1
|
Castillo-Mancho V, Atienza-Manuel A, Sarmiento-Jiménez J, Ruiz-Gómez M, Culi J. Phospholipid scramblase 1: an essential component of the nephrocyte slit diaphragm. Cell Mol Life Sci 2024; 81:261. [PMID: 38878170 DOI: 10.1007/s00018-024-05287-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/03/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024]
Abstract
Blood ultrafiltration in nephrons critically depends on specialized intercellular junctions between podocytes, named slit diaphragms (SDs). Here, by studying a homologous structure found in Drosophila nephrocytes, we identify the phospholipid scramblase Scramb1 as an essential component of the SD, uncovering a novel link between membrane dynamics and SD formation. In scramb1 mutants, SDs fail to form. Instead, the SD components Sticks and stones/nephrin, Polychaetoid/ZO-1, and the Src-kinase Src64B/Fyn associate in cortical foci lacking the key SD protein Dumbfounded/NEPH1. Scramb1 interaction with Polychaetoid/ZO-1 and Flotillin2, the presence of essential putative palmitoylation sites and its capacity to oligomerize, suggest a function in promoting SD assembly within lipid raft microdomains. Furthermore, Scramb1 interactors as well as its functional sensitivity to temperature, suggest an active involvement in membrane remodeling processes during SD assembly. Remarkably, putative Ca2+-binding sites in Scramb1 are essential for its activity raising the possibility that Ca2+ signaling may control the assembly of SDs by impacting on Scramb1 activity.
Collapse
Affiliation(s)
- Vicente Castillo-Mancho
- Centro de Biología Molecular Severo Ochoa, CSIC and UAM, Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Alexandra Atienza-Manuel
- Centro de Biología Molecular Severo Ochoa, CSIC and UAM, Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Jorge Sarmiento-Jiménez
- Centro de Biología Molecular Severo Ochoa, CSIC and UAM, Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Mar Ruiz-Gómez
- Centro de Biología Molecular Severo Ochoa, CSIC and UAM, Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain.
| | - Joaquim Culi
- Centro de Biología Molecular Severo Ochoa, CSIC and UAM, Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain.
| |
Collapse
|
2
|
Unger Avila P, Padvitski T, Leote AC, Chen H, Saez-Rodriguez J, Kann M, Beyer A. Gene regulatory networks in disease and ageing. Nat Rev Nephrol 2024:10.1038/s41581-024-00849-7. [PMID: 38867109 DOI: 10.1038/s41581-024-00849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/14/2024]
Abstract
The precise control of gene expression is required for the maintenance of cellular homeostasis and proper cellular function, and the declining control of gene expression with age is considered a major contributor to age-associated changes in cellular physiology and disease. The coordination of gene expression can be represented through models of the molecular interactions that govern gene expression levels, so-called gene regulatory networks. Gene regulatory networks can represent interactions that occur through signal transduction, those that involve regulatory transcription factors, or statistical models of gene-gene relationships based on the premise that certain sets of genes tend to be coexpressed across a range of conditions and cell types. Advances in experimental and computational technologies have enabled the inference of these networks on an unprecedented scale and at unprecedented precision. Here, we delineate different types of gene regulatory networks and their cell-biological interpretation. We describe methods for inferring such networks from large-scale, multi-omics datasets and present applications that have aided our understanding of cellular ageing and disease mechanisms.
Collapse
Affiliation(s)
- Paula Unger Avila
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tsimafei Padvitski
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ana Carolina Leote
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - He Chen
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Martin Kann
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
| |
Collapse
|
3
|
Chen J, Wang X, He Q, Yang HC, Fogo AB, Harris RC. Inhibition of transcriptional coactivator YAP Impairs the expression and function of transcription factor WT1 in diabetic podocyte injury. Kidney Int 2024; 105:1200-1211. [PMID: 38423183 DOI: 10.1016/j.kint.2024.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Podocyte injury and loss are hallmarks of diabetic nephropathy (DN). However, the molecular mechanisms underlying these phenomena remain poorly understood. YAP (Yes-associated protein) is an important transcriptional coactivator that binds with various other transcription factors, including the TEAD family members (nuclear effectors of the Hippo pathway), that regulate cell proliferation, differentiation, and apoptosis. The present study found an increase in YAP phosphorylation at S127 of YAP and a reduction of nuclear YAP localization in podocytes of diabetic mouse and human kidneys, suggesting dysregulation of YAP may play a role in diabetic podocyte injury. Tamoxifen-inducible podocyte-specific Yap gene knockout mice (YappodKO) exhibited accelerated and worsened diabetic kidney injury. YAP inactivation decreased transcription factor WT1 expression with subsequent reduction of Tead1 and other well-known targets of WT1 in diabetic podocytes. Thus, our study not only sheds light on the pathophysiological roles of the Hippo pathway in diabetic podocyte injury but may also lead to the development of new therapeutic strategies to prevent and/or treat DN by targeting the Hippo signaling pathway.
