1
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Dissanayake LV, Kravtsova O, Lowe M, McCrorey MK, Van Beusecum JP, Palygin O, Staruschenko A. The presence of xanthine dehydrogenase is crucial for the maturation of the rat kidneys. Clin Sci (Lond) 2024; 138:269-288. [PMID: 38358003 DOI: 10.1042/cs20231144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/24/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
The development of the kidney involves essential cellular processes, such as cell proliferation and differentiation, which are led by interactions between multiple signaling pathways. Xanthine dehydrogenase (XDH) catalyzes the reaction producing uric acid in the purine catabolism, which plays a multifaceted role in cellular metabolism. Our previous study revealed that the genetic ablation of the Xdh gene in rats leads to smaller kidneys, kidney damage, decline of renal functions, and failure to thrive. Rats, unlike humans, continue their kidney development postnatally. Therefore, we explored whether XDH plays a critical role in kidney development using SS-/- rats during postnatal development phase. XDH expression was significantly increased from postnatal day 5 to 15 in wild-type but not homozygote rat kidneys. The transcriptomic profile of renal tissue revealed several dysregulated pathways due to the lack of Xdh expression with the remodeling in inflammasome, purinergic signaling, and redox homeostasis. Further analysis suggested that lack of Xdh affects kidney development, likely via dysregulation of epidermal growth factor and its downstream STAT3 signaling. The present study showed that Xdh is essential for kidney maturation. Our data, alongside the previous research, suggests that loss of Xdh function leads to developmental issues, rendering them vulnerable to kidney diseases in adulthood.
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Affiliation(s)
- Lashodya V Dissanayake
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Olha Kravtsova
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Melissa Lowe
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Marice K McCrorey
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Justin P Van Beusecum
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
- Ralph H. Johnson Veterans Affairs Healthcare System, Charleston, SC 29403, U.S.A
| | - Oleg Palygin
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Alexander Staruschenko
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
- Hypertension and Kidney Research Center, University of South Florida, Tampa, FL 33602, U.S.A
- James A. Haley Veterans' Hospital, Tampa, FL 33612, U.S.A
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2
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Wang SX, Streit A. Shared features in ear and kidney development - implications for oto-renal syndromes. Dis Model Mech 2024; 17:dmm050447. [PMID: 38353121 PMCID: PMC10886756 DOI: 10.1242/dmm.050447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
The association between ear and kidney anomalies has long been recognized. However, little is known about the underlying mechanisms. In the last two decades, embryonic development of the inner ear and kidney has been studied extensively. Here, we describe the developmental pathways shared between both organs with particular emphasis on the genes that regulate signalling cross talk and the specification of progenitor cells and specialised cell types. We relate this to the clinical features of oto-renal syndromes and explore links to developmental mechanisms.
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Affiliation(s)
- Scarlet Xiaoyan Wang
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
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3
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Bronstein R, Pace J, Gowthaman Y, Salant DJ, Mallipattu SK. Podocyte-Parietal Epithelial Cell Interdependence in Glomerular Development and Disease. J Am Soc Nephrol 2023; 34:737-750. [PMID: 36800545 PMCID: PMC10125654 DOI: 10.1681/asn.0000000000000104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
Podocytes and parietal epithelial cells (PECs) are among the few principal cell types within the kidney glomerulus, the former serving as a crucial constituent of the kidney filtration barrier and the latter representing a supporting epithelial layer that adorns the inner wall of Bowman's capsule. Podocytes and PECs share a circumscript developmental lineage that only begins to diverge during the S-shaped body stage of nephron formation-occurring immediately before the emergence of the fully mature nephron. These two cell types, therefore, share a highly conserved gene expression program, evidenced by recently discovered intermediate cell types occupying a distinct spatiotemporal gene expression zone between podocytes and PECs. In addition to their homeostatic functions, podocytes and PECs also have roles in kidney pathogenesis. Rapid podocyte loss in diseases, such as rapidly progressive GN and collapsing and cellular subtypes of FSGS, is closely allied with PEC proliferation and migration toward the capillary tuft, resulting in the formation of crescents and pseudocrescents. PECs are thought to contribute to disease progression and severity, and the interdependence between these two cell types during development and in various manifestations of kidney pathology is the primary focus of this review.
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Affiliation(s)
- Robert Bronstein
- Division of Nephrology, Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York
| | - Jesse Pace
- Division of Nephrology, Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York
| | - Yogesh Gowthaman
- Division of Nephrology, Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York
| | - David J. Salant
- Division of Nephrology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Sandeep K. Mallipattu
- Division of Nephrology, Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York
- Renal Section, Northport VA Medical Center, Northport, New York
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4
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Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development. Sci Rep 2022; 12:19548. [PMID: 36380228 PMCID: PMC9666651 DOI: 10.1038/s41598-022-24147-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme-a transient kidney-specific progenitor state-undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms' tumor that mimics normal kidney development. While human kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. Therefore, in this study, we performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms' tumor patient-derived xenografts. Using this newly generated RNAseq data, we identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms' tumor xenografts. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate alternative mRNA splicing during human kidney development. These findings illuminate new molecular mechanisms involved in human kidney development and pediatric kidney cancer.
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5
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Mechanisms of ion transport regulation by HNF1β in the kidney: beyond transcriptional regulation of channels and transporters. Pflugers Arch 2022; 474:901-916. [PMID: 35554666 PMCID: PMC9338905 DOI: 10.1007/s00424-022-02697-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 01/01/2023]
Abstract
Hepatocyte nuclear factor 1β (HNF1β) is a transcription factor essential for the development and function of the kidney. Mutations in and deletions of HNF1β cause autosomal dominant tubule interstitial kidney disease (ADTKD) subtype HNF1β, which is characterized by renal cysts, diabetes, genital tract malformations, and neurodevelopmental disorders. Electrolyte disturbances including hypomagnesemia, hyperuricemia, and hypocalciuria are common in patients with ADTKD-HNF1β. Traditionally, these electrolyte disturbances have been attributed to HNF1β-mediated transcriptional regulation of gene networks involved in ion transport in the distal part of the nephron including FXYD2, CASR, KCNJ16, and FXR. In this review, we propose additional mechanisms that may contribute to the electrolyte disturbances observed in ADTKD-HNF1β patients. Firstly, kidney development is severely affected in Hnf1b-deficient mice. HNF1β is required for nephron segmentation, and the absence of the transcription factor results in rudimentary nephrons lacking mature proximal tubule, loop of Henle, and distal convoluted tubule cluster. In addition, HNF1β is proposed to be important for apical-basolateral polarity and tight junction integrity in the kidney. Interestingly, cilia formation is unaffected by Hnf1b defects in several models, despite the HNF1β-mediated transcriptional regulation of many ciliary genes. To what extent impaired nephron segmentation, apical-basolateral polarity, and cilia function contribute to electrolyte disturbances in HNF1β patients remains elusive. Systematic phenotyping of Hnf1b mouse models and the development of patient-specific kidney organoid models will be essential to advance future HNF1β research.
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6
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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7
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Generation of Induced Nephron Progenitor-like Cells from Human Urine-Derived Cells. Int J Mol Sci 2021; 22:ijms222413449. [PMID: 34948246 PMCID: PMC8708572 DOI: 10.3390/ijms222413449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023] Open
Abstract
Background: Regenerative medicine strategies employing nephron progenitor cells (NPCs) are a viable approach that is worthy of substantial consideration as a promising cell source for kidney diseases. However, the generation of induced nephron progenitor-like cells (iNPCs) from human somatic cells remains a major challenge. Here, we describe a novel method for generating NPCs from human urine-derived cells (UCs) that can undergo long-term expansion in a serum-free condition. Results: Here, we generated iNPCs from human urine-derived cells by forced expression of the transcription factors OCT4, SOX2, KLF4, c-MYC, and SLUG, followed by exposure to a cocktail of defined small molecules. These iNPCs resembled human embryonic stem cell-derived NPCs in terms of their morphology, biological characteristics, differentiation potential, and global gene expression and underwent a long-term expansion in serum-free conditions. Conclusion: This study demonstrates that human iNPCs can be readily generated and expanded, which will facilitate their broad applicability in a rapid, efficient, and patient-specific manner, particularly holding the potential as a transplantable cell source for patients with kidney disease.
