ATP/ADP ratio oscillates reproducibly throughout the cell cycle, and cell proliferation is associated with a decreased intracellular ATP/ADP ratio. In vivo, transcriptomic data from transplanted kidneys revealed that proliferation was strongly associated with a decrease in the expression of the mitochondria-encoded genes of the oxidative phosphorylation pathway, but not of the nucleus-encoded ones. These observations suggest that mitochondrial function is a limiting factor for energy production in proliferative kidney cells after injury. The association of increased proliferation and decreased mitochondrial function was indeed associated with poor renal outcomes. In summary, proliferation is an energy-demanding process impairing the cellular ability to cope with an injury, highlighting proliferative repair and metabolic recovery as indispensable and interdependent features for successful kidney repair.NEW & NOTEWORTHY ATP depletion is a hallmark of acute kidney injury. Proliferation is instrumental to kidney repair. We show that ATP levels vary during the cell cycle and that proliferation sensitizes renal epithelial cells to superimposed injuries in vitro. More proliferation and less energy production by the mitochondria are associated with adverse outcomes in injured kidney allografts. This suggests that controlling the timing of kidney repair might be beneficial to mitigate the extent of acute kidney injury.
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Affiliation(s)
- Pierre Galichon
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
- Medical School, Sorbonne Université, Paris, France
| | - Morgane Lannoy
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Li Li
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Justine Serre
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Sophie Vandermeersch
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - David Legouis
- Laboratory of Nephrology, Division of Intensive Care, Department of Medicine and Cell Physiology, University Hospital of Geneva, Geneva, Switzerland
| | - M Todd Valerius
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Juliette Hadchouel
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Joseph V Bonventre
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
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3
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Shi M, McCracken KW, Patel AB, Zhang W, Ester L, Valerius MT, Bonventre JV. Human ureteric bud organoids recapitulate branching morphogenesis and differentiate into functional collecting duct cell types. Nat Biotechnol 2023; 41:252-261. [PMID: 36038632 PMCID: PMC9957856 DOI: 10.1038/s41587-022-01429-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [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: 01/25/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
Directed differentiation of human pluripotent stem cells (hPSCs) into functional ureteric and collecting duct (CD) epithelia is essential to kidney regenerative medicine. Here we describe highly efficient, serum-free differentiation of hPSCs into ureteric bud (UB) organoids and functional CD cells. The hPSCs are first induced into pronephric progenitor cells at 90% efficiency and then aggregated into spheres with a molecular signature similar to the nephric duct. In a three-dimensional matrix, the spheres form UB organoids that exhibit branching morphogenesis similar to the fetal UB and correct distal tip localization of RET expression. Organoid-derived cells incorporate into the UB tips of the progenitor niche in chimeric fetal kidney explant culture. At later stages, the UB organoids differentiate into CD organoids, which contain >95% CD cell types as estimated by single-cell RNA sequencing. The CD epithelia demonstrate renal electrophysiologic functions, with ENaC-mediated vectorial sodium transport by principal cells and V-type ATPase proton pump activity by FOXI1-induced intercalated cells.
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Affiliation(s)
- Min Shi
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu, China
| | - Kyle W McCracken
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Division of Nephrology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, USA.
| | - Ankit B Patel
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weitao Zhang
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lioba Ester
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department II of Internal Medicine, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Cologne, Germany
| | - M Todd Valerius
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge and Boston, Boston, MA, USA
| | - Joseph V Bonventre
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge and Boston, Boston, MA, USA. .,Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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4
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Hiratsuka K, Miyoshi T, Kroll KT, Gupta NR, Valerius MT, Ferrante T, Yamashita M, Lewis JA, Morizane R. Organoid-on-a-chip model of human ARPKD reveals mechanosensing pathomechanisms for drug discovery. Sci Adv 2022; 8:eabq0866. [PMID: 36129975 PMCID: PMC9491724 DOI: 10.1126/sciadv.abq0866] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/03/2022] [Indexed: 05/23/2023]
Abstract
Organoids serve as a novel tool for disease modeling in three-dimensional multicellular contexts. Static organoids, however, lack the requisite biophysical microenvironment such as fluid flow, limiting their ability to faithfully recapitulate disease pathology. Here, we unite organoids with organ-on-a-chip technology to unravel disease pathology and develop therapies for autosomal recessive polycystic kidney disease. PKHD1-mutant organoids-on-a-chip are subjected to flow that induces clinically relevant phenotypes of distal nephron dilatation. Transcriptomics discover 229 signal pathways that are not identified by static models. Mechanosensing molecules, RAC1 and FOS, are identified as potential therapeutic targets and validated by patient kidney samples. On the basis of this insight, we tested two U.S. Food and Drug Administration-approved and one investigational new drugs that target RAC1 and FOS in our organoid-on-a-chip model, which suppressed cyst formation. Our observations highlight the vast potential of organoid-on-a-chip models to elucidate complex disease mechanisms for therapeutic testing and discovery.
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Affiliation(s)
- Ken Hiratsuka
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Tomoya Miyoshi
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Katharina T. Kroll
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Navin R. Gupta
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - M. Todd Valerius
- Harvard Medical School, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - Thomas Ferrante
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michifumi Yamashita
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer A. Lewis
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - Ryuji Morizane
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
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5
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Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU. A reference tissue atlas for the human kidney. Sci Adv 2022; 8:eabn4965. [PMID: 35675394 PMCID: PMC9176741 DOI: 10.1126/sciadv.abn4965] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 05/08/2023]
Abstract
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
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Affiliation(s)
- Jens Hansen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Sealfon
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | - Rajasree Menon
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Becky Steck
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kavya Anjani
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Samir Parikh
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Tara K. Sigdel
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Guanshi Zhang
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | | | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Dejan Dobi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Priyanka Rashmi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Edgar A. Otto
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Miguel Rivera
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Michael P. Rose
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Christopher R. Anderton
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John P. Shapiro
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Pamreddy
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Seth Winfree
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yuguang Xiong
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yongqun He
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ian H. de Boer
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Abhijit S. Naik
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kumar Sharma
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Minnie M. Sarwal
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Himmelfarb
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | - Brad Rovin
- Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Zoltan Laszik
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - M. Todd Valerius
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sanjay Jain
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
| | - Lisa M. Satlin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | | | - Ravi Iyengar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kidney Precision Medicine Project
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
- University of Michigan School of Medicine, Ann Arbor, MI, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- University of California San Francisco School of Medicine, San Francisco, CA, USA
- Ohio State University College of Medicine, Columbus, OH, USA
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
- European Molecular Biology Laboratory, Heidelberg, Germany
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Duke University School of Medicine, Durham, NC, USA
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
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6
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Naved BA, Bonventre JV, Hubbell JA, Hukriede NA, Humphreys BD, Kesselman C, Valerius MT, McMahon AP, Shankland SJ, Wertheim JA, White MJV, de Caestecker MP, Drummond IA. Kidney repair and regeneration: perspectives of the NIDDK (Re)Building a Kidney consortium. Kidney Int 2022; 101:845-853. [PMID: 35276204 PMCID: PMC9045003 DOI: 10.1016/j.kint.2022.02.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 11/15/2021] [Revised: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022]
Abstract
Acute kidney injury impacts ∼13.3 million individuals and causes ∼1.7 million deaths per year globally. Numerous injury pathways contribute to acute kidney injury, including cell cycle arrest, senescence, inflammation, mitochondrial dysfunction, and endothelial injury and dysfunction, and can lead to chronic inflammation and fibrosis. However, factors enabling productive repair versus nonproductive, persistent injury states remain less understood. The (Re)Building a Kidney (RBK) consortium is a National Institute of Diabetes and Digestive and Kidney Diseases consortium focused on both endogenous kidney repair mechanisms and the generation of new kidney tissue. This short review provides an update on RBK studies of endogenous nephron repair, addressing the following questions: (i) What is productive nephron repair? (ii) What are the cellular sources and drivers of repair? and (iii) How do RBK studies promote development of therapeutics? Also, we provide a guide to RBK's open access data hub for accessing, downloading, and further analyzing data sets.