Collapse
Affiliation(s)
- Jianchun Chen
- Department of Veterans Affairs, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease, Nashville, Tennessee, USA.
| | - Xiaoyong Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Qian He
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Hai-Chun Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Agnes B Fogo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Raymond C Harris
- Department of Veterans Affairs, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
4
|
Torban E, Goodyer P. Wilms' tumor gene 1: lessons from the interface between kidney development and cancer. Am J Physiol Renal Physiol 2024; 326:F3-F19. [PMID: 37916284 DOI: 10.1152/ajprenal.00248.2023] [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: 08/17/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
In 1990, mutations of the Wilms' tumor-1 gene (WT1), encoding a transcription factor in the embryonic kidney, were found in 10-15% of Wilms' tumors; germline WT1 mutations were associated with hereditary syndromes involving glomerular and reproductive tract dysplasia. For more than three decades, these discoveries prompted investigators to explore the embryonic role of WT1 and the mechanisms by which loss of WT1 leads to malignant transformation. Here, we discuss how alternative splicing of WT1 generates isoforms that act in a context-specific manner to activate or repress target gene transcription. WT1 also regulates posttranscriptional regulation, alters the epigenetic landscape, and activates miRNA expression. WT1 functions at multiple stages of kidney development, including the transition from resting stem cells to committed nephron progenitor, which it primes to respond to WNT9b signals from the ureteric bud. WT1 then drives nephrogenesis by activating WNT4 expression and directing the development of glomerular podocytes. We review the WT1 mutations that account for Denys-Drash syndrome, Frasier syndrome, and WAGR syndrome. Although the WT1 story began with Wilms' tumors, an understanding of the pathways that link aberrant kidney development to malignant transformation still has some important gaps. Loss of WT1 in nephrogenic rests may leave these premalignant clones with inadequate DNA repair enzymes and may disturb the epigenetic landscape. Yet none of these observations provide a complete picture of Wilms' tumor pathogenesis. It appears that the WT1 odyssey is unfinished and still holds a great deal of untilled ground to be explored.
Collapse
Affiliation(s)
- Elena Torban
- Department of Medicine, McGill University and Research Institute of McGill University Health Center, Montreal, Quebec, Canada
| | - Paul Goodyer
- Department of Human Genetics, Montreal Children's Hospital and McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Montreal Children's Hospital and McGill University, Montreal, Quebec, Canada
| |
Collapse
|
5
|
Ester L, Cabrita I, Ventzke M, Kieckhöfer E, Christodoulou M, Mandel AM, Diefenhardt P, Fabretti F, Benzing T, Habbig S, Schermer B. The role of the FSGS disease gene product and nuclear pore protein NUP205 in regulating nuclear localization and activity of transcriptional regulators YAP and TAZ. Hum Mol Genet 2023; 32:3153-3165. [PMID: 37565816 PMCID: PMC10630254 DOI: 10.1093/hmg/ddad135] [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: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
Mutations in genes encoding nuclear pore proteins (NUPs) lead to the development of steroid-resistant nephrotic syndrome and focal segmental glomerulosclerosis (FSGS). However, the precise molecular mechanisms by which NUP dysfunction contributes to podocyte injury preceding FSGS remain unclear. The tightly regulated activity of Yes-associated protein (YAP) and WW-domain-containing transcription regulator 1 (TAZ), the transcriptional effectors of the Hippo pathway, is crucial for podocytes and the maintenance of the glomerular filter. In this study, we investigate the impact of NUPs on the regulation of YAP/TAZ nuclear import and activity in podocytes. In unbiased interactome studies using quantitative label-free mass spectrometry, we identify the FSGS disease gene products NUP107, NUP133, NUP205, and Exportin-5 (XPO5) as components of YAP and TAZ protein complexes in podocytes. Moreover, we demonstrate that NUP205 is essential for YAP/TAZ nuclear import. Consistently, both the nuclear interaction of YAP/TAZ with TEA domain transcription factor 1 and their transcriptional activity were dependent on NUP205 expression. Additionally, we elucidate a regulatory feedback mechanism whereby YAP activity is modulated in response to TAZ-mediated NUP205 expression. In conclusion, this study establishes a connection between the FSGS disease protein NUP205 and the activity of the transcriptional regulators and Hippo effectors YAP and TAZ and it proposes a potential pathological role of YAP/TAZ dysregulation in podocytes of patients with pathogenic NUP205 variants.