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8
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PBRM1 loss in kidney cancer unbalances the proximal tubule master transcription factor hub to repress proximal tubule differentiation. Cell Rep 2021; 36:109747. [PMID: 34551289 PMCID: PMC8561673 DOI: 10.1016/j.celrep.2021.109747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/20/2021] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
PBRM1, a subunit of the PBAF coactivator complex that transcription factors use to activate target genes, is genetically inactivated in almost all clear cell renal cell cancers (RCCs). Using unbiased proteomic analyses, we find that PAX8, a master transcription factor driver of proximal tubule epithelial fates, recruits PBRM1/PBAF. Reverse analyses of the PAX8 interactome confirm recruitment specifically of PBRM1/PBAF and not functionally similar BAF. More conspicuous in the PAX8 hub in RCC cells, however, are corepressors, which functionally oppose coactivators. Accordingly, key PAX8 target genes are repressed in RCC versus normal kidneys, with the loss of histone lysine-27 acetylation, but intact lysine-4 trimethylation, activation marks. Re-introduction of PBRM1, or depletion of opposing corepressors using siRNA or drugs, redress coregulator imbalance and release RCC cells to terminal epithelial fates. These mechanisms thus explain RCC resemblance to the proximal tubule lineage but with suppression of the late-epithelial program that normally terminates lineage-precursor proliferation. Gu et al. identify that transcription factor PAX8 needs the PBRM1/PBAF coactivator to activate proximal tubule genes. PBRM1 mutation/deletion thus explains the resemblance of clear cell kidney cancer to proximal tubule tissue but with suppressed terminal epithelial markers. This oncogenic mechanism could be repaired using drugs to inhibit corepressors.
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9
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Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Single cell derived mRNA signals across human kidney tumors. Nat Commun 2021; 12:3896. [PMID: 34162837 PMCID: PMC8222373 DOI: 10.1038/s41467-021-23949-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/25/2021] [Indexed: 01/16/2023] Open
Abstract
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer.
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Affiliation(s)
- Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Francisco Morales-Rodriguez
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eleonora Khabirova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerda Kildisiute
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alice Piapi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Christina Burke
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirsty Ambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ignacio Del Valle
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials office, Cambridge Biomedical Campus Cambridge CB2 0QQ University of Cambridge, Cambridge, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil Sebire
- NIHR Great Ormond Street Hospital BRC and Institute of Child Health, London, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Anne Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Intitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
- Heidelberg University Hospital, Department of Pediatric Hematology and Oncology, Heidelberg, Germany
| | - John C Achermann
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Xiaoling He
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Frank C Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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10
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Schuh MP, Alkhudairy L, Potter A, Potter SS, Chetal K, Thakkar K, Salomonis N, Kopan R. The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis. J Am Soc Nephrol 2021; 32:1097-1112. [PMID: 33789950 PMCID: PMC8259676 DOI: 10.1681/asn.2020101459] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/18/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Most nephrons are added in late gestation. Truncated extrauterine nephrogenesis in premature infants results in fewer nephrons and significantly increased risk for CKD in adulthood. To overcome the ethical and technical difficulties associated with studies of late-gestation human fetal kidney development, third-trimester rhesus macaques served as a model to understand lateral branch nephrogenesis (LBN) at the molecular level. METHODS Immunostaining and 3D rendering assessed morphology. Single-cell (sc) and single-nucleus (sn) RNA-Seq were performed on four cortically enriched fetal rhesus kidneys of 129-131 days gestational age (GA). An integrative bioinformatics strategy was applied across single-cell modalities, species, and time. RNAScope validation studies were performed on human archival tissue. RESULTS Third-trimester rhesus kidney undergoes human-like LBN. scRNA-Seq of 23,608 cells revealed 37 transcriptionally distinct cell populations, including naïve nephron progenitor cells (NPCs), with the prior noted marker genes CITED1, MEOX1, and EYA1 (c25). These same populations and markers were reflected in snRNA-Seq of 5972 nuclei. Late-gestation rhesus NPC markers resembled late-gestation murine NPC, whereas early second-trimester human NPC markers aligned to midgestation murine NPCs. New, age-specific rhesus NPCs (SHISA8) and ureteric buds (POU3F4 and TWIST) predicted markers were verified in late-gestation human archival samples. CONCLUSIONS Rhesus macaque is the first model of bona fide LBN, enabling molecular studies of late gestation, human-like nephrogenesis. These molecular findings support the hypothesis that aging nephron progenitors have a distinct molecular signature and align to their earlier human counterparts, with unique markers highlighting LBN-specific progenitor maturation.
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Affiliation(s)
- Meredith P. Schuh
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Nephrology and Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Lyan Alkhudairy
- Division of Nephrology and Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Andrew Potter
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - S. Steven Potter
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Raphael Kopan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
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11
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Dworschak GC, Reutter HM, Ludwig M. Currarino syndrome: a comprehensive genetic review of a rare congenital disorder. Orphanet J Rare Dis 2021; 16:167. [PMID: 33836786 PMCID: PMC8034116 DOI: 10.1186/s13023-021-01799-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background The triad of a presacral mass, sacral agenesis and an anorectal anomaly constitutes the rare Currarino syndrome (CS), which is caused by dorsal–ventral patterning defects during embryonic development. The major causative CS gene is MNX1, encoding a homeobox protein. Main body In the majority of patients, CS occurs as an autosomal dominant trait; however, a female predominance observed, implies that CS may underlie an additional mode(s) of inheritance. Often, the diagnosis of CS is established solely by clinical findings, impacting a detailed analysis of the disease. Our combined data, evaluating more than 60 studies reporting patients with CS-associated mutations, revealed a slightly higher incidence rate in females with a female-to-male ratio of 1.39:1. Overall, MNX1 mutation analysis was successful in only 57.4% of all CS patients investigated, with no mutation detected in 7.7% of the familial and 68% of the sporadic patients. Our studies failed to detect the presence of an expressed MNX1 isoform that might explain at least some of these mutation-negative cases. Conclusion Aside from MNX1, other genes or regulatory regions may contribute to CS and we discuss several cytogenetic studies and whole-exome sequencing data that have implicated further loci/genes in its etiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01799-0.
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Affiliation(s)
- Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany. .,Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany. .,Department of Pediatrics, University Hospital Bonn, 53127, Bonn, Germany.
| | - Heiko M Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, University Hospital Bonn, 53127, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, 53127, Bonn, Germany
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12
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Abstract
The kidney plays an integral role in filtering the blood-removing metabolic by-products from the body and regulating blood pressure. This requires the establishment of large numbers of efficient and specialized blood filtering units (nephrons) that incorporate a system for vascular exchange and nutrient reabsorption as well as a collecting duct system to remove waste (urine) from the body. Kidney development is a dynamic process which generates these structures through a delicately balanced program of self-renewal and commitment of nephron progenitor cells that inhabit a constantly evolving cellular niche at the tips of a branching ureteric "tree." The former cells build the nephrons and the latter the collecting duct system. Maintaining these processes across fetal development is critical for establishing the normal "endowment" of nephrons in the kidney and perturbations to this process are associated both with mutations in integral genes and with alterations to the fetal environment.
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Affiliation(s)
- Ian M Smyth
- Department of Anatomy and Developmental Biology, Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
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13
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Abstract
Uromodulin, a protein exclusively produced by the kidney, is the most abundant urinary protein in physiological conditions. Already described several decades ago, uromodulin has gained the spotlight in recent years, since the discovery that mutations in its encoding gene UMOD cause a renal Mendelian disease (autosomal dominant tubulointerstitial kidney disease) and that common polymorphisms are associated with multifactorial disorders, such as chronic kidney disease, hypertension, and cardiovascular diseases. Moreover, variations in uromodulin levels in urine and/or blood reflect kidney functioning mass and are of prognostic value for renal function, cardiovascular events, and overall mortality. The clinical relevance of uromodulin reflects its multifunctional nature, playing a role in renal ion transport and immunomodulation, in protection against urinary tract infections and renal stones, and possibly as a systemic antioxidant. Here, we discuss the multifaceted roles of this protein in kidney physiology and its translational relevance.
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Affiliation(s)
- Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy;
| | - Olivier Devuyst
- Mechanisms of Inherited Kidney Disorders Group, University of Zurich, CH-8057 Zurich, Switzerland
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy;
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14
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Short KM, Smyth IM. Branching morphogenesis as a driver of renal development. Anat Rec (Hoboken) 2020; 303:2578-2587. [PMID: 32790143 DOI: 10.1002/ar.24486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022]
Abstract
Branching morphogenesis is an integral developmental mechanism central to the formation of a range of organs including the kidney, lung, pancreas and mammary gland. The ramified networks of epithelial tubules it establishes are critical for the processes of secretion, excretion and exchange mediated by these tissues. In the kidney, branching serves to establish the collecting duct system that transports urine from the nephrons into the renal pelvis, ureter and finally the bladder. Generally speaking, the formation of these networks in different organs begins with the specification and differentiation of simple bud-like organ anlage, which then undergo a process of elaboration, typically by bifurcation. This process is often governed by the interaction of progenitor cells at the tips of the epithelia with neighboring mesenchymal cell populations which direct the branching process and which often themselves differentiate to form part of the adult organ. In the kidney, the tips of ureteric bud elaborate through a dynamic cell signaling relationship with overlying nephron progenitor cell populations. These cells sequentially commit to differentiation and the resulting nephrons reintegrate with the ureteric epithelium as development progresses. This review will describe recent advances in understanding the how the elaboration of the ureteric bud is patterned and consider the extent to which this process is shared with other organs.