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Affiliation(s)
- Bilal A Naved
- Medical Science Training Program, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Joseph V Bonventre
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey A Hubbell
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Benjamin D Humphreys
- Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Carl Kesselman
- Informatics Systems Research Division, Information Sciences Institute, University of Southern California, Los Angeles, California, USA
| | - M Todd Valerius
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Stuart J Shankland
- Division of Nephrology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jason A Wertheim
- Department of Biomedical Engineering, College of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Michael J V White
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, USA
| | - Mark P de Caestecker
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Iain A Drummond
- Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, Maine, USA.
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7
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Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol 2021; 23:1117-1128. [PMID: 34750582 PMCID: PMC10079270 DOI: 10.1038/s41556-021-00788-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked parts of the HRA: (1) three-dimensional representations of anatomy that are linked to (2) tables that name and interlink major anatomical structures, cell types, plus biomarkers (ASCT+B). We discuss four examples that demonstrate the practical utility of the HRA.
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Affiliation(s)
- Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen Browne
- Department of Health and Human Services, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Bruce W Herr
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Hrishikesh Paul
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Shin Lin
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Avinash Boppana
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Teri A Longacre
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - John Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yiing Lin
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - M Todd Valerius
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yongqun He
- Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Xin Sun
- Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Marda Jorgensen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Andrea J Radtke
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Clive Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Fiona Ginty
- Biology and Applied Physics, General Electric Research, Niskayuna, NY, USA
| | - Jonhan Ho
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel Sunshine
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca T Beuschel
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Rajeev Malhotra
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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8
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Li L, Galichon P, Xiao X, Figueroa-Ramirez AC, Tamayo D, Lee JJK, Kalocsay M, Gonzalez-Sanchez D, Chancay MS, McCracken KW, Lee NN, Ichimura T, Mori Y, Valerius MT, Wilflingseder J, Lemos DR, Edelman ER, Bonventre JV. Orphan nuclear receptor COUP-TFII enhances myofibroblast glycolysis leading to kidney fibrosis. EMBO Rep 2021; 22:e51169. [PMID: 34031962 DOI: 10.15252/embr.202051169] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/28/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
Recent studies demonstrate that metabolic disturbance, such as augmented glycolysis, contributes to fibrosis. The molecular regulation of this metabolic perturbation in fibrosis, however, has been elusive. COUP-TFII (also known as NR2F2) is an important regulator of glucose and lipid metabolism. Its contribution to organ fibrosis is undefined. Here, we found increased COUP-TFII expression in myofibroblasts in human fibrotic kidneys, lungs, kidney organoids, and mouse kidneys after injury. Genetic ablation of COUP-TFII in mice resulted in attenuation of injury-induced kidney fibrosis. A non-biased proteomic study revealed the suppression of fatty acid oxidation and the enhancement of glycolysis pathways in COUP-TFII overexpressing fibroblasts. Overexpression of COUP-TFII in fibroblasts also induced production of alpha-smooth muscle actin (αSMA) and collagen 1. Knockout of COUP-TFII decreased glycolysis and collagen 1 levels in fibroblasts. Chip-qPCR revealed the binding of COUP-TFII on the promoter of PGC1α. Overexpression of COUP-TFII reduced the cellular level of PGC1α. Targeting COUP-TFII serves as a novel treatment approach for mitigating fibrosis in chronic kidney disease and potentially fibrosis in other organs.
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Affiliation(s)
- Li Li
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre Galichon
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiaoyan Xiao
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Diana Tamayo
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jake J-K Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Maria S Chancay
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kyle W McCracken
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nathan N Lee
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Takaharu Ichimura
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yutaro Mori
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - M Todd Valerius
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | | | - Dario R Lemos
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elazer R Edelman
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph V Bonventre
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
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9
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Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y. Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. Nat Rev Nephrol 2020; 16:686-696. [PMID: 32939051 PMCID: PMC8012202 DOI: 10.1038/s41581-020-00335-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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] [Accepted: 07/24/2020] [Indexed: 12/29/2022]
Abstract
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient's phenotype. The development of two new ontologies - the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation - will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lucy L Wang
- Allen Institute for Artificial Intelligence, Seattle, WA, USA
| | - Jennifer Schaub
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John F O'Toole
- Department of Nephrology and Hypertension, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Becky Steck
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Frederick Dowd
- UW Medicine Research IT, University of Washington, Seattle, WA, USA
| | - Jens Hansen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Barisoni
- Division of AI/Computational Pathology, Department of Pathology, and Division of Nephrology, Department of Medicine, Duke University, Durham, NC, USA
| | - Sanjay Jain
- Division of Nephrology, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Ian H de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - M Todd Valerius
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University Medical Center, Boston, MA, USA
| | - Christopher Park
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Christian Stoeckert
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, PA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Alexander D Diehl
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Haendel
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sean Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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10
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Wilflingseder J, Willi M, Lee HK, Olauson H, Jankowski J, Ichimura T, Erben R, Valerius MT, Hennighausen L, Bonventre JV. Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury. Nat Commun 2020; 11:3383. [PMID: 32636391 PMCID: PMC7341735 DOI: 10.1038/s41467-020-17205-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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: 04/08/2019] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
The endogenous repair process can result in recovery after acute kidney injury (AKI) with adaptive proliferation of tubular epithelial cells, but repair can also lead to fibrosis and progressive kidney disease. There is currently limited knowledge about transcriptional regulators regulating these repair programs. Herein we establish the enhancer and super-enhancer landscape after AKI by ChIP-seq in uninjured and repairing kidneys on day two after ischemia reperfusion injury (IRI). We identify key transcription factors including HNF4A, GR, STAT3 and STAT5, which show specific binding at enhancer and super-enhancer sites, revealing enhancer dynamics and transcriptional changes during kidney repair. Loss of bromodomain-containing protein 4 function before IRI leads to impaired recovery after AKI and increased mortality. Our comprehensive analysis of epigenetic changes after kidney injury in vivo has the potential to identify targets for therapeutic intervention. Importantly, our data also call attention to potential caveats involved in use of BET inhibitors in patients at risk for AKI.
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Affiliation(s)
- Julia Wilflingseder
- Brigham and Women's Hospital, Renal Division, Harvard Medical School, 4 Blackfan Circle, Boston, MA, 02115, USA.
- Laboratory of Genetics and Physiology, NIDDK, NIH, 8 Center Dr, Bethesda, MD, 20814, USA.
- Department of Physiology and Pathophysiology, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Michaela Willi
- Laboratory of Genetics and Physiology, NIDDK, NIH, 8 Center Dr, Bethesda, MD, 20814, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, NIDDK, NIH, 8 Center Dr, Bethesda, MD, 20814, USA
| | - Hannes Olauson
- Brigham and Women's Hospital, Renal Division, Harvard Medical School, 4 Blackfan Circle, Boston, MA, 02115, USA
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Solnavägen 1, 171 77, Stockholm, Sweden
| | - Jakub Jankowski
- Laboratory of Genetics and Physiology, NIDDK, NIH, 8 Center Dr, Bethesda, MD, 20814, USA
- Department of Physiology and Pathophysiology, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Takaharu Ichimura
- Brigham and Women's Hospital, Renal Division, Harvard Medical School, 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Reinhold Erben
- Department of Physiology and Pathophysiology, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - M Todd Valerius
- Brigham and Women's Hospital, Renal Division, Harvard Medical School, 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, NIDDK, NIH, 8 Center Dr, Bethesda, MD, 20814, USA
| | - Joseph V Bonventre
- Brigham and Women's Hospital, Renal Division, Harvard Medical School, 4 Blackfan Circle, Boston, MA, 02115, USA.
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11
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Wilflingseder J, Willi M, Lee HK, Olauson H, Jankowsky J, Ichimura T, Erben R, Valerius MT, Hennighausen L, Bonventre JV. P0511ENHANCER AND SUPER-ENHANCER DYNAMICS IN REPAIR AFTER ISCHEMIC ACUTE KIDNEY INJURY. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa143.p0511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background and Aims
The endogenous repair process of the mammalian kidney allows rapid recovery after acute kidney injury (AKI) through robust proliferation of tubular epithelial cells. There is currently limited understanding of which transcriptional regulators activate these repair programs and how transcriptional dysregulation leads to maladaptive repair. Here we investigate the existence of enhancer dynamics in the regenerating mouse kidney.