Collapse
Affiliation(s)
- Lioba Ester
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Inês Cabrita
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Michel Ventzke
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Emilia Kieckhöfer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Marita Christodoulou
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Paul Diefenhardt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Sandra Habbig
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| |
Collapse
|
6
|
Tatsumoto N, Saito S, Rifkin IR, Bonegio RG, Leal DN, Sen GC, Arditi M, Yamashita M. EGF-Receptor-Dependent TLR7 Signaling in Macrophages Promotes Glomerular Injury in Crescentic Glomerulonephritis. J Transl Med 2023; 103:100190. [PMID: 37268107 PMCID: PMC10527264 DOI: 10.1016/j.labinv.2023.100190] [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: 12/20/2022] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
Glomerulonephritis (GN) is a group of inflammatory diseases and an important cause of morbidity and mortality worldwide. The initiation of the inflammatory process is quite different for each type of GN; however, each GN is characterized commonly and variably by acute inflammation with neutrophils and macrophages and crescent formation, leading to glomerular death. Toll-like receptor (TLR) 7 is a sensor for self-RNA and implicated in the pathogenesis of human and murine GN. Here, we show that TLR7 exacerbates glomerular injury in nephrotoxic serum nephritis (NTN), a murine model of severe crescentic GN. TLR7-/- mice were resistant to NTN, although TLR7-/- mice manifested comparable immune-complex deposition to wild-type mice without significant defects in humoral immunity, suggesting that endogenous TLR7 ligands accelerate glomerular injury. TLR7 was expressed exclusively in macrophages in glomeruli in GN but not in glomerular resident cells or neutrophils. Furthermore, we discovered that epidermal growth factor receptor (EGFR), a receptor-type tyrosine kinase, is essential for TLR7 signaling in macrophages. Mechanistically, EGFR physically interacted with TLR7 upon TLR7 stimulation, and EGFR inhibitor completely blocked the phosphorylation of TLR7 tyrosine residue(s). EGFR inhibitor attenuated glomerular damage in wild-type mice, and no additional glomerular protective effects by EGFR inhibitor were observed in TLR7-/- mice. Finally, mice lacking EGFR in macrophages were resistant to NTN. This study clearly demonstrated that EGFR-dependent TLR7 signaling in macrophages is essential for glomerular injury in crescentic GN.