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Affiliation(s)
- Kieran M Short
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
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15
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Wineberg Y, Bar-Lev TH, Futorian A, Ben-Haim N, Armon L, Ickowicz D, Oriel S, Bucris E, Yehuda Y, Pode-Shakked N, Gilad S, Benjamin S, Hohenstein P, Dekel B, Urbach A, Kalisky T. Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development. J Am Soc Nephrol 2020; 31:2278-2291. [PMID: 32651222 DOI: 10.1681/asn.2019080770] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 05/23/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates. METHODS Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys. RESULTS Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. CONCLUSIONS Discovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development.
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Affiliation(s)
- Yishay Wineberg
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Tali Hana Bar-Lev
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Anna Futorian
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nissim Ben-Haim
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Leah Armon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Debby Ickowicz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Oriel
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Efrat Bucris
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yishai Yehuda
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Naomi Pode-Shakked
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Division of Pediatric Nephrology, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shlomit Gilad
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Sima Benjamin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Division of Pediatric Nephrology, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tomer Kalisky
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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16
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Chung JJ, Goldstein L, Chen YJJ, Lee J, Webster JD, Roose-Girma M, Paudyal SC, Modrusan Z, Dey A, Shaw AS. Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury. J Am Soc Nephrol 2020; 31:2341-2354. [PMID: 32651223 DOI: 10.1681/asn.2020020220] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/07/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The glomerulus is a specialized capillary bed that is involved in urine production and BP control. Glomerular injury is a major cause of CKD, which is epidemic and without therapeutic options. Single-cell transcriptomics has radically improved our ability to characterize complex organs, such as the kidney. Cells of the glomerulus, however, have been largely underrepresented in previous single-cell kidney studies due to their paucity and intractability. METHODS Single-cell RNA sequencing comprehensively characterized the types of cells in the glomerulus from healthy mice and from four different disease models (nephrotoxic serum nephritis, diabetes, doxorubicin toxicity, and CD2AP deficiency). RESULTS All cell types in the glomerulus were identified using unsupervised clustering analysis. Novel marker genes and gene signatures of mesangial cells, vascular smooth muscle cells of the afferent and efferent arterioles, parietal epithelial cells, and three types of endothelial cells were identified. Analysis of the disease models revealed cell type-specific and injury type-specific responses in the glomerulus, including acute activation of the Hippo pathway in podocytes after nephrotoxic immune injury. Conditional deletion of YAP or TAZ resulted in more severe and prolonged proteinuria in response to injury, as well as worse glomerulosclerosis. CONCLUSIONS Generation of comprehensive high-resolution, single-cell transcriptomic profiles of the glomerulus from healthy and injured mice provides resources to identify novel disease-related genes and pathways.
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Affiliation(s)
- Jun-Jae Chung
- Department of Research Biology, Genentech, South San Francisco, California
| | - Leonard Goldstein
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Ying-Jiun J Chen
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Jiyeon Lee
- Department of Research Biology, Genentech, South San Francisco, California
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, California
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Sharad C Paudyal
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Anwesha Dey
- Department of Molecular Oncology, Genentech, South San Francisco, California
| | - Andrey S Shaw
- Department of Research Biology, Genentech, South San Francisco, California
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17
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Wood-Bradley RJ, Henry SL, Barrand S, Giot A, Eipper L, Bertram JF, Cullen-McEwen LA, Armitage JA. Analysis of structure and gene expression in developing kidneys of male and female rats exposed to low protein diets in utero. Anat Rec (Hoboken) 2020; 303:2657-2667. [PMID: 32567250 DOI: 10.1002/ar.24417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/24/2019] [Accepted: 01/17/2020] [Indexed: 01/10/2023]
Abstract
A maternal low protein (LP) diet in rodents often results in low nephron endowment and renal pathophysiology in adult life, with outcomes often differing between male and female offspring. Precisely how a maternal LP diet results in low nephron endowment is unknown. We conducted morphological and molecular studies of branching morphogenesis and nephrogenesis to identify mechanisms and timepoints that might give rise to low nephron endowment. Sprague-Dawley rats were fed a normal protein (19.4% protein, NP) or LP (9% protein) diet for 3 weeks prior to mating and throughout gestation. Embryonic day 14.25 (E14.25) kidneys from males and females were either cultured for 2 days after which branching morphogenesis was quantified, or frozen for gene expression analysis. Real-time PCR was used to quantify expression of key nephrogenesis and branching morphogenesis genes at E14.25 and 17.25. At E17.25, nephron number was determined in fixed tissue. There was no effect of either maternal diet or sex on branching morphogenesis. Nephron number at E17.25 was 14% lower in male and female LP offspring than in NP controls. At E14.25 expression levels of genes involved in branching morphogenesis (Gfrα1, Bmp4, Gdnf) and nephrogenesis (Hnf4a, Pax2, Wnt4) were similar in the dietary groups, but significant differences between sexes were identified. At E17.25, expression of Gfrα1, Gdnf, Bmp4, Pax2 and Six2 was lower in LP offspring than NP offspring, in both male and female offspring. These findings provide new insights into how a LP diet leads to low nephron endowment and renal sexual dimorphism.
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Affiliation(s)
- Ryan J Wood-Bradley
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia.,Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Sarah L Henry
- Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Sanna Barrand
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Anais Giot
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Luke Eipper
- Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - John F Bertram
- Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Luise A Cullen-McEwen
- Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - James A Armitage
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia.,Department of Anatomy and Developmental Biology, and Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
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18
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Abstract
Human kidney tissue can now be generated via the directed differentiation of human pluripotent stem cells. This advance is anticipated to facilitate the modeling of human kidney diseases, provide platforms for nephrotoxicity screening, enable cellular therapy, and potentially generate tissue for renal replacement. All such applications will rely upon the accuracy and reliability of the model and the capacity for stem cell-derived kidney tissue to recapitulate both normal and diseased states. In this review, we discuss the models available, how well they recapitulate the human kidney, and how far we are from application of these cells for use in cellular therapies.
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Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia; .,Department of Paediatrics, University of Melbourne, Victoria 3010, Australia.,Department of Anatomy and Neuroscience, University of Melbourne, Victoria 3010, Australia
| | - Lorna J Hale
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia;
| | - Sara E Howden
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia; .,Department of Paediatrics, University of Melbourne, Victoria 3010, Australia
| | - Santhosh V Kumar
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia; .,Department of Paediatrics, University of Melbourne, Victoria 3010, Australia
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19
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Little MH. Diving Deep into the Adult Mouse Kidney. Dev Cell 2020; 51:293-294. [PMID: 31689383 DOI: 10.1016/j.devcel.2019.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this issue of Developmental Cell, Ransick et al. (2019) provide a comprehensive anatomically guided single-cell dataset from adult mouse kidney, representing the most detailed analysis of the cellular heterogeneity and lineage relationship of cells in the adult mouse kidney published to date.
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Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia.
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20
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Lakhia R, Yheskel M, Flaten A, Ramalingam H, Aboudehen K, Ferrè S, Biggers L, Mishra A, Chaney C, Wallace DP, Carroll T, Igarashi P, Patel V. Interstitial microRNA miR-214 attenuates inflammation and polycystic kidney disease progression. JCI Insight 2020; 5:133785. [PMID: 32182218 DOI: 10.1172/jci.insight.133785] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/11/2020] [Indexed: 12/20/2022] Open
Abstract
Renal cysts are the defining feature of autosomal dominant polycystic kidney disease (ADPKD); however, the substantial interstitial inflammation is an often-overlooked aspect of this disorder. Recent studies suggest that immune cells in the cyst microenvironment affect ADPKD progression. Here we report that microRNAs (miRNAs) are new molecular signals in this crosstalk. We found that miR-214 and its host long noncoding RNA Dnm3os are upregulated in orthologous ADPKD mouse models and cystic kidneys from humans with ADPKD. In situ hybridization revealed that interstitial cells in the cyst microenvironment are the primary source of miR-214. While genetic deletion of miR-214 does not affect kidney development or homeostasis, surprisingly, its inhibition in Pkd2- and Pkd1-mutant mice aggravates cyst growth. Mechanistically, the proinflammatory TLR4/IFN-γ/STAT1 pathways transactivate the miR-214 host gene. miR-214, in turn as a negative feedback loop, directly inhibits Tlr4. Accordingly, miR-214 deletion is associated with increased Tlr4 expression and enhanced pericystic macrophage accumulation. Thus, miR-214 upregulation is a compensatory protective response in the cyst microenvironment that restrains inflammation and cyst growth.