Method
RNA-seq and ChIP-seq (H3K27ac, H3K4m3, BRD4, POL2 and selected transcription factors) were performed on samples from repairing kidney cortex 2 days after ischemia/reperfusion injury (IRI) to identify activated genes, transcription factors, enhancer and super-enhancers associated with kidney repair. Further we investigated the role of super-enhancer activation in kidney repair through pharmacological BET inhibition using the small molecule JQ1 in vitro and in acute kidney injury models in vivo.
Results
Response to kidney injury leads to genome-wide alteration in enhancer repertoire in-vivo. We identified 16,781 enhancer sites (H3K27ac and BRD4 positive, H3K4me3 negative binding) active in SHAM and IRI samples; 6,512 lost and 9,774 gained after IRI. The lost and gained enhancer sites can be annotated to 62% and 63% of down- and up-regulated transcripts at day 2 after kidney injury, respectively. Super-enhancer analysis revealed 164 lost and 216 gained super-enhancer sites at IRI day 2. 385 super-enhancers maintain activity before and after injury. ChIP-seq profiles of selected transcription factors based on motif analysis show specific binding at corresponding enhancer sites. We observed lost enhancer binding of HNF4A and GR mainly at kidney related enhancer elements. In contrast, STAT3 showed increased binding at injury induces enhancer elements. No dynamic was observed for STAT5. Both transcription factor groups show corresponding mRNA changes after injury. Pharmacological inhibition of enhancer and super-enhancer activity by BRD4 inhibition (JQ1: 50mg/kg/day) before IRI leads to suppression of 40% of injury-induced transcripts associated with cell cycle regulation and significantly increased mortality between days 2 and 3 after AKI.
Conclusion
This is the first demonstration of enhancer and super-enhancer function in the repairing kidney. In addition, our data call attention to potential caveats for use of small molecule inhibitors of BET proteins that are currently being tested in clinical trials in cancer patients who are at risk for AKI. Our analyses of enhancer dynamics after kidney injury in vivo have the potential to identify new targets for therapeutic intervention.
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Affiliation(s)
- Julia Wilflingseder
- Brigham and Women's Hospital, Harvard Medical School, Renal Division, Boston, United States of America
- National Institute of Diabestes, Digestive and Kidney Disease, NIH, Laboratory of Genetics and Physiology, Bethesda, United States of America
- University of Veterinary Medicine, Physiology, Vienna, Austria
| | - Michaela Willi
- National Institute of Diabestes, Digestive and Kidney Disease, NIH, Laboratory of Genetics and Physiology, Bethesda, United States of America
| | - Hye Kyung Lee
- National Institute of Diabestes, Digestive and Kidney Disease, NIH, Laboratory of Genetics and Physiology, Bethesda, United States of America
| | - Hannes Olauson
- Brigham and Women's Hospital, Harvard Medical School, Renal Division, Boston, United States of America
- Karolinska Institutet, Division of Renal Medicine, Department of Clinical Sciences, Intervetion and Technology, Stockholm, Sweden
| | - Jakub Jankowsky
- University of Veterinary Medicine, Physiology, Vienna, Austria
| | - Takaharu Ichimura
- Brigham and Women's Hospital, Harvard Medical School, Renal Division, Boston, United States of America
| | - Reinhold Erben
- University of Veterinary Medicine, Physiology, Vienna, Austria
| | - M Todd Valerius
- Brigham and Women's Hospital, Harvard Medical School, Renal Division, Boston, United States of America
| | - Lothar Hennighausen
- National Institute of Diabestes, Digestive and Kidney Disease, NIH, Laboratory of Genetics and Physiology, Bethesda, United States of America
| | - Joseph Vincent Bonventre
- Brigham and Women's Hospital, Harvard Medical School, Renal Division, Boston, United States of America
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12
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Homan KA, Gupta N, Kroll KT, Kolesky DB, Skylar-Scott M, Miyoshi T, Mau D, Valerius MT, Ferrante T, Bonventre JV, Lewis JA, Morizane R. Flow-enhanced vascularization and maturation of kidney organoids in vitro. Nat Methods 2019; 16:255-262. [PMID: 30742039 PMCID: PMC6488032 DOI: 10.1038/s41592-019-0325-y] [Citation(s) in RCA: 466] [Impact Index Per Article: 93.2] [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: 10/09/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023]
Abstract
Kidney organoids derived from human pluripotent stem cells have glomerular- and tubular-like compartments that are largely avascular and immature in static culture. Here we report an in vitro method for culturing kidney organoids under flow on millifluidic chips, which expands their endogenous pool of endothelial progenitor cells and generates vascular networks with perfusable lumens surrounded by mural cells. We found that vascularized kidney organoids cultured under flow had more mature podocyte and tubular compartments with enhanced cellular polarity and adult gene expression compared with that in static controls. Glomerular vascular development progressed through intermediate stages akin to those involved in the embryonic mammalian kidney's formation of capillary loops abutting foot processes. The association of vessels with these compartments was reduced after disruption of the endogenous VEGF gradient. The ability to induce substantial vascularization and morphological maturation of kidney organoids in vitro under flow opens new avenues for studies of kidney development, disease, and regeneration.
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Affiliation(s)
- Kimberly A Homan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Navin Gupta
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Katharina T Kroll
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - David B Kolesky
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Mark Skylar-Scott
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Tomoya Miyoshi
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Donald Mau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - M Todd Valerius
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Joseph V Bonventre
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Lewis
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Ryuji Morizane
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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13
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Gupta N, Susa K, Yoda Y, Bonventre JV, Valerius MT, Morizane R. CRISPR/Cas9-based Targeted Genome Editing for the Development of Monogenic Diseases Models with Human Pluripotent Stem Cells. Curr Protoc Stem Cell Biol 2018; 45:e50. [PMID: 30040245 PMCID: PMC6060633 DOI: 10.1002/cpsc.50] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells (hPSCs) represent a formidable tool for disease modeling, drug discovery, and regenerative medicine using human cells and tissues in vitro. Evolving techniques of targeted genome editing, specifically the CRISPR/Cas9 system, allow for the generation of cell lines bearing gene-specific knock-outs, knock-in reporters, and precise mutations. However, there are increasing concerns related to the transfection efficiency, cell viability, and maintenance of pluripotency provided by genome-editing techniques. The procedure presented here employs transient antibiotic selection that overcomes reduced transfection efficiency, avoids cytotoxic flow sorting for increased viability, and generates multiple genome-edited pluripotent hPSC lines expanded from a single parent cell. Avoidance of xenogeneic contamination from feeder cells and reduced operator workload, owing to single-cell passaging rather than clump passaging, are additional benefits. The outlined methods may enable researchers with limited means and technical experience to create human stem cell lines containing desired gene-specific mutations. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Navin Gupta
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Koichiro Susa
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yoko Yoda
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Joseph V Bonventre
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - M Todd Valerius
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Ryuji Morizane
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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14
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Ramalingam H, Fessler AR, Das A, Valerius MT, Basta J, Robbins L, Brown AC, Oxburgh L, McMahon AP, Rauchman M, Carroll TJ. Disparate levels of beta-catenin activity determine nephron progenitor cell fate. Dev Biol 2018; 440:13-21. [PMID: 29705331 DOI: 10.1016/j.ydbio.2018.04.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/11/2018] [Accepted: 04/24/2018] [Indexed: 10/17/2022]
Abstract
Formation of a functional kidney depends on the balance between renewal and differentiation of nephron progenitors. Failure to sustain this balance can lead to kidney failure or stem cell tumors. For nearly 60 years, we have known that signals from an epithelial structure known as the ureteric bud were essential for maintaining this balance. More recently it was discovered that one molecule, Wnt9b, was necessary for both renewal and differentiation of the nephron progenitor cells. How one ligand signaling through one transcription factor promoted two seemingly contradictory cellular processes was unclear. In this study, we show that Wnt9b/beta-catenin signaling alone is sufficient to promote both renewal and differentiation. Moreover, we show that discrete levels of beta-catenin can promote these two disparate fates, with low levels fostering progenitor renewal and high levels driving differentiation. These results provide insight into how Wnt9b regulates distinct target genes that balance nephron progenitor renewal and differentiation.