Collapse
Affiliation(s)
- Narihito Tatsumoto
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Suguru Saito
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ian R Rifkin
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts; Renal Section, Department of Medicine, VA Boston Healthcare System, Boston, Massachusetts
| | - Ramon G Bonegio
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts; Renal Section, Department of Medicine, VA Boston Healthcare System, Boston, Massachusetts
| | - Daniel N Leal
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ganes C Sen
- Department of Inflammation & Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Moshe Arditi
- Division of Infectious Diseases and Immunology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California; Infectious and Immunologic Diseases Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michifumi Yamashita
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| |
Collapse
|
7
|
Hagmann H, Khayyat NH, Oezel C, Papadakis A, Kuczkowski A, Benzing T, Gulbins E, Dryer S, Brinkkoetter PT. Paraoxonase 2 (PON2) Deficiency Reproduces Lipid Alterations of Diabetic and Inflammatory Glomerular Disease and Affects TRPC6 Signaling. Cells 2022; 11:cells11223625. [PMID: 36429053 PMCID: PMC9688324 DOI: 10.3390/cells11223625] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/31/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Diabetes and inflammatory diseases are associated with an altered cellular lipid composition due to lipid peroxidation. The pathogenic potential of these lipid alterations in glomerular kidney diseases remains largely obscure as suitable cell culture and animal models are lacking. In glomerular disease, a loss of terminally differentiated glomerular epithelial cells called podocytes refers to irreversible damage. Podocytes are characterized by a complex ramified cellular architecture and highly active transmembrane signaling. Alterations in lipid composition in states of disease have been described in podocytes but the pathophysiologic mechanisms mediating podocyte damage are unclear. In this study, we employ a genetic deletion of the anti-oxidative, lipid-modifying paraoxonase 2 enzyme (PON2) as a model to study altered cellular lipid composition and its effects on cellular signaling in glomerular disease. PON2 deficiency reproduces features of an altered lipid composition of glomerular disease, characterized by an increase in ceramides and cholesterol. PON2 knockout mice are more susceptible to glomerular damage in models of aggravated oxidative stress such as adriamycin-induced nephropathy. Voltage clamp experiments in cultured podocytes reveal a largely increased TRPC6 conductance after a membrane stretch in PON2 deficiency. Correspondingly, a concomitant knockout of TRPC6 and PON2 partially rescues the aggravated glomerular phenotype of a PON2 knockout in the adriamycin model. This study establishes PON2 deficiency as a model to investigate the pathophysiologic mechanisms of podocyte dysfunction related to alterations in the lipid composition, as seen in diabetic and inflammatory glomerular disease. Expanding the knowledge on these routes and options of intervention could lead to novel treatment strategies for glomerular disease.
Collapse
Affiliation(s)
- Henning Hagmann
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
- Correspondence:
| | | | - Cem Oezel
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
| | - Antonios Papadakis
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany
| | - Alexander Kuczkowski
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), 50931 Cologne, Germany
| | - Erich Gulbins
- Department of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Stuart Dryer
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
- Department of Biomedical Sciences, Tilman J. Fertitta Family College of Medicine, University of Houston, Houston, TX 77204, USA
| | - Paul T. Brinkkoetter
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
| |
Collapse
|
8
|
Schnell J, Achieng M, Lindström NO. Principles of human and mouse nephron development. Nat Rev Nephrol 2022; 18:628-642. [PMID: 35869368 DOI: 10.1038/s41581-022-00598-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 12/17/2022]
Abstract
The mechanisms underlying kidney development in mice and humans is an area of intense study. Insights into kidney organogenesis have the potential to guide our understanding of the origin of congenital anomalies and enable the assembly of genetic diagnostic tools. A number of studies have delineated signalling nodes that regulate positional identities and cell fates of nephron progenitor and precursor cells, whereas cross-species comparisons have markedly enhanced our understanding of conserved and divergent features of mammalian kidney organogenesis. Greater insights into the complex cellular movements that occur as the proximal-distal axis is established have challenged our understanding of nephron patterning and provided important clues to the elaborate developmental context in which human kidney diseases can arise. Studies of kidney development in vivo have also facilitated efforts to recapitulate nephrogenesis in kidney organoids in vitro, by providing a detailed blueprint of signalling events, cell movements and patterning mechanisms that are required for the formation of correctly patterned nephrons and maturation of physiologically functional apparatus that are responsible for maintaining human health.