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Affiliation(s)
- Ronak Lakhia
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Matanel Yheskel
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Andrea Flaten
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Harini Ramalingam
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Karam Aboudehen
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis, Minnesota, USA
| | - Silvia Ferrè
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA.,Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Laurence Biggers
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Abheepsa Mishra
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Christopher Chaney
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Darren P Wallace
- Department of Medicine and the Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Thomas Carroll
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA.,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Peter Igarashi
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis, Minnesota, USA
| | - Vishal Patel
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
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21
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Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Braga FAV, Botting RA, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera MDC, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Spatiotemporal immune zonation of the human kidney. Science 2019; 365:1461-1466. [PMID: 31604275 PMCID: PMC7343525 DOI: 10.1126/science.aat5031] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 01/31/2019] [Accepted: 09/04/2019] [Indexed: 11/02/2022]
Abstract
Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly or by cross-talk with immune cells. We used single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. We reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, our study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.
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Affiliation(s)
- Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Alexandra M Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Gordon L Frazer
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Joy UL Staniforth
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | | | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Charlotte Guzzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Grace Collord
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Antony CP Riddick
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Marc Bajenoff
- Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Sam Behjati
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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22
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Faraj R, Irizarry-Alfonzo A, Puri P. Molecular characterization of nephron progenitors and their early epithelial derivative structures in the nephrogenic zone of the canine fetal kidney. Eur J Histochem 2019; 63. [PMID: 31544449 PMCID: PMC6763752 DOI: 10.4081/ejh.2019.3049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/10/2019] [Indexed: 01/14/2023] Open
Abstract
Nephron progenitors (NPs) and nephrogenesis have been extensively studied in mice and humans and have provided insights into the mechanisms of renal development, disease and possibility of NP-based therapies. However, molecular features of NPs and their derivatives in the canine fetal kidney (CFK) remain unknown. This study was focused to characterize the expression of potential markers of canine NPs and their derivatives by immuno-fluorescence and western blot analysis. Transcription factors (TFs) SIX1 and SIX2, well-characterized human NP markers, were expressed in NPs surrounding the ureteric bud in the CFK. Canine NPs also expressed ITGA8 and NCAM1, surface markers previously used to isolate NPs from the mouse and human fetal kidneys. TF, PAX2 was detected in the ureteric bud, NPs and their derivative structures such as renal vesicle and S-shaped body. This study highlights the similarities in dog, mouse and human renal development and characterizes markers to identify canine NPs and their derivatives. These results will facilitate the isolation of canine NPs and their functional characterization to develop NP-based therapies for canine renal diseases.
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Affiliation(s)
- Rawah Faraj
- Department of Biomedical Sciences, College of Veterinary Medicine, Tuskegee University, Tuskegee.
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23
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Sung SSJ, Fu SM. Interactions among glomerulus infiltrating macrophages and intrinsic cells via cytokines in chronic lupus glomerulonephritis. J Autoimmun 2019; 106:102331. [PMID: 31495649 DOI: 10.1016/j.jaut.2019.102331] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Inflammation plays a key role in the pathogenesis of lupus nephritis (LN) and inflammatory cytokines within the glomeruli are critical in this process. However, little information is available for the identities of the cell types that are primarily responsible for the production and function of the various cytokines. We have devised a novel method to visualize cytokine signals in the kidney by confocal microscopy and found that cytokine production within the glomerulus is cell type-specific and under translational control. In the lupus-prone NZM2328 mice with chronic glomerulonephritis, IL-6, IL-1β, and TNF-α in the glomerulus were produced predominantly by mesangial cells, podocytes, and glomerulus-infiltrating blood-derived macrophages, respectively. Microarray and RNASeq analyses showed that these cells expressed the receptors for these cytokines. Together the 3 cell types form a cytokine circuit in amplifying cytokine responses in LN. The intrinsic cells and infiltrating macrophages also produced other cytokines including M-CSF, SCF, and IL-34 that constituted within the enclosed glomerular space the soluble effector milieu which may mediate cellular damage and proliferation, and cytokine transcriptional and translation regulation. IL-10 and IL-1β were translationally regulated in the glomeruli in the intact kidney in a cell type-specific manner. The production of these 2 cytokines by infiltrating macrophages was undetectable in a visualization system for in situ protein accumulation despite high mRNA expression levels. However, these macrophages in isolated glomeruli which are released from Bowman's capsules produced large amounts of IL-10 and IL-1β. These data reveal the complexity of cytokine regulation, production, and function in the glomerulus and provide a model in which cytokine blocking may be beneficial in LN treatment.
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Affiliation(s)
- Sun-Sang J Sung
- Center for Immunity, Inflammation, and Regenerative Medicine, Departments of Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Shu Man Fu
- Center for Immunity, Inflammation, and Regenerative Medicine, Departments of Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA; Division of Rheumatology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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24
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Sander V, Salleh L, Naylor RW, Schierding W, Sontam D, O’Sullivan JM, Davidson AJ. Transcriptional profiling of the zebrafish proximal tubule. Am J Physiol Renal Physiol 2019; 317:F478-F488. [DOI: 10.1152/ajprenal.00174.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The hepatocyte nuclear factor-1β (Hnf1b) transcription factor is a key regulator of kidney tubule formation and is associated with a syndrome of renal cysts and early onset diabetes. To further our understanding of Hnf1b in the developing zebrafish kidney, we performed RNA sequencing analysis of proximal tubules from hnf1b-deficient larvae. This analysis revealed an enrichment of gene transcripts encoding transporters of the solute carrier (SLC) superfamily, including multiple members of slc2 and slc5 glucose transporters. An investigation of expression of slc2a1a, slc2a2, and slc5a2 as well as a poorly studied glucose/mannose transporter encoded by slc5a9 revealed that these genes undergo dynamic spatiotemporal changes during tubule formation and maturation. A comparative analysis of zebrafish SLC genes with those expressed in mouse proximal tubules showed a substantial overlap at the level of gene families, indicating a high degree of functional conservation between zebrafish and mammalian proximal tubules. Taken together, our findings are consistent with a role for Hnf1b as a critical determinant of proximal tubule transport function by acting upstream of a large number of SLC genes and validate the zebrafish as a physiologically relevant model of the mammalian proximal tubule.
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Affiliation(s)
- Veronika Sander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Liam Salleh
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Richard W. Naylor
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | | | - Dharani Sontam
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Alan J. Davidson
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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25
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Combes AN, Phipson B, Lawlor KT, Dorison A, Patrick R, Zappia L, Harvey RP, Oshlack A, Little MH. Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development 2019; 146:dev.178673. [PMID: 31118232 DOI: 10.1242/dev.178673] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]
Abstract
Recent advances in the generation of kidney organoids and the culture of primary nephron progenitors from mouse and human have been based on knowledge of the molecular basis of kidney development in mice. Although gene expression during kidney development has been intensely investigated, single cell profiling provides new opportunities to further subsect component cell types and the signalling networks at play. Here, we describe the generation and analysis of 6732 single cell transcriptomes from the fetal mouse kidney [embryonic day (E)18.5] and 7853 sorted nephron progenitor cells (E14.5). These datasets provide improved resolution of cell types and specific markers, including subdivision of the renal stroma and heterogeneity within the nephron progenitor population. Ligand-receptor interaction and pathway analysis reveals novel crosstalk between cellular compartments and associates new pathways with differentiation of nephron and ureteric epithelium cell types. We identify transcriptional congruence between the distal nephron and ureteric epithelium, showing that most markers previously used to identify ureteric epithelium are not specific. Together, this work improves our understanding of metanephric kidney development and provides a template to guide the regeneration of renal tissue.
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Affiliation(s)
- Alexander N Combes
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia .,Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia
| | - Belinda Phipson
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kynan T Lawlor
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia
| | - Aude Dorison
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Ralph Patrick
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Kensington, New South Wales 2033, Australia
| | - Luke Zappia
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard P Harvey
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Kensington, New South Wales 2033, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, New South Wales 2010, Australia
| | - Alicia Oshlack
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia.,School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Melissa H Little
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia .,Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
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26
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Yosypiv IV, Sequeira-Lopez MLS, Song R, De Goes Martini A. Stromal prorenin receptor is critical for normal kidney development. Am J Physiol Regul Integr Comp Physiol 2019; 316:R640-R650. [PMID: 30943054 DOI: 10.1152/ajpregu.00320.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formation of the metanephric kidney requires coordinated interaction among the stroma, ureteric bud, and cap mesenchyme. The transcription factor Foxd1, a specific marker of renal stromal cells, is critical for normal kidney development. The prorenin receptor (PRR), a receptor for renin and prorenin, is also an accessory subunit of the vacuolar proton pump V-ATPase. Global loss of PRR is embryonically lethal in mice, indicating an essential role of the PRR in embryonic development. Here, we report that conditional deletion of the PRR in Foxd1+ stromal progenitors in mice (cKO) results in neonatal mortality. The kidneys of surviving mice show reduced expression of stromal markers Foxd1 and Meis1 and a marked decrease in arterial and arteriolar development with the subsequent decreased number of glomeruli, expansion of Six2+ nephron progenitors, and delay in nephron differentiation. Intrarenal arteries and arterioles in cKO mice were fewer and thinner and showed a marked decrease in the expression of renin, suggesting a central role for the PRR in the development of renin-expressing cells, which in turn are essential for the proper formation of the renal arterial tree. We conclude that stromal PRR is crucial for the appropriate differentiation of the renal arterial tree, which in turn may restrict excessive expansion of nephron progenitors to promote a coordinated and proper morphogenesis of the nephrovascular structures of the mammalian kidney.