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Affiliation(s)
- Harini Ramalingam
- Departments of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA; Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA
| | - Alicia R Fessler
- Departments of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA; Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA
| | - Amrita Das
- Departments of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA; Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA
| | - M Todd Valerius
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jeannine Basta
- Department of Internal Medicine, Saint Louis University, St Louis, MO 63104, USA; Department of Biochemistry and Molecular Biology, Saint Louis University, St Louis, MO 63104, USA; VA St. Louis Health Care System, John Cochran Division, St Louis, MO 63106, USA
| | - Lynn Robbins
- Department of Internal Medicine, Saint Louis University, St Louis, MO 63104, USA; Department of Biochemistry and Molecular Biology, Saint Louis University, St Louis, MO 63104, USA; VA St. Louis Health Care System, John Cochran Division, St Louis, MO 63106, USA
| | - Aaron C Brown
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, W.M. Keck School of Medicine of the University of Southern California,1425 San Pablo Street, Los Angeles, CA 90033, USA; Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA
| | - Michael Rauchman
- Department of Internal Medicine, Saint Louis University, St Louis, MO 63104, USA; Department of Biochemistry and Molecular Biology, Saint Louis University, St Louis, MO 63104, USA; VA St. Louis Health Care System, John Cochran Division, St Louis, MO 63106, USA
| | - Thomas J Carroll
- Departments of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA; Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA.
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15
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Naiman N, Fujioka K, Fujino M, Valerius MT, Potter SS, McMahon AP, Kobayashi A. Repression of Interstitial Identity in Nephron Progenitor Cells by Pax2 Establishes the Nephron-Interstitium Boundary during Kidney Development. Dev Cell 2017; 41:349-365.e3. [PMID: 28535371 DOI: 10.1016/j.devcel.2017.04.022] [Citation(s) in RCA: 47] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 03/10/2017] [Accepted: 04/24/2017] [Indexed: 12/31/2022]
Abstract
The kidney contains the functional units, the nephrons, surrounded by the renal interstitium. Previously we discovered that, once Six2-expressing nephron progenitor cells and Foxd1-expressing renal interstitial progenitor cells form at the onset of kidney development, descendant cells from these populations contribute exclusively to the main body of nephrons and renal interstitial tissues, respectively, indicating a lineage boundary between the nephron and renal interstitial compartments. Currently it is unclear how lineages are regulated during kidney organogenesis. We demonstrate that nephron progenitor cells lacking Pax2 fail to differentiate into nephron cells but can switch fates into renal interstitium-like cell types. These data suggest that Pax2 function maintains nephron progenitor cells by repressing a renal interstitial cell program. Thus, the lineage boundary between the nephron and renal interstitial compartments is maintained by the Pax2 activity in nephron progenitor cells during kidney organogenesis.
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Affiliation(s)
- Natalie Naiman
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kaoru Fujioka
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Mari Fujino
- Department of Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, 750 Republican Street, Seattle, WA 98109, USA
| | - M Todd Valerius
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA
| | - Akio Kobayashi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, 750 Republican Street, Seattle, WA 98109, USA.
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16
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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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17
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Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA. (Re)Building a Kidney. J Am Soc Nephrol 2017; 28:1370-1378. [PMID: 28096308 DOI: 10.1681/asn.2016101077] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
(Re)Building a Kidney is a National Institute of Diabetes and Digestive and Kidney Diseases-led consortium to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and the integration of these cells into complex structures that replicate human kidney function. The ultimate goals of the consortium are two-fold: to develop and implement strategies for in vitro engineering of replacement kidney tissue, and to devise strategies to stimulate regeneration of nephrons in situ to restore failing kidney function. Projects within the consortium will answer fundamental questions regarding human gene expression in the developing kidney, essential signaling crosstalk between distinct cell types of the developing kidney, how to derive the many cell types of the kidney through directed differentiation of human pluripotent stem cells, which bioengineering or scaffolding strategies have the most potential for kidney tissue formation, and basic parameters of the regenerative response to injury. As these projects progress, the consortium will incorporate systematic investigations in physiologic function of in vitro and in vivo differentiated kidney tissue, strategies for engraftment in experimental animals, and development of therapeutic approaches to activate innate reparative responses.
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Affiliation(s)
- Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine;
| | - Thomas J Carroll
- Department of Molecular Biology and.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ondine Cleaver
- Department of Molecular Biology and.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Daniel R Gossett
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Deborah K Hoshizaki
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey A Hubbell
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Benjamin D Humphreys
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Sanjay Jain
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Jan Jensen
- Department of Stem Cell Biology and Regenerative Medicine and.,Trailhead Biosystems, Inc, Cleveland, Ohio
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Carl Kesselman
- Epstein Department of Industrial and Systems Engineering and Information Sciences Institute, Viterbi School of Engineering and.,Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Christian J Ketchum
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Melissa H Little
- Cell Biology Theme, Murdoch Childrens Research Institute, Parkville, Melbourne, Australia.,Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology and.,Department of Cell and Developmental Biology and Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan
| | - M Todd Valerius
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jason A Wertheim
- Department of Surgery, Jesse Brown VA Medical Center, and.,Comprehensive Transplant Center, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and
| | - Oliver Wessely
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Ying Zheng
- Department of Bioengineering, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
| | - Iain A Drummond
- Nephrology Division, Massachusetts General Hospital, Charlestown, Massachusetts
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18
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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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19
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Masuzaki R, Zhao S, Valerius MT, Tsugawa D, Oya Y, Ray KC, Karp SJ. SOCS2 Balances Metabolic and Restorative Requirements during Liver Regeneration. J Biol Chem 2015; 291:3346-58. [PMID: 26703468 DOI: 10.1074/jbc.m115.703264] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 11/09/2015] [Indexed: 01/01/2023] Open
Abstract
After significant injury, the liver must maintain homeostasis during the regenerative process. We hypothesized the existence of mechanisms to limit hepatocyte proliferation after injury to maintain metabolic and synthetic function. A screen for candidates revealed suppressor of cytokine signaling 2 (SOCS2), an inhibitor of growth hormone (GH) signaling, was strongly induced after partial hepatectomy. Using genetic deletion and administration of various factors we investigated the role of SOCS2 during liver regeneration. SOCS2 preserves liver function by restraining the first round of hepatocyte proliferation after partial hepatectomy by preventing increases in growth hormone receptor (GHR) via ubiquitination, suppressing GH pathway activity. At later times, SOCS2 enhances hepatocyte proliferation by modulating a decrease in serum insulin-like growth factor 1 (IGF-1) that allows GH release from the pituitary. SOCS2, therefore, plays a dual role in modulating the rate of hepatocyte proliferation. In particular, this is the first demonstration of an endogenous mechanism to limit hepatocyte proliferation after injury.
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Affiliation(s)
- Ryota Masuzaki
- From the Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Sophia Zhao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - M Todd Valerius
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, and Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138
| | - Daisuke Tsugawa
- From the Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Yuki Oya
- From the Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Kevin C Ray
- From the Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Seth J Karp
- From the Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37232,
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20
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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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21
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Baek JH, Zeng R, Weinmann-Menke J, Valerius MT, Wada Y, Ajay AK, Colonna M, Kelley VR. IL-34 mediates acute kidney injury and worsens subsequent chronic kidney disease. J Clin Invest 2015; 125:3198-214. [PMID: 26121749 DOI: 10.1172/jci81166] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/14/2015] [Indexed: 12/12/2022] Open
Abstract
Macrophages (Mø) are integral in ischemia/reperfusion injury-incited (I/R-incited) acute kidney injury (AKI) that leads to fibrosis and chronic kidney disease (CKD). IL-34 and CSF-1 share a receptor (c-FMS), and both cytokines mediate Mø survival and proliferation but also have distinct features. CSF-1 is central to kidney repair and destruction. We tested the hypothesis that IL-34-dependent, Mø-mediated mechanisms promote persistent ischemia-incited AKI that worsens subsequent CKD. In renal I/R, the time-related magnitude of Mø-mediated AKI and subsequent CKD were markedly reduced in IL-34-deficient mice compared with controls. IL-34, c-FMS, and a second IL-34 receptor, protein-tyrosine phosphatase ζ (PTP-ζ) were upregulated in the kidney after I/R. IL-34 was generated by tubular epithelial cells (TECs) and promoted Mø-mediated TEC destruction during AKI that worsened subsequent CKD via 2 distinct mechanisms: enhanced intrarenal Mø proliferation and elevated BM myeloid cell proliferation, which increases circulating monocytes that are drawn into the kidney by chemokines. CSF-1 expression in TECs did not compensate for IL-34 deficiency. In patients, kidney transplants subject to I/R expressed IL-34, c-FMS, and PTP-ζ in TECs during AKI that increased with advancing injury. Moreover, IL-34 expression increased, along with more enduring ischemia in donor kidneys. In conclusion, IL-34-dependent, Mø-mediated, CSF-1 nonredundant mechanisms promote persistent ischemia-incited AKI that worsens subsequent CKD.