Collapse
Affiliation(s)
- Jack Schnell
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA
| | - MaryAnne Achieng
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA
| | - Nils Olof Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
9
|
Hutzfeldt AD, Tan Y, Bonin LL, Beck BB, Baumbach J, Lassé M, Demir F, Rinschen MM. Consensus draft of the native mouse podocyte-ome. Am J Physiol Renal Physiol 2022; 323:F182-F197. [PMID: 35796460 DOI: 10.1152/ajprenal.00058.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The podocyte is a key cell in maintaining renal filtration barrier integrity. Several recent studies have analyzed the entity of genome-coded molecules in the podocyte at deep resolution. This avenue of "podocyte-ome" research was enabled by a variety of techniques, including single-cell transcriptomics, FACS-sorting with and without genetically encoded markers, and deep acquisition of proteomics. However, data across various omics studies are not well-integrated with each other. Here, we aim to establish a common, simplified knowledgebase for the mouse "podocyte-ome" by integrating bulk RNA sequencing and bulk proteomics of sorted podocytes and single cell transcriptomics. Three datasets of each omics type from different laboratories, respectively, were integrated, visualized and bioinformatically analyzed. The procedure sheds light on conserved processes of podocytes, but also on limitations and specific features of the used technologies. High expression of glycan GPI anchor synthesis and turnover, and retinol metabolism was identified as a relatively understudied feature of podocytes, while there are both podocyte-enriched and podocyte-depleted actin binding molecules. We compiled aggregated data in an application that illustrates the features of the dataset and allows for exploratory analyses through individual gene query of podocyte identity in absolute and relative quantification towards other glomerular cell types, keywords, GO-terms and gene set enrichments. This consensus draft is a first step towards common molecular omics knowledge of kidney cells.
Collapse
Affiliation(s)
- Arvid D Hutzfeldt
- III Department of Medicine, grid.13648.38University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yifan Tan
- Department of Biomedicine, grid.7048.bAarhus University, Aarhus, Denmark
| | - Léna Lydie Bonin
- Department of Biomedicine, grid.7048.bAarhus University, Aarhus, Denmark
| | - Bodo B Beck
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, grid.6190.eUniversity of Cologne, Cologne, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, grid.9026.dUniversität Hamburg, Hamburg, Germany
| | - Moritz Lassé
- III Department of Medicine, grid.13648.38University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fatih Demir
- Department of Biomedicine, grid.7048.bAarhus University, Aarhus, Denmark
| | - Markus M Rinschen
- Department of Biomedicine, grid.7048.bAarhus University, Aarhus, Denmark
| |
Collapse
|
10
|
Tran T, Song CJ, Nguyen T, Cheng SY, McMahon JA, Yang R, Guo Q, Der B, Lindström NO, Lin DCH, McMahon AP. A scalable organoid model of human autosomal dominant polycystic kidney disease for disease mechanism and drug discovery. Cell Stem Cell 2022; 29:1083-1101.e7. [PMID: 35803227 PMCID: PMC11088748 DOI: 10.1016/j.stem.2022.06.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Human pluripotent stem-cell-derived organoids are models for human development and disease. We report a modified human kidney organoid system that generates thousands of similar organoids, each consisting of 1-2 nephron-like structures. Single-cell transcriptomic profiling and immunofluorescence validation highlighted patterned nephron-like structures utilizing similar pathways, with distinct morphogenesis, to human nephrogenesis. To examine this platform for therapeutic screening, the polycystic kidney disease genes PKD1 and PKD2 were inactivated by gene editing. PKD1 and PKD2 mutant models exhibited efficient and reproducible cyst formation. Cystic outgrowths could be propagated for months to centimeter-sized cysts. To shed new light on cystogenesis, 247 protein kinase inhibitors (PKIs) were screened in a live imaging assay identifying compounds blocking cyst formation but not overall organoid growth. Scaling and further development of the organoid platform will enable a broader capability for kidney disease modeling and high-throughput drug screens.