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Affiliation(s)
- Ihor V Yosypiv
- Department of Pediatrics, Tulane University School of Medicine , New Orleans, Louisiana
| | | | - Renfang Song
- Department of Pediatrics, Tulane University School of Medicine , New Orleans, Louisiana
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27
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Bhattacharyya S, Sathe AA, Bhakta M, Xing C, Munshi NV. PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues. PLoS One 2019; 14:e0214677. [PMID: 30939177 PMCID: PMC6445515 DOI: 10.1371/journal.pone.0214677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Recent studies have highlighted the extraordinary cell type diversity that exists within mammalian organs, yet the molecular drivers of such heterogeneity remain elusive. To address this issue, much attention has been focused on profiling the transcriptome and epigenome of individual cell types. However, standard cell type isolation methods based on surface or fluorescent markers remain problematic for cells residing within organs with significant connective tissue. Since the nucleus contains both genomic and transcriptomic information, the isolation of nuclei tagged in specific cell types (INTACT) method provides an attractive solution. Although INTACT has been successfully applied to plants, flies, zebrafish, frogs, and mouse brain and adipose tissue, broad use across mammalian organs remains challenging. Here we describe the PAN-INTACT method, which can be used to isolate cell type specific nuclei from fibrous mouse organs, which are particularly problematic. As a proof-of-concept, we demonstrate successful isolation of cell type-specific nuclei from the mouse heart, which contains substantial connective tissue and harbors multiple cell types, including cardiomyocytes, fibroblasts, endothelial cells, and epicardial cells. Compared to established techniques, PAN-INTACT allows more rapid isolation of cardiac nuclei to facilitate downstream applications. We show cell type-specific isolation of nuclei from the hearts of Nkx2-5Cre/+; R26Sun1-2xsf-GFP-6xmyc/+ mice, which we confirm by expression of lineage markers. Furthermore, we perform Assay for Transposase Accessible Chromatin (ATAC)-Seq to provide high-fidelity chromatin accessibility maps of Nkx2-5+ nuclei. To extend the applicability of PAN-INTACT, we also demonstrate successful isolation of Wt1+ podocytes from adult kidney. Taken together, our data suggest that PAN-INTACT is broadly applicable for profiling the transcriptional and epigenetic landscape of specific cell types. Thus, we envision that our method can be used to systematically probe mechanistic details of cell type-specific functions within individual organs of intact mice.
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Affiliation(s)
- Samadrita Bhattacharyya
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adwait A. Sathe
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, Texas, United States of America
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, Dallas, Texas, United States of America
- * E-mail:
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28
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Tubuloids derived from human adult kidney and urine for personalized disease modeling. Nat Biotechnol 2019; 37:303-313. [PMID: 30833775 DOI: 10.1038/s41587-019-0048-8] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/23/2019] [Indexed: 01/10/2023]
Abstract
Adult stem cell-derived organoids are three-dimensional epithelial structures that recapitulate fundamental aspects of their organ of origin. We describe conditions for the long-term growth of primary kidney tubular epithelial organoids, or 'tubuloids'. The cultures are established from human and mouse kidney tissue and can be expanded for at least 20 passages (>6 months) while retaining a normal number of chromosomes. In addition, cultures can be established from human urine. Human tubuloids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. We apply tubuloids to model infectious, malignant and hereditary kidney diseases in a personalized fashion. BK virus infection of tubuloids recapitulates in vivo phenomena. Tubuloids are established from Wilms tumors. Kidney tubuloids derived from the urine of a subject with cystic fibrosis allow ex vivo assessment of treatment efficacy. Finally, tubuloids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active (trans-)epithelial transport function.
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29
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Sieber KB, Batorsky A, Siebenthall K, Hudkins KL, Vierstra JD, Sullivan S, Sur A, McNulty M, Sandstrom R, Reynolds A, Bates D, Diegel M, Dunn D, Nelson J, Buckley M, Kaul R, Sampson MG, Himmelfarb J, Alpers CE, Waterworth D, Akilesh S. Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci. J Am Soc Nephrol 2019; 30:421-441. [PMID: 30760496 PMCID: PMC6405142 DOI: 10.1681/asn.2018030309] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 12/26/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Linking genetic risk loci identified by genome-wide association studies (GWAS) to their causal genes remains a major challenge. Disease-associated genetic variants are concentrated in regions containing regulatory DNA elements, such as promoters and enhancers. Although researchers have previously published DNA maps of these regulatory regions for kidney tubule cells and glomerular endothelial cells, maps for podocytes and mesangial cells have not been available. METHODS We generated regulatory DNA maps (DNase-seq) and paired gene expression profiles (RNA-seq) from primary outgrowth cultures of human glomeruli that were composed mainly of podocytes and mesangial cells. We generated similar datasets from renal cortex cultures, to compare with those of the glomerular cultures. Because regulatory DNA elements can act on target genes across large genomic distances, we also generated a chromatin conformation map from freshly isolated human glomeruli. RESULTS We identified thousands of unique regulatory DNA elements, many located close to transcription factor genes, which the glomerular and cortex samples expressed at different levels. We found that genetic variants associated with kidney diseases (GWAS) and kidney expression quantitative trait loci were enriched in regulatory DNA regions. By combining GWAS, epigenomic, and chromatin conformation data, we functionally annotated 46 kidney disease genes. CONCLUSIONS We demonstrate a powerful approach to functionally connect kidney disease-/trait-associated loci to their target genes by leveraging unique regulatory DNA maps and integrated epigenomic and genetic analysis. This process can be applied to other kidney cell types and will enhance our understanding of genome regulation and its effects on gene expression in kidney disease.
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Affiliation(s)
| | - Anna Batorsky
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | | | | | - Jeff D Vierstra
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | | | - Aakash Sur
- Phase Genomics Inc., Seattle, Washington
- Department of Biomedical and Health Informatics, and
| | - Michelle McNulty
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | | | - Alex Reynolds
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Douglass Dunn
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Matthew G Sampson
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Seattle, Washington
| | - Charles E Alpers
- Department of Anatomic Pathology
- Kidney Research Institute, Seattle, Washington
| | | | - Shreeram Akilesh
- Department of Anatomic Pathology,
- Kidney Research Institute, Seattle, Washington
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30
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Munro DAD, Wineberg Y, Tarnick J, Vink CS, Li Z, Pridans C, Dzierzak E, Kalisky T, Hohenstein P, Davies JA. Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development. eLife 2019; 8:43271. [PMID: 30758286 PMCID: PMC6374076 DOI: 10.7554/elife.43271] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/29/2019] [Indexed: 12/17/2022] Open
Abstract
The origins and functions of kidney macrophages in the adult have been explored, but their roles during development remain largely unknown. Here we characterise macrophage arrival, localisation, heterogeneity, and functions during kidney organogenesis. Using genetic approaches to ablate macrophages, we identify a role for macrophages in nephron progenitor cell clearance as mouse kidney development begins. Throughout renal organogenesis, most kidney macrophages are perivascular and express F4/80 and CD206. These macrophages are enriched for mRNAs linked to developmental processes, such as blood vessel morphogenesis. Using antibody-mediated macrophage-depletion, we show macrophages support vascular anastomoses in cultured kidney explants. We also characterise a subpopulation of galectin-3+ (Gal3+) myeloid cells within the developing kidney. Our findings may stimulate research into macrophage-based therapies for renal developmental abnormalities and have implications for the generation of bioengineered kidney tissues. The kidneys clean our blood by filtering out waste products while ensuring that useful components, like nutrients, remain in the bloodstream. Blood enters the kidneys through a network of intricately arranged blood vessels, which associate closely with the ‘cleaning tubes’ that carry out filtration. Human kidneys start developing during the early phases of embryonic development. During this process, the newly forming blood vessels and cleaning tubes must grow in the right places for the adult kidney to work properly. Macrophages are cells of the immune system that clear away foreign, diseased, or damaged cells. They are also thought to encourage growth of the developing kidney, but how exactly they do this has remained unknown. Munro et al. therefore wanted to find out when macrophages first appeared in the embryonic kidney and how they might help control their development. Experiments using mice revealed that the first macrophages arrived in the kidney early during its development, alongside newly forming blood vessels. Further investigation using genetically modified mice that did not have macrophages revealed that these immune cells were needed at this stage to clear away misplaced kidney cells and help ‘set the scene’ for future development. At later stages, macrophages in the kidney interacted closely with growing blood vessels. As well as producing molecules linked with blood vessel formation, the macrophages wrapped around the vessels themselves, sometimes even eating cells lining the vessels and the blood cells carried within them. These observations suggested that macrophages actively shaped the network of blood vessels developing within the kidneys. Experiments removing macrophages from kidney tissue confirmed this: in normal kidneys, the blood vessels grew into a continuous network, but in kidneys lacking macrophages, far fewer connections formed between the vessels. This work sheds new light on how the complex structures in the adult kidney first arise and could be useful in future research. For example, adding macrophages to simplified, laboratory-grown ‘mini-kidneys’ could make them better models to study kidney growth, while patients suffering from kidney diseases might benefit from new drugs targeting macrophages.