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22
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Lindström NO, Chang CH, Valerius MT, Hohenstein P, Davies JA. Node retraction during patterning of the urinary collecting duct system. J Anat 2014; 226:13-21. [PMID: 25292187 PMCID: PMC4299504 DOI: 10.1111/joa.12239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2014] [Indexed: 11/28/2022] Open
Abstract
This report presents a novel mechanism for remodelling a branched epithelial tree. The mouse renal collecting duct develops by growth and repeated branching of an initially unbranched ureteric bud: this mechanism initially produces an almost fractal form with young branches connected to the centre of the kidney via a sequence of nodes (branch points) distributed widely throughout the developing organ. The collecting ducts of a mature kidney have a different form: from the nephrons in the renal cortex, long, straight lengths of collecting duct run almost parallel to one another through the renal medulla, and open together to the renal pelvis. Here we present time-lapse studies of E11.5 kidneys growing in culture: after about 5 days, the collecting duct trees show evidence of ‘node retraction’, in which the node of a ‘Y’-shaped branch moves downwards, shortening the stalk of the ‘Y’, lengthening its arms and narrowing their divergence angle so that the ‘Y’ becomes a ‘V’. Computer simulation suggests that node retraction can transform a spread tree, like that of an early kidney, into one with long, almost-parallel medullary rays similar to those seen in a mature real kidney.
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23
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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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24
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Wiese CB, Ireland S, Fleming NL, Yu J, Valerius MT, Georgas K, Chiu HS, Brennan J, Armstrong J, Little MH, McMahon AP, Southard-Smith EM. A genome-wide screen to identify transcription factors expressed in pelvic Ganglia of the lower urinary tract. Front Neurosci 2012; 6:130. [PMID: 22988430 PMCID: PMC3439845 DOI: 10.3389/fnins.2012.00130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 08/22/2012] [Indexed: 12/16/2022] Open
Abstract
Relative positions of neurons within mature murine pelvic ganglia based on expression of neurotransmitters have been described. However the spatial organization of developing innervation in the murine urogenital tract (UGT) and the gene networks that regulate specification and maturation of neurons within the pelvic ganglia of the lower urinary tract (LUT) are unknown. We used whole-mount immunohistochemistry and histochemical stains to localize neural elements in 15.5 days post coitus (dpc) fetal mice. To identify potential regulatory factors expressed in pelvic ganglia, we surveyed expression patterns for known or probable transcription factors (TF) annotated in the mouse genome by screening a whole-mount in situ hybridization library of fetal UGTs. Of the 155 genes detected in pelvic ganglia, 88 encode TFs based on the presence of predicted DNA-binding domains. Neural crest (NC)-derived progenitors within the LUT were labeled by Sox10, a well-known regulator of NC development. Genes identified were categorized based on patterns of restricted expression in pelvic ganglia, pelvic ganglia and urethral epithelium, or pelvic ganglia and urethral mesenchyme. Gene expression patterns and the distribution of Sox10+, Phox2b+, Hu+, and PGP9.5+ cells within developing ganglia suggest previously unrecognized regional segregation of Sox10+ progenitors and differentiating neurons in early development of pelvic ganglia. Reverse transcription-PCR of pelvic ganglia RNA from fetal and post-natal stages demonstrated that multiple TFs maintain post-natal expression, although Pax3 is extinguished before weaning. Our analysis identifies multiple potential regulatory genes including TFs that may participate in segregation of discrete lineages within pelvic ganglia. The genes identified here are attractive candidate disease genes that may now be further investigated for their roles in malformation syndromes or in LUT dysfunction.
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Affiliation(s)
- Carrie B Wiese
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA
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Park JS, Ma W, O'Brien LL, Chung E, Guo JJ, Cheng JG, Valerius MT, McMahon JA, Wong WH, McMahon AP. Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. Dev Cell 2012; 23:637-51. [PMID: 22902740 DOI: 10.1016/j.devcel.2012.07.008] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [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: 07/12/2011] [Revised: 05/24/2012] [Accepted: 07/15/2012] [Indexed: 01/09/2023]
Abstract
A balance between Six2-dependent self-renewal and canonical Wnt signaling-directed commitment regulates mammalian nephrogenesis. Intersectional studies using chromatin immunoprecipitation and transcriptional profiling identified direct target genes shared by each pathway within nephron progenitors. Wnt4 and Fgf8 are essential for progenitor commitment; cis-regulatory modules flanking each gene are cobound by Six2 and β-catenin and are dependent on conserved Lef/Tcf binding sites for activity. In vitro and in vivo analyses suggest that Six2 and Lef/Tcf factors form a regulatory complex that promotes progenitor maintenance while entry of β-catenin into this complex promotes nephrogenesis. Alternative transcriptional responses associated with Six2 and β-catenin cobinding events occur through non-Lef/Tcf DNA binding mechanisms, highlighting the regulatory complexity downstream of Wnt signaling in the developing mammalian kidney.
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Affiliation(s)
- Joo-Seop Park
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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26
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Yu J, Valerius MT, Duah M, Staser K, Hansard JK, Guo JJ, McMahon J, Vaughan J, Faria D, Georgas K, Rumballe B, Ren Q, Krautzberger AM, Junker JP, Thiagarajan RD, Machanick P, Gray PA, van Oudenaarden A, Rowitch DH, Stiles CD, Ma Q, Grimmond SM, Bailey TL, Little MH, McMahon AP. Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development 2012; 139:1863-73. [PMID: 22510988 DOI: 10.1242/dev.074005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Lengthy developmental programs generate cell diversity within an organotypic framework, enabling the later physiological actions of each organ system. Cell identity, cell diversity and cell function are determined by cell type-specific transcriptional programs; consequently, transcriptional regulatory factors are useful markers of emerging cellular complexity, and their expression patterns provide insights into the regulatory mechanisms at play. We performed a comprehensive genome-scale in situ expression screen of 921 transcriptional regulators in the developing mammalian urogenital system. Focusing on the kidney, analysis of regional-specific expression patterns identified novel markers and cell types associated with development and patterning of the urinary system. Furthermore, promoter analysis of synexpressed genes predicts transcriptional control mechanisms that regulate cell differentiation. The annotated informational resource (www.gudmap.org) will facilitate functional analysis of the mammalian kidney and provides useful information for the generation of novel genetic tools to manipulate emerging cell populations.
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Affiliation(s)
- Jing Yu
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
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Balasubramanian S, Jansen M, Valerius MT, Humphreys BD, Strom TB. Orphan nuclear receptor Nur77 promotes acute kidney injury and renal epithelial apoptosis. J Am Soc Nephrol 2012; 23:674-86. [PMID: 22343121 DOI: 10.1681/asn.2011070646] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [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
Nur77 and its family members Nurr1 and Nor-1 are inducible orphan nuclear receptors that orchestrate cellular responses to diverse extracellular signals. In epithelia, Nur77 can act as a potent proapoptotic molecule in response to cellular stress, suggesting a possible role for this nuclear receptor in the tissue response to injury. Here, we found that Nur77 promotes epithelial cell apoptosis after AKI. Injury of proximal tubular epithelial cells rapidly and strongly induced Nur77, Nor-1, and Nurr1 both in vitro and in vivo. After renal ischemia-reperfusion, Nurr77-deficient mice exhibited less apoptosis of tubular epithelial cells and better renal function than wild-type mice. Nur77-mediated renal injury involved a conformational change of Bcl2 and an increase in the protein levels of proapoptotic Bcl-xS. Ligand-activated retinoic acid receptors repressed Nur77 induction and function. Pretreatment of wild-type mice with retinoic acid before renal ischemia-reperfusion blunted the induction of Nur77, conferred protection of renal function, attenuated renal histologic injury, and reduced the expression of epithelial-derived proinflammatory cytokines. Retinoic acid also inhibited hypoxia-mediated induction of proinflammatory cytokines in cultured renal epithelial cells. Results obtained from proximal tubule cultures derived from Nur77-deficient mice suggested that the inhibition of Nur77 expression mediated the renoprotective effects of retinoic acid. In summary, Nur77 promotes epithelial apoptosis after ischemia-reperfusion injury, and retinoic acid-mediated inhibition of Nur77 expression is a promising therapeutic strategy for the prevention of AKI.