Collapse
Affiliation(s)
- Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Cheng Jack Song
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Amgen Research, Cardiometabolic Disorders, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Trang Nguyen
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Shun-Yang Cheng
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rui Yang
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Balint Der
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel C-H Lin
- Amgen Research, Cardiometabolic Disorders, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
11
|
Alquraishi M, Chahed S, Alani D, Puckett DL, Dowker PD, Hubbard K, Zhao Y, Kim JY, Nodit L, Fatima H, Donohoe D, Voy B, Chowanadisai W, Bettaieb A. Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin. Cell Commun Signal 2022; 20:76. [PMID: 35637461 PMCID: PMC9150347 DOI: 10.1186/s12964-022-00884-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is associated with a severe decline in kidney function caused by abnormalities within the podocytes' glomerular matrix. Recently, AKI has been linked to alterations in glycolysis and the activity of glycolytic enzymes, including pyruvate kinase M2 (PKM2). However, the contribution of this enzyme to AKI remains largely unexplored. METHODS Cre-loxP technology was used to examine the effects of PKM2 specific deletion in podocytes on the activation status of key signaling pathways involved in the pathophysiology of AKI by lipopolysaccharides (LPS). In addition, we used lentiviral shRNA to generate murine podocytes deficient in PKM2 and investigated the molecular mechanisms mediating PKM2 actions in vitro. RESULTS Specific PKM2 deletion in podocytes ameliorated LPS-induced protein excretion and alleviated LPS-induced alterations in blood urea nitrogen and serum albumin levels. In addition, PKM2 deletion in podocytes alleviated LPS-induced structural and morphological alterations to the tubules and to the brush borders. At the molecular level, PKM2 deficiency in podocytes suppressed LPS-induced inflammation and apoptosis. In vitro, PKM2 knockdown in murine podocytes diminished LPS-induced apoptosis. These effects were concomitant with a reduction in LPS-induced activation of β-catenin and the loss of Wilms' Tumor 1 (WT1) and nephrin. Notably, the overexpression of a constitutively active mutant of β-catenin abolished the protective effect of PKM2 knockdown. Conversely, PKM2 knockdown cells reconstituted with the phosphotyrosine binding-deficient PKM2 mutant (K433E) recapitulated the effect of PKM2 depletion on LPS-induced apoptosis, β-catenin activation, and reduction in WT1 expression. CONCLUSIONS Taken together, our data demonstrates that PKM2 plays a key role in podocyte injury and suggests that targetting PKM2 in podocytes could serve as a promising therapeutic strategy for AKI. TRIAL REGISTRATION Not applicable. Video abstract.
Collapse
Affiliation(s)
- Mohammed Alquraishi
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA.,Department of Community Health Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Samah Chahed
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Dina Alani
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Dexter L Puckett
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Presley D Dowker
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Katelin Hubbard
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Yi Zhao
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA.,Kellogg Eye Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Ji Yeon Kim
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Laurentia Nodit
- Department of Pathology, University of Tennessee Medical Center, Knoxville, TN, 37920, USA
| | - Huma Fatima
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dallas Donohoe
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Brynn Voy
- Tennessee Agricultural Experiment Station, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996-0840, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Winyoo Chowanadisai
- Department of Nutrition, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Ahmed Bettaieb
- Department of Nutrition, The University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA. .,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996-0840, USA. .,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA.
| |
Collapse
|
12
|
Bezdicka M, Kaufman F, Krizova I, Dostalkova A, Rumlova M, Seeman T, Vondrak K, Fencl F, Zieg J, Soucek O. Alteration in DNA-binding affinity of Wilms tumor 1 protein due to WT1 genetic variants associated with steroid - resistant nephrotic syndrome in children. Sci Rep 2022; 12:8704. [PMID: 35610319 PMCID: PMC9130146 DOI: 10.1038/s41598-022-12760-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Approximately one third of children with steroid-resistant nephrotic syndrome (SRNS) carry pathogenic variants in one of the many associated genes. The WT1 gene coding for the WT1 transcription factor is among the most frequently affected genes. Cases from the Czech national SRNS database were sequenced for exons 8 and 9 of the WT1 gene. Eight distinct exonic WT1 variants in nine children were found. Three children presented with isolated SRNS, while the other six manifested with additional features. To analyze the impact of WT1 genetic variants, wild type and mutant WT1 proteins were prepared and the DNA-binding affinity of these proteins to the target EGR1 sequence was measured by microscale thermophoresis. Three WT1 mutants showed significantly decreased DNA-binding affinity (p.Arg439Pro, p.His450Arg and p.Arg463Ter), another three mutants showed significantly increased binding affinity (p.Gln447Pro, p.Asp469Asn and p.His474Arg), and the two remaining mutants (p.Cys433Tyr and p.Arg467Trp) showed no change of DNA-binding affinity. The protein products of WT1 pathogenic variants had variable DNA-binding affinity, and no clear correlation with the clinical symptoms of the patients. Further research is needed to clarify the mechanisms of action of the distinct WT1 mutants; this could potentially lead to individualized treatment of a so far unfavourable disease.
Collapse
Affiliation(s)
- Martin Bezdicka
- Vera Vavrova Lab/VIAL, Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague, Czech Republic.
| | - Filip Kaufman
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ivana