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Affiliation(s)
- David AD Munro
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yishay Wineberg
- Department of Bioengineering, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Julia Tarnick
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Chris S Vink
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Zhuan Li
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Clare Pridans
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elaine Dzierzak
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tomer Kalisky
- Department of Bioengineering, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Peter Hohenstein
- Leiden University Medical Center, Leiden University, Leiden, The Netherlands.,The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
| | - Jamie A Davies
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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31
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Genetic variant rs17185536 regulates SIM1 gene expression in human brain hypothalamus. Proc Natl Acad Sci U S A 2019; 116:3347-3348. [PMID: 30755538 DOI: 10.1073/pnas.1821550116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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32
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Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics. Cell Stem Cell 2018; 23:869-881.e8. [PMID: 30449713 DOI: 10.1016/j.stem.2018.10.010] [Citation(s) in RCA: 337] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/09/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
Kidney organoids derived from human pluripotent stem cells have great utility for investigating organogenesis and disease mechanisms and, potentially, as a replacement tissue source, but how closely organoids derived from current protocols replicate adult human kidney is undefined. We compared two directed differentiation protocols by single-cell transcriptomics of 83,130 cells from 65 organoids with single-cell transcriptomes of fetal and adult kidney cells. Both protocols generate a diverse range of kidney cells with differing ratios, but organoid-derived cell types are immature, and 10%-20% of cells are non-renal. Reconstructing lineage relationships by pseudotemporal ordering identified ligands, receptors, and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its cognate receptor NTRK2 were expressed in the neuronal lineage during organoid differentiation. Inhibiting this pathway improved organoid formation by reducing neurons by 90% without affecting kidney differentiation, highlighting the power of single-cell technologies to characterize and improve organoid differentiation.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kohei Uchimura
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Erinn L Donnelly
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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33
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Recapitulating kidney development: Progress and challenges. Semin Cell Dev Biol 2018; 91:153-168. [PMID: 30184476 DOI: 10.1016/j.semcdb.2018.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022]
Abstract
Decades of research into the molecular and cellular regulation of kidney morphogenesis in rodent models, particularly the mouse, has provided both an atlas of the mammalian kidney and a roadmap for recreating kidney cell types with potential applications for the treatment of kidney disease. With advances in both our capacity to maintain nephron progenitors in culture, reprogram to kidney cell types and direct the differentiation of human pluripotent stem cells to kidney endpoints, renal regeneration via cellular therapy or tissue engineering may be possible. Human kidney models also have potential for disease modelling and drug screening. Such applications will rely upon the accuracy of the model at the cellular level and the capacity for stem-cell derived kidney tissue to recapitulate both normal and diseased kidney tissue. In this review, we will discuss the available cell sources, how well they model the human kidney and how far we are from application either as models or for tissue engineering.
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34
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Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen YC, Troyanskaya O, Spence JR, Kretzler M, Cebrián C. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development 2018; 145:145/16/dev164038. [PMID: 30166318 PMCID: PMC6124540 DOI: 10.1242/dev.164038] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/30/2018] [Indexed: 12/11/2022]
Abstract
The mammalian kidney develops through reciprocal interactions between the ureteric bud and the metanephric mesenchyme to give rise to the entire collecting system and the nephrons. Most of our knowledge of the developmental regulators driving this process arises from the study of gene expression and functional genetics in mice and other animal models. In order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell populations, and to study individual cell dynamics and lineage trajectories during development. Single-cell transcriptome analyses of 6414 cells from five individual specimens identified 11 initial clusters of specific renal cell types as defined by their gene expression profile. Further subclustering identifies progenitors, and mature and intermediate stages of differentiation for several renal lineages. Other lineages identified include mesangium, stroma, endothelial and immune cells. Novel markers for these cell types were revealed in the analysis, as were components of key signaling pathways driving renal development in animal models. Altogether, we provide a comprehensive and dynamic gene expression profile of the developing human kidney at the single-cell level. Summary: New markers for specific cell types in the developing human kidney are identified and computational approaches infer developmental trajectories and interrogate the complex network of signaling pathways and cellular transitions.
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Affiliation(s)
- Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Austin Kokoruda
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jian Zhou
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zidong Zhang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ 08544, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olga Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Flatiron Institute, Simons Foundation, New York, NY 10010, USA.,Department of Computer Science, Princeton University, Princeton, NJ
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA .,Department of Cell and Developmental Biology, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cristina Cebrián
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
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35
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Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018; 361:594-599. [PMID: 30093597 PMCID: PMC6104812 DOI: 10.1126/science.aat1699] [Citation(s) in RCA: 434] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.
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Affiliation(s)
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | | | | | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James N Armitage
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | | | - Menna Clatworthy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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36
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Geometry of Gene Expression Space of Wilms' Tumors From Human Patients. Neoplasia 2018; 20:871-881. [PMID: 30029183 PMCID: PMC6076422 DOI: 10.1016/j.neo.2018.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 02/05/2023] Open
Abstract
Wilms' tumor is a pediatric malignancy that is thought to originate from faulty kidney development during the embryonic stage. However, there is a large variation between tumors from different patients in both histology and gene expression that is not well characterized. Here we use a meta-analysis of published microarray datasets to show that Favorable Histology Wilms' Tumors (FHWT's) fill a triangle-shaped continuum in gene expression space of which the vertices represent three idealized “archetypes”. We show that these archetypes have predominantly renal blastemal, stromal, and epithelial characteristics and that they correlate well with the three major lineages of the developing embryonic kidney. Moreover, we show that advanced stage tumors shift towards the renal blastemal archetype. These results illustrate the potential of this methodology for characterizing the cellular composition of Wilms' tumors and for assessing disease progression.
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37
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Chang-Panesso M, Kadyrov FF, Machado FG, Kumar A, Humphreys BD. Meis1 is specifically upregulated in kidney myofibroblasts during aging and injury but is not required for kidney homeostasis or fibrotic response. Am J Physiol Renal Physiol 2018; 315:F275-F290. [PMID: 29592525 DOI: 10.1152/ajprenal.00030.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The homeobox transcription factor Meis1 is required for mammalian development, and its overexpression plays a role in tumorigenesis, especially leukemia. Meis1 is known to be expressed in kidney stroma, but its function in kidney is undefined. We hypothesized that Meis1 may regulate stromal cell proliferation in kidney development and disease and tested the hypothesis using cell lineage tracing and cell-specific Meis1 deletion in development, aging, and fibrotic disease. We observed strong expression of Meis1 in platelet-derived growth factor receptor-β-positive pericytes and perivascular fibroblasts, both in adult mouse kidney and to a lesser degree in human kidney. Either bilateral ischemia-reperfusion injury or aging itself led to strong upregulation of Meis1 protein and mRNA in kidney myofibroblasts, and genetic lineage analysis confirmed that Meis1-positive cells proliferate as they differentiate into myofibroblasts after injury. Conditional deletion of Meis1 in all kidney stroma with two separate tamoxifen-inducible Cre recombinase drivers had no phenotype with the exception of consistent induction of the tubular injury marker kidney injury molecule-1 (Kim-1) only in Meis1 mutants. Further examination of Kim-1 expression revealed linkage disequilibrium of Kim-1 and Meis1, such that Meis1 mutants carried the longer BALB/c Kim-1 allele. Unexpectedly, we report that this Kim-1 allele is expressed at baseline in wild-type BALB/c mice, without any associated abnormalities, including long-term fibrosis, as predicted from the literature. We conclude that Meis1 is specifically expressed in stroma and myofibroblasts of mouse and human kidney, that it is not required for kidney development, disease, or aging, and that BALB/c mice unexpectedly express Kim-1 protein at baseline without other kidney abnormality.