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Affiliation(s)
- Savithri Balasubramanian
- Department of Medicine, The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Boyle SC, Kim M, Valerius MT, McMahon AP, Kopan R. Notch pathway activation can replace the requirement for Wnt4 and Wnt9b in mesenchymal-to-epithelial transition of nephron stem cells. Development 2011; 138:4245-54. [PMID: 21852398 DOI: 10.1242/dev.070433] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The primary excretory organ in vertebrates is the kidney, which is responsible for blood filtration, solute homeostasis and pH balance. These functions are carried out by specialized epithelial cells organized into tubules called nephrons. Each of these cell types arise during embryonic development from a mesenchymal stem cell pool through a process of mesenchymal-to-epithelial transition (MET) that requires sequential action of specific Wnt signals. Induction by Wnt9b directs cells to exit the stem cell niche and express Wnt4, which is both necessary and sufficient for the formation of epithelia. Without either factor, MET fails, nephrons do not form and newborn mice die owing to kidney failure. Ectopic Notch activation in stem cells induces mass differentiation and exhaustion of the stem cell pool. To investigate whether this reflected an interaction between Notch and Wnt, we employed a novel gene manipulation strategy in cultured embryonic kidneys. We show that Notch activation is capable of inducing MET in the absence of both Wnt4 and Wnt9b. Following MET, the presence of Notch directs cells primarily to the proximal tubule fate. Only nephron stem cells have the ability to undergo MET in response to Wnt or Notch, as activation in the closely related stromal mesenchyme has no inductive effect. These data demonstrate that stem cells for renal epithelia are uniquely poised to undergo MET, and that Notch activation can replace key inductive Wnt signals in this process. After MET, Notch provides an instructive signal directing cells towards the proximal tubule lineage at the expense of other renal epithelial fates.
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Affiliation(s)
- Scott C Boyle
- Departments of Developmental Biology and Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
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30
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Balasubramanian S, Kota SK, Valerius MT. The rejection barrier to induced pluripotent stem cells. J Am Soc Nephrol 2011; 22:1583-6. [PMID: 21836145 DOI: 10.1681/asn.2011070707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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31
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Humphreys BD, Lin SL, Kobayashi A, Hudson TE, Nowlin BT, Bonventre JV, Valerius MT, McMahon AP, Duffield JS. Fate tracing reveals the pericyte and not epithelial origin of myofibroblasts in kidney fibrosis. Am J Pathol 2009; 176:85-97. [PMID: 20008127 DOI: 10.2353/ajpath.2010.090517] [Citation(s) in RCA: 1094] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the origin of myofibroblasts in kidney is of great interest because these cells are responsible for scar formation in fibrotic kidney disease. Recent studies suggest epithelial cells are an important source of myofibroblasts through a process described as the epithelial-to-mesenchymal transition; however, confirmatory studies in vivo are lacking. To quantitatively assess the contribution of renal epithelial cells to myofibroblasts, we used Cre/Lox techniques to genetically label and fate map renal epithelia in models of kidney fibrosis. Genetically labeled primary proximal epithelial cells cultured in vitro from these mice readily induce markers of myofibroblasts after transforming growth factor beta(1) treatment. However, using either red fluorescent protein or beta-galactosidase as fate markers, we found no evidence that epithelial cells migrate outside of the tubular basement membrane and differentiate into interstitial myofibroblasts in vivo. Thus, although renal epithelial cells can acquire mesenchymal markers in vitro, they do not directly contribute to interstitial myofibroblast cells in vivo. Lineage analysis shows that during nephrogenesis, FoxD1-positive((+)) mesenchymal cells give rise to adult CD73(+), platelet derived growth factor receptor beta(+), smooth muscle actin-negative interstitial pericytes, and these FoxD1-derivative interstitial cells expand and differentiate into smooth muscle actin(+) myofibroblasts during fibrosis, accounting for a large majority of myofibroblasts. These data indicate that therapeutic strategies directly targeting pericyte differentiation in vivo may productively impact fibrotic kidney disease.
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Affiliation(s)
- Benjamin D Humphreys
- Renal Division, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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32
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Kobayashi A, Valerius MT, Mugford JW, Carroll TJ, Self M, Oliver G, McMahon AP. Six2 defines and regulates a multipotent self-renewing nephron progenitor population throughout mammalian kidney development. Cell Stem Cell 2009; 3:169-81. [PMID: 18682239 DOI: 10.1016/j.stem.2008.05.020] [Citation(s) in RCA: 677] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 04/23/2008] [Accepted: 05/29/2008] [Indexed: 12/20/2022]
Abstract
Nephrons, the basic functional units of the kidney, are generated repetitively during kidney organogenesis from a mesenchymal progenitor population. Which cells within this pool give rise to nephrons and how multiple nephron lineages form during this protracted developmental process are unclear. We demonstrate that the Six2-expressing cap mesenchyme represents a multipotent nephron progenitor population. Six2-expressing cells give rise to all cell types of the main body of the nephron during all stages of nephrogenesis. Pulse labeling of Six2-expressing nephron progenitors at the onset of kidney development suggests that the Six2-expressing population is maintained by self-renewal. Clonal analysis indicates that at least some Six2-expressing cells are multipotent, contributing to multiple domains of the nephron. Furthermore, Six2 functions cell autonomously to maintain a progenitor cell status, as cap mesenchyme cells lacking Six2 activity contribute to ectopic nephron tubules, a mechanism dependent on a Wnt9b inductive signal. Taken together, our observations suggest that Six2 activity cell-autonomously regulates a multipotent nephron progenitor population.
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Affiliation(s)
- Akio Kobayashi
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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33
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Georgas K, Rumballe B, Valerius MT, Chiu HS, Thiagarajan RD, Lesieur E, Aronow BJ, Brunskill EW, Combes AN, Tang D, Taylor D, Grimmond SM, Potter SS, McMahon AP, Little MH. Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment. Dev Biol 2009; 332:273-86. [PMID: 19501082 DOI: 10.1016/j.ydbio.2009.05.578] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 05/28/2009] [Accepted: 05/29/2009] [Indexed: 01/04/2023]
Abstract
While nephron formation is known to be initiated by a mesenchyme-to-epithelial transition of the cap mesenchyme to form a renal vesicle (RV), the subsequent patterning of the nephron and fusion with the ureteric component of the kidney to form a patent contiguous uriniferous tubule has not been fully characterized. Using dual section in situ hybridization (SISH)/immunohistochemistry (IHC) we have revealed distinct distal/proximal patterning of Notch, BMP and Wnt pathway components within the RV stage nephron. Quantitation of mitoses and Cyclin D1 expression indicated that cell proliferation was higher in the distal RV, reflecting the differential developmental programs of the proximal and distal populations. A small number of RV genes were also expressed in the early connecting segment of the nephron. Dual ISH/IHC combined with serial section immunofluorescence and 3D reconstruction revealed that fusion occurs between the late RV and adjacent ureteric tip via a process that involves loss of the intervening ureteric epithelial basement membrane and insertion of cells expressing RV markers into the ureteric tip. Using Six2-eGFPCre x R26R-lacZ mice, we demonstrate that these cells are derived from the cap mesenchyme and not the ureteric epithelium. Hence, both nephron patterning and patency are evident at the late renal vesicle stage.
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Affiliation(s)
- Kylie Georgas
- NHMRC Principal Research Fellow, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
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Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius MT, Aronow J, Kaimal V, Jegga AG, Yu J, Grimmond S, McMahon AP, Patterson LT, Little MH, Potter SS. Atlas of Gene Expression in the Developing Kidney at Microanatomic Resolution. Dev Cell 2009. [DOI: 10.1016/j.devcel.2009.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius MT, Aronow J, Kaimal V, Jegga AG, Yu J, Grimmond S, McMahon AP, Patterson LT, Little MH, Potter SS. Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell 2009; 15:781-91. [PMID: 19000842 DOI: 10.1016/j.devcel.2008.09.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 08/29/2008] [Accepted: 09/22/2008] [Indexed: 01/03/2023]
Abstract
Kidney development is based on differential cell-type-specific expression of a vast number of genes. While multiple critical genes and pathways have been elucidated, a genome-wide analysis of gene expression within individual cellular and anatomic structures is lacking. Accomplishing this could provide significant new insights into fundamental developmental mechanisms such as mesenchymal-epithelial transition, inductive signaling, branching morphogenesis, and segmentation. We describe here a comprehensive gene expression atlas of the developing mouse kidney based on the isolation of each major compartment by either laser capture microdissection or fluorescence-activated cell sorting, followed by microarray profiling. The resulting data agree with known expression patterns and additional in situ hybridizations. This kidney atlas allows a comprehensive analysis of the progression of gene expression states during nephrogenesis, as well as discovery of potential growth factor-receptor interactions. In addition, the results provide deeper insight into the genetic regulatory mechanisms of kidney development.
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Affiliation(s)
- Eric W Brunskill
- Division of Developmental Biology, Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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36
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Humphreys BD, Valerius MT, Kobayashi A, Mugford JW, Soeung S, Duffield JS, McMahon AP, Bonventre JV. Intrinsic epithelial cells repair the kidney after injury. Cell Stem Cell 2008; 2:284-91. [PMID: 18371453 DOI: 10.1016/j.stem.2008.01.014] [Citation(s) in RCA: 610] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 12/17/2007] [Accepted: 01/22/2008] [Indexed: 12/17/2022]
Abstract
Understanding the mechanisms of nephron repair is critical for the design of new therapeutic approaches to treat kidney disease. The kidney can repair after even a severe insult, but whether adult stem or progenitor cells contribute to epithelial renewal after injury and the cellular origin of regenerating cells remain controversial. Using genetic fate-mapping techniques, we generated transgenic mice in which 94%-95% of tubular epithelial cells, but no interstitial cells, were labeled with either beta-galactosidase (lacZ) or red fluorescent protein (RFP). Two days after ischemia-reperfusion injury (IRI), 50.5% of outer medullary epithelial cells coexpress Ki67 and RFP, indicating that differentiated epithelial cells that survived injury undergo proliferative expansion. After repair was complete, 66.9% of epithelial cells had incorporated BrdU, compared to only 3.5% of cells in the uninjured kidney. Despite this extensive cell proliferation, no dilution of either cell-fate marker was observed after repair. These results indicate that regeneration by surviving tubular epithelial cells is the predominant mechanism of repair after ischemic tubular injury in the adult mammalian kidney.
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Affiliation(s)
- Benjamin D Humphreys
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Institutes of Medicine, Room 550, 4 Blackfan Circle, Boston, MA 02115, USA.
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Valerius MT, McMahon AP. Transcriptional profiling of Wnt4 mutant mouse kidneys identifies genes expressed during nephron formation. Gene Expr Patterns 2008; 8:297-306. [DOI: 10.1016/j.gep.2008.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/30/2008] [Accepted: 02/02/2008] [Indexed: 01/26/2023]
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Cheng HT, Kim M, Valerius MT, Surendran K, Schuster-Gossler K, Gossler A, McMahon AP, Kopan R. Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron. Development 2007. [DOI: 10.1242/dev.02887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Little MH, Brennan J, Georgas K, Davies JA, Davidson DR, Baldock RA, Beverdam A, Bertram JF, Capel B, Chiu HS, Clements D, Cullen-McEwen L, Fleming J, Gilbert T, Herzlinger D, Houghton D, Kaufman MH, Kleymenova E, Koopman PA, Lewis AG, McMahon AP, Mendelsohn CL, Mitchell EK, Rumballe BA, Sweeney DE, Valerius MT, Yamada G, Yang Y, Yu J. Corrigendum to “A high-resolution anatomical ontology of the developing murine genitourinary tract” [Gene Expression Patterns 7 (2007) 680–699]. Gene Expr Patterns 2007. [DOI: 10.1016/j.modgep.2007.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
Mammalian nephrons form as a result of a complex morphogenesis and patterning of a simple epithelial precursor, the renal vesicle. Renal vesicles are established from a mesenchymal progenitor population in response to inductive signals. Several lines of evidence support the sequential roles of two Wnt family members, Wnt9b and Wnt4, in renal vesicle induction. Using genetic approaches to specifically manipulate the activity of β-catenin within the mesenchymal progenitor pool in mice, we investigated the potential role of the canonical Wnt pathway in these inductive events. Progenitor-cell-specific removal of β-catenin activity completely blocked both the formation of renal vesicles and the expected molecular signature of an earlier inductive response. By contrast, activation of stabilizedβ-catenin in the same cell population causes ectopic expression of mesenchymal induction markers in vitro and functionally replaces the requirement for Wnt9b and Wnt4 in their inductive roles in vivo. Thus, canonical Wnt signaling is both necessary and sufficient for initiating and maintaining inductive pathways mediated by Wnt9b and Wnt4. However, the failure of induced mesenchyme with high levels of β-catenin activity to form epithelial structures suggests that modulating canonical signaling may be crucial for the cellular transition to the renal vesicle.
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Affiliation(s)
- Joo-Seop Park
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Little MH, Brennan J, Georgas K, Davies JA, Davidson DR, Baldock RA, Beverdam A, Bertram JF, Capel B, Chiu HS, Clements D, Cullen-McEwen L, Fleming J, Gilbert T, Herzlinger D, Houghton D, Kaufman MH, Kleymenova E, Koopman PA, Lewis AG, McMahon AP, Mendelsohn CL, Mitchell EK, Rumballe BA, Sweeney DE, Valerius MT, Yamada G, Yang Y, Yu J. A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expr Patterns 2007; 7:680-99. [PMID: 17452023 PMCID: PMC2117077 DOI: 10.1016/j.modgep.2007.03.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [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: 01/12/2007] [Revised: 03/14/2007] [Accepted: 03/14/2007] [Indexed: 11/24/2022]
Abstract
Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided.
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Affiliation(s)
- Melissa H Little
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia.
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Cheng HT, Kim M, Valerius MT, Surendran K, Schuster-Gossler K, Gossler A, McMahon AP, Kopan R. Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron. Development 2007; 134:801-11. [PMID: 17229764 PMCID: PMC2613851 DOI: 10.1242/dev.02773] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [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] [Indexed: 12/16/2022]
Abstract
The Notch pathway regulates cell fate determination in numerous developmental processes. Here we report that Notch2 acts non-redundantly to control the processes of nephron segmentation through an Rbp-J-dependent process. Notch1 and Notch2 are detected in the early renal vesicle. Genetic analysis reveals that only Notch2 is required for the differentiation of proximal nephron structures (podocytes and proximal convoluted tubules) despite the presence of activated Notch1 in the nuclei of putative proximal progenitors. The inability of endogenous Notch1 to compensate for Notch2 deficiency may reflect sub-threshold Notch1 levels in the nucleus. In line with this view, forced expression of a gamma-secretase-independent form of Notch1 intracellular domain drives the specification of proximal fates where all endogenous, ligand-dependent Notch signaling is blocked by a gamma-secretase inhibitor. These results establish distinct (non-redundant), instructive roles for Notch receptors in nephron segmentation.
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Affiliation(s)
- Hui-Teng Cheng
- Department of Molecular Biology and Pharmacology at Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8103, St Louis, MO 63110, USA
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Gray PA, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, Tenzen T, Yuk DI, Tsung EF, Cai Z, Alberta JA, Cheng LP, Liu Y, Stenman JM, Valerius MT, Billings N, Kim HA, Greenberg ME, McMahon AP, Rowitch DH, Stiles CD, Ma Q. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 2005; 306:2255-7. [PMID: 15618518 DOI: 10.1126/science.1104935] [Citation(s) in RCA: 336] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In the developing brain, transcription factors (TFs) direct the formation of a diverse array of neurons and glia. We identifed 1445 putative TFs in the mouse genome. We used in situ hybridization to map the expression of over 1000 of these TFs and TF-coregulator genes in the brains of developing mice. We found that 349 of these genes showed restricted expression patterns that were adequate to describe the anatomical organization of the brain. We provide a comprehensive inventory of murine TFs and their expression patterns in a searchable brain atlas database.