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Affiliation(s)
- Monica Chang-Panesso
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine , St. Louis, Missouri
| | - Farid F Kadyrov
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine , St. Louis, Missouri
| | - Flavia G Machado
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine , St. Louis, Missouri
| | - Ashish Kumar
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine , St. Louis, Missouri
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38
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Lindström NO, McMahon JA, Guo J, Tran T, Guo Q, Rutledge E, Parvez RK, Saribekyan G, Schuler RE, Liao C, Kim AD, Abdelhalim A, Ruffins SW, Thornton ME, Baskin L, Grubbs B, Kesselman C, McMahon AP. Conserved and Divergent Features of Human and Mouse Kidney Organogenesis. J Am Soc Nephrol 2018; 29:785-805. [PMID: 29449453 DOI: 10.1681/asn.2017080887] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/27/2017] [Indexed: 01/22/2023] Open
Abstract
Human kidney function is underpinned by approximately 1,000,000 nephrons, although the number varies substantially, and low nephron number is linked to disease. Human kidney development initiates around 4 weeks of gestation and ends around 34-37 weeks of gestation. Over this period, a reiterative inductive process establishes the nephron complement. Studies have provided insightful anatomic descriptions of human kidney development, but the limited histologic views are not readily accessible to a broad audience. In this first paper in a series providing comprehensive insight into human kidney formation, we examined human kidney development in 135 anonymously donated human kidney specimens. We documented kidney development at a macroscopic and cellular level through histologic analysis, RNA in situ hybridization, immunofluorescence studies, and transcriptional profiling, contrasting human development (4-23 weeks) with mouse development at selected stages (embryonic day 15.5 and postnatal day 2). The high-resolution histologic interactive atlas of human kidney organogenesis generated can be viewed at the GUDMAP database (www.gudmap.org) together with three-dimensional reconstructions of key components of the data herein. At the anatomic level, human and mouse kidney development differ in timing, scale, and global features such as lobe formation and progenitor niche organization. The data also highlight differences in molecular and cellular features, including the expression and cellular distribution of anchor gene markers used to identify key cell types in mouse kidney studies. These data will facilitate and inform in vitro efforts to generate human kidney structures and comparative functional analyses across mammalian species.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Elisabeth Rutledge
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Gohar Saribekyan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | | | - Christopher Liao
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Ahmed Abdelhalim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Seth W Ruffins
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Laurence Baskin
- Department of Urology and Pediatrics, University of California San Francisco, San Francisco, California
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering.,Epstein Department of Industrial and Systems Engineering and Information Sciences Institute, Viterbi School of Engineering and Department of Preventive Medicine, Keck School of Medicine, and
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine,
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39
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Cazorla-Vázquez S, Engel FB. Adhesion GPCRs in Kidney Development and Disease. Front Cell Dev Biol 2018; 6:9. [PMID: 29468160 PMCID: PMC5808184 DOI: 10.3389/fcell.2018.00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/23/2018] [Indexed: 12/25/2022] Open
Abstract
Chronic kidney disease (CKD) represents the fastest growing pathology worldwide with a prevalence of >10% in many countries. In addition, kidney cancer represents 5% of all new diagnosed cancers. As currently no effective therapies exist to restore kidney function after CKD- as well as cancer-induced renal damage, it is important to elucidate new regulators of kidney development and disease as new therapeutic targets. G protein-coupled receptors (GPCRs) represent the most successful class of pharmaceutical targets. In recent years adhesion GPCRs (aGPCRs), the second largest GPCR family, gained significant attention as they are present on almost all mammalian cells, are associated to a plethora of diseases and regulate important cellular processes. aGPCRs regulate for example cell polarity, mitotic spindle orientation, cell migration, and cell aggregation; all processes that play important roles in kidney development and/or disease. Moreover, polycystin-1, a major regulator of kidney development and disease, contains a GAIN domain, which is otherwise only found in aGPCRs. In this review, we assess the potential of aGPCRs as therapeutic targets for kidney disease. For this purpose we have summarized the available literature and analyzed data from the databases The Human Protein Atlas, EURExpress, Nephroseq, FireBrowse, cBioPortal for Cancer Genomics and the National Cancer Institute Genomic Data Commons data portal (NCIGDC). Our data indicate that most aGPCRs are expressed in different spatio-temporal patterns during kidney development and that altered aGPCR expression is associated with a variety of kidney diseases including CKD, diabetic nephropathy, lupus nephritis as well as renal cell carcinoma. We conclude that aGPCRs present a promising new class of therapeutic targets and/or might be useful as diagnostic markers in kidney disease.
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Affiliation(s)
- Salvador Cazorla-Vázquez
- Department of Nephropathology, Experimental Renal and Cardiovascular Research, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Felix B Engel
- Department of Nephropathology, Experimental Renal and Cardiovascular Research, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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40
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Troy/TNFRSF19 marks epithelial progenitor cells during mouse kidney development that continue to contribute to turnover in adult kidney. Proc Natl Acad Sci U S A 2017; 114:E11190-E11198. [PMID: 29237753 DOI: 10.1073/pnas.1714145115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
During kidney development, progressively committed progenitor cells give rise to the distinct segments of the nephron, the functional unit of the kidney. Similar segment-committed progenitor cells are thought to be involved in the homeostasis of adult kidney. However, markers for most segment-committed progenitor cells remain to be identified. Here, we evaluate Troy/TNFRSF19 as a segment-committed nephron progenitor cell marker. Troy is expressed in the ureteric bud during embryonic development. During postnatal nephrogenesis, Troy+ cells are present in the cortex and papilla and display an immature tubular phenotype. Tracing of Troy+ cells during nephrogenesis demonstrates that Troy+ cells clonally give rise to tubular structures that persist for up to 2 y after induction. Troy+ cells have a 40-fold higher capacity than Troy- cells to form organoids, which is considered a stem cell property in vitro. In the adult kidney, Troy+ cells are present in the papilla and these cells continue to contribute to collecting duct formation during homeostasis. The number of Troy-derived cells increases after folic acid-induced injury. Our data show that Troy marks a renal stem/progenitor cell population in the developing kidney that in adult kidney contributes to homeostasis, predominantly of the collecting duct, and regeneration.
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41
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Magella B, Adam M, Potter AS, Venkatasubramanian M, Chetal K, Hay SB, Salomonis N, Potter SS. Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. Dev Biol 2017; 434:36-47. [PMID: 29183737 DOI: 10.1016/j.ydbio.2017.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022]
Abstract
The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages.
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Affiliation(s)
- Bliss Magella
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Mike Adam
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Andrew S Potter
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Kashish Chetal
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Stuart B Hay
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Nathan Salomonis
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA.
| | - S Steven Potter
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA.
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42
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Munro DAD, Hohenstein P, Coate TM, Davies JA. Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney. Dev Dyn 2017; 246:1047-1056. [PMID: 28929539 DOI: 10.1002/dvdy.24592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 09/16/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND During murine kidney development, new cortical blood vessels form and pattern in cycles that coincide with cycles of collecting duct branching and the accompanying splitting of the cap mesenchyme (nephron progenitor cell populations that "cap" collecting duct ends). At no point in the patterning cycle do blood vessels enter the cap mesenchyme. We hypothesized that the exclusion of blood vessels from the cap mesenchyme may be controlled, at least in part, by an anti-angiogenic signal expressed by the cap mesenchyme cells. RESULTS We show that semaphorin-3f (Sema3f), a known anti-angiogenic factor, is expressed in cap mesenchymal cells and its receptor, neuropilin-2 (Nrp2), is expressed by newly forming blood vessels in the cortex of the developing kidney. We hypothesized that Sema3f/Nrp2 signaling excludes vessels from the cap mesenchyme. Genetic ablation of Sema3f and of Nrp2, however, failed to result in vessels invading the cap mesenchyme. CONCLUSIONS Despite complementary expression patterns, our data suggest that Sema3f and Nrp2 are dispensable for the exclusion of vessels from the cap mesenchyme during kidney development. These results should provoke additional experiments to ascertain the biological significance of Sema3f/Nrp2 expression in the developing kidney. Developmental Dynamics 246:1047-1056, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- David A D Munro
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Hohenstein
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas M Coate
- Georgetown University, Department of Biology, Washington, DC
| | - Jamie A Davies
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
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43
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Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ. A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat Genet 2017; 49:1487-1494. [PMID: 28825729 PMCID: PMC5712232 DOI: 10.1038/ng.3940] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
Genome-wide sequencing, mRNA and miRNA expression, DNA copy number and methylation analyses were performed on 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, FAM123B, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), mutations were identified in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A. DNA copy number changes resulted in recurrent 1q gain, MYCN amplification, LIN28B gain, and let-7a loss. Unexpected germline variants involved PALB2 and CHEK2. Integrated analyses support two major classes of genetic changes that preserve the progenitor state and/or interrupt normal development.