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Affiliation(s)
- Paul A Gray
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Recent functional studies in mouse further illustrate the importance of the epithelial-mesenchymal interaction between the ureteric bud epithelium and the metanephric mesenchyme in kidney formation. Genetic ablation of Gdf11, Six1, Slit2/Robo2 reveal a role of these genes in regulating the outgrowth of a single ureteric bud from the Wolffian duct. Studies of Wnt11 and Fras1/Grip1, all expressed in the ureteric bud, show a role for these genes in regulating events in the adjacent metanephric mesenchyme. Furthermore, various approaches were used to address the function of Pod1, Pbx1, the Notch pathway and Brn1 in nephron formation.
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Affiliation(s)
- Jing Yu
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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Abstract
Mutation of the functionally redundant Hoxa 11/Hoxd 11 genes gives absent or rudimentary kidneys resulting from a dramatic reduction of the growth and branching of the ureteric bud. To understand better the molecular mechanisms of Hoxa 11/Hoxd 11 function in kidney development, it is necessary to identify the downstream target genes regulated by their encoded transcription factors. To this end, we conducted a screen for Hoxa 11-responsive genes in two kidney cell lines. HEK293 cells, which usually do not express Hoxa 11, were modified to allow inducible Hoxa 11 expression. The mK10 cells, derived specifically for this study from Hoxa 11/Hoxd 11 double-mutant mice, were also modified to give cell populations with and without Hoxa 11 expression. Differential display, Gene Discovery Arrays, and Affymetrix genechip probe arrays were used to screen for genes up- or down-regulated by Hoxa 11. Nine genes, PDGF A, Cathepsin L, annexin A1, Mm.112139, Est2 repressor factor, NrCAM, ZNF192, integrin-associated protein, and GCM1, showed reproducible 3-fold or smaller changes in gene expression in response to Hoxa 11. One gene, the Integrin alpha8, was up-regulated approximately 20-fold after Hoxa 11 expression. The Integrin alpha8 gene is expressed together with Hoxa 11 in metanephric mesenchyme cells, and mutation of Integrin alpha8 gives a bud-branching morphogenesis defect very similar to that observed in Hoxa 11/Hoxd 11 mutant mice. In situ hybridizations showed a dramatic regional reduction in Integrin alpha8 expression in the developing kidneys of Hoxa 11/Hoxd 11 mutant mice. This work suggests that the Integrin alpha8 gene may be a major effector of Hoxa 11/Hoxd 11 function in the developing kidney.
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Affiliation(s)
- M Todd Valerius
- Division of Developmental Biology, Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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46
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Potter SS, Valerius MT, Brunskill EW. Using progenitor cells and gene chips to define genetic pathways. Methods Mol Biol 2002; 185:269-84. [PMID: 11768995 DOI: 10.1385/1-59259-241-4:269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- S S Potter
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH, USA
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47
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Abstract
Clonal cell lines representing different developmental stages of the metanephric mesenchyme were made from transgenic mice with the Simian Virus 40 T-antigen (SV40 Tag) gene driven by the Hoxa 11 promoter. The resulting mK3 cell line represented early metanephric mesenchyme, prior to induction by the ureteric bud. These cells showed a spindle-shaped, fibroblast morphology. They expressed genes characteristic of early mesenchyme, including Hoxa 11, Hoxd 11, collagen I, and vimentin. Moreover, the mK3 cells displayed early metanephric mesenchyme biological function. In organ co-culture experiments they were able to induce growth and branching of the ureteric bud. Another cell line, mK4, represented later, induced metanephric mesenchyme undergoing epithelial conversion. These cells were more polygonal, or epithelial in shape, and expressed genes diagnostic of late mesenchyme, including Pax-2, Pax-8, Wnt-4, Cadherin-6, Collagen IV, and LFB3. To better define the gene expression patterns of kidney metanephric mesenchyme cells at these two stages of development, RNAs from the mK3 and mK4 cells were hybridized to Affymetrix GeneChip probe arrays. Over 4000 expressed genes were identified and thereby implicated in kidney formation. Comparison of the mK3 and mK4 gene expression profiles revealed 121 genes showing greater than a ten-fold difference in expression level. Several are known to be expressed during metanephric mesenchyme differentiation, but most had not been previously associated with this process. In situ hybridizations were used to confirm that selected novel genes were expressed in the developing kidney.
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Affiliation(s)
- M Todd Valerius
- Division of Developmental Biology, Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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48
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Abstract
Clonal cell lines representing different developmental stages of the metanephric mesenchyme were made from transgenic mice with the Simian Virus 40 T-antigen (SV40 Tag) gene driven by the Hoxa 11 promoter. The resulting mK3 cell line represented early metanephric mesenchyme, prior to induction by the ureteric bud. These cells showed a spindle-shaped, fibroblast morphology. They expressed genes characteristic of early mesenchyme, including Hoxa 11, Hoxd 11, collagen I, and vimentin. Moreover, the mK3 cells displayed early metanephric mesenchyme biological function. In organ co-culture experiments they were able to induce growth and branching of the ureteric bud. Another cell line, mK4, represented later, induced metanephric mesenchyme undergoing epithelial conversion. These cells were more polygonal, or epithelial in shape, and expressed genes diagnostic of late mesenchyme, including Pax-2, Pax-8, Wnt-4, Cadherin-6, Collagen IV, and LFB3. To better define the gene expression patterns of kidney metanephric mesenchyme cells at these two stages of development, RNAs from the mK3 and mK4 cells were hybridized to Affymetrix GeneChip probe arrays. Over 4000 expressed genes were identified and thereby implicated in kidney formation. Comparison of the mK3 and mK4 gene expression profiles revealed 121 genes showing greater than a ten-fold difference in expression level. Several are known to be expressed during metanephric mesenchyme differentiation, but most had not been previously associated with this process. In situ hybridizations were used to confirm that selected novel genes were expressed in the developing kidney.
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Affiliation(s)
- M Todd Valerius
- Division of Developmental Biology, Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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49
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Abstract
Spx1, a novel mouse homeobox gene, encodes a homeodomain characteristic of the paired-like class of homeobox genes and has been mapped to the distal end of the X chromosome. Northern blot hybridization of adult tissues detected high levels of a single Spx1 transcript in the testis. Further analysis by in situ hybridization revealed predominant Spx1 expression within the spermatogonia/preleptotene spermatocytes and round spermatids of spermatogenic stages IV-VII. These expression data suggest SPX1 may play a role in the regulation of spermatogenesis.
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Affiliation(s)
- W W Branford
- Children's Hospital Research Foundation, Developmental Biology, Cincinnati, OH 45229, USA
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50
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Haynes TL, Thomas MB, Dusing MR, Valerius MT, Potter SS, Wiginton DA. An enhancer LEF-1/TCF-1 site is essential for insertion site-independent transgene expression in thymus. Nucleic Acids Res 1996; 24:5034-44. [PMID: 9016677 PMCID: PMC146351 DOI: 10.1093/nar/24.24.5034] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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] [Indexed: 02/03/2023] Open
Abstract
Transcriptional activation of eukaryotic genes involves assembly of specific multiprotein complexes on the promoters and enhancers of the genes. Recently, it has been proposed that the role of some of the proteins in the complex may be architectural, involving DNA bending, orchestration of protein-protein interaction and modulation of nucleosome structure. This role has been proposed for the HMG proteins LEF-1 and TCF-1. We examined the role of a LEF-1/TCF-1 binding site in the human adenosine deaminase (ADA) thymic enhancer. Mutational analysis demonstrated that a functional LEF-1/TCF-1 binding site is not required for enhancer-mediated transcriptional activation in transient transfection studies, but is essential for enhancer function in the in vivo chromatin context of transgenic mice. Mutation of the LEF-1/TCF-1 site destroyed the ability of the ADA enhancer/locus control region to specify high level, insertion site-independent transgene expression in thymus. DNase I and DpnII accessibility experiments indicated dramatic changes in the chromatin organization of the ADA enhancer in transgenic mice with a mutated LEF-1/TCF-1 site. This supports the hypothesis that factors binding the LEF-1/TCF-1 site play an architectural role during the in vivo activation of the ADA enhancer, possibly involving chromatin modification.
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Affiliation(s)
- T L Haynes
- Department of Pediatrics, University of Cincinnati, OH 45229, USA
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