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Affiliation(s)
- Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy L Walz
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ariadne H A G Ooms
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA.,Department of Pathology, Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Amy E Armstrong
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Tanja Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey S Dome
- Division of Pediatric Hematology/Oncology, Children's National Medical Center, Washington DC, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Stefan T Arold
- Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA
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44
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Devuyst O, Olinger E, Rampoldi L. Uromodulin: from physiology to rare and complex kidney disorders. Nat Rev Nephrol 2017; 13:525-544. [PMID: 28781372 DOI: 10.1038/nrneph.2017.101] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Uromodulin (also known as Tamm-Horsfall protein) is exclusively produced in the kidney and is the most abundant protein in normal urine. The function of uromodulin remains elusive, but the available data suggest that this protein might regulate salt transport, protect against urinary tract infection and kidney stones, and have roles in kidney injury and innate immunity. Interest in uromodulin was boosted by genetic studies that reported involvement of the UMOD gene, which encodes uromodulin, in a spectrum of rare and common kidney diseases. Rare mutations in UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD), which leads to chronic kidney disease (CKD). Moreover, genome-wide association studies have identified common variants in UMOD that are strongly associated with risk of CKD and also with hypertension and kidney stones in the general population. These findings have opened up a new field of kidney research. In this Review we summarize biochemical, physiological, genetic and pathological insights into the roles of uromodulin; the mechanisms by which UMOD mutations cause ADTKD, and the association of common UMOD variants with complex disorders.
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Affiliation(s)
- Olivier Devuyst
- Institute of Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Eric Olinger
- Institute of Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Luca Rampoldi
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
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45
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Martin KR, Zhou W, Bowman MJ, Shih J, Au KS, Dittenhafer-Reed KE, Sisson KA, Koeman J, Weisenberger DJ, Cottingham SL, DeRoos ST, Devinsky O, Winn ME, Cherniack AD, Shen H, Northrup H, Krueger DA, MacKeigan JP. The genomic landscape of tuberous sclerosis complex. Nat Commun 2017. [PMID: 28643795 PMCID: PMC5481739 DOI: 10.1038/ncomms15816] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a rare genetic disease causing multisystem growth of benign tumours and other hamartomatous lesions, which leads to diverse and debilitating clinical symptoms. Patients are born with TSC1 or TSC2 mutations, and somatic inactivation of wild-type alleles drives MTOR activation; however, second hits to TSC1/TSC2 are not always observed. Here, we present the genomic landscape of TSC hamartomas. We determine that TSC lesions contain a low somatic mutational burden relative to carcinomas, a subset feature large-scale chromosomal aberrations, and highly conserved molecular signatures for each type exist. Analysis of the molecular signatures coupled with computational approaches reveals unique aspects of cellular heterogeneity and cell origin. Using immune data sets, we identify significant neuroinflammation in TSC-associated brain tumours. Taken together, this molecular catalogue of TSC serves as a resource into the origin of these hamartomas and provides a framework that unifies genomic and transcriptomic dimensions for complex tumours.
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Affiliation(s)
- Katie R Martin
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Megan J Bowman
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Kit Sing Au
- Department of Pediatrics, University of Texas Health Science Center at Houston-McGovern Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | - Kristin E Dittenhafer-Reed
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Kellie A Sisson
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Julie Koeman
- Cytogenetics and Pathology Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Daniel J Weisenberger
- Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, California 90033, USA
| | - Sandra L Cottingham
- Department of Pathology, Spectrum Health System, 100 Michigan Street NE, Grand Rapids, Michigan 49503, USA
| | - Steven T DeRoos
- Division of Pediatric Neurology, Helen DeVos Children's Hospital, Spectrum Health System, 100 Michigan Street NE, Grand Rapids, Michigan 49503, USA
| | - Orrin Devinsky
- Department of Neurology, New York University School of Medicine, 223 E 34 Street, New York, New York 10016, USA
| | - Mary E Winn
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Hope Northrup
- Department of Pediatrics, University of Texas Health Science Center at Houston-McGovern Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | - Darcy A Krueger
- Division of Neurology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
| | - Jeffrey P MacKeigan
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA.,College of Human Medicine, Michigan State University, 220 Trowbridge Road, East Lansing, Michigan 48824, USA
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46
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McClelland KS, Yao HHC. Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case. Sex Dev 2017; 11:1-20. [PMID: 28196369 PMCID: PMC6171109 DOI: 10.1159/000455113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2016] [Indexed: 01/03/2023] Open
Abstract
With each new microarray or RNA-seq experiment, massive quantities of transcriptomic information are generated with the purpose to produce a list of candidate genes for functional analyses. Yet an effective strategy remains elusive to prioritize the genes on these candidate lists. In this review, we outline a prioritizing strategy by taking a step back from the bench and leveraging the rich range of public databases. This in silico approach provides an economical, less biased, and more effective solution. We discuss the publicly available online resources that can be used to answer a range of questions about a gene. Is the gene of interest expressed in the system of interest (using expression databases)? Where else is this gene expressed (using added-value transcriptomic resources)? What pathways and processes is the gene involved in (using enriched gene pathway analysis and mouse knockout databases)? Is this gene correlated with human diseases (using human disease variant databases)? Using mouse fetal testis as an example, our strategies identified 298 genes annotated as expressed in the fetal testis. We cross-referenced these genes to existing microarray data and narrowed the list down to cell-type-specific candidates (35 for Sertoli cells, 11 for Leydig cells, and 25 for germ cells). Our strategies can be customized so that they allow researchers to effectively and confidently prioritize genes for functional analysis.
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Affiliation(s)
- Kathryn S McClelland
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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47
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Song R, Janssen A, Li Y, El-Dahr S, Yosypiv IV. Prorenin receptor controls renal branching morphogenesis via Wnt/β-catenin signaling. Am J Physiol Renal Physiol 2016; 312:F407-F417. [PMID: 28031172 DOI: 10.1152/ajprenal.00563.2016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 11/22/2022] Open
Abstract
The prorenin receptor (PRR) is a receptor for renin and prorenin, and an accessory subunit of the vacuolar proton pump H+-ATPase. Renal branching morphogenesis, defined as growth and branching of the ureteric bud (UB), is essential for mammalian kidney development. Previously, we demonstrated that conditional ablation of the PRR in the UB in PRRUB-/- mice causes severe defects in UB branching, resulting in marked kidney hypoplasia at birth. Here, we investigated the UB transcriptome using whole genome-based analysis of gene expression in UB cells, FACS-isolated from PRRUB-/-, and control kidneys at birth (P0) to determine the primary role of the PRR in terminal differentiation and growth of UB-derived collecting ducts. Three genes with expression in UB cells that previously shown to regulate UB branching morphogenesis, including Wnt9b, β-catenin, and Fgfr2, were upregulated, whereas the expression of Wnt11, Bmp7, Etv4, and Gfrα1 was downregulated. We next demonstrated that infection of immortalized UB cells with shPRR in vitro or deletion of the UB PRR in double-transgenic PRRUB-/-/BatGal+ mice, a reporter strain for β-catenin transcriptional activity, in vivo increases β-catenin activity in the UB epithelia. In addition to UB morphogenetic genes, the functional groups of differentially expressed genes within the downregulated gene set included genes involved in molecular transport, metabolic disease, amino acid metabolism, and energy production. Together, these data demonstrate that UB PRR performs essential functions during UB branching and collecting duct morphogenesis via control of a hierarchy of genes that control UB branching and terminal differentiation of the collecting duct cells.
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Affiliation(s)
- Renfang Song
- Division of Pediatric Nephrology, Department of Pediatrics, Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Lousiana
| | - Adam Janssen
- Division of Pediatric Nephrology, Department of Pediatrics, Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Lousiana
| | - Yuwen Li
- Division of Pediatric Nephrology, Department of Pediatrics, Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Lousiana
| | - Samir El-Dahr
- Division of Pediatric Nephrology, Department of Pediatrics, Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Lousiana
| | - Ihor V Yosypiv
- Division of Pediatric Nephrology, Department of Pediatrics, Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Lousiana
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48
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Short KM, Smyth IM. The contribution of branching morphogenesis to kidney development and disease. Nat Rev Nephrol 2016; 12:754-767. [DOI: 10.1038/nrneph.2016.157] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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49
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Abstract
Over a decade ago, it was proposed that the regulation of tubular repair in the kidney might involve the recapitulation of developmental pathways. Although the kidney cannot generate new nephrons after birth, suggesting a low level of regenerative competence, the tubular epithelial cells of the nephrons can proliferate to repair the damage after AKI. However, the debate continues over whether this repair involves a persistent progenitor population or any mature epithelial cell remaining after injury. Recent reports have highlighted the expression of Sox9, a transcription factor critical for normal kidney development, during postnatal epithelial repair in the kidney. Indeed, the proliferative response of the epithelium involves expression of several pathways previously described as being involved in kidney development. In some instances, these pathways are also apparently involved in the maladaptive responses observed after repeated injury. Whether development and repair in the kidney are the same processes or we are misinterpreting the similar expression of genes under different circumstances remains unknown. Here, we review the evidence for this link, concluding that such parallels in expression may more correctly represent the use of the same pathways in a distinct context, likely triggered by similar stressors.
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Affiliation(s)
- Melissa Helen Little
- Murdoch Children's Research Institute, Melbourne, Australia; and .,Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Pamela Kairath
- Murdoch Children's Research Institute, Melbourne, Australia; and.,Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
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50
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Little MH, Kairath P. Regenerative medicine in kidney disease. Kidney Int 2016; 90:289-299. [DOI: 10.1016/j.kint.2016.03.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022]
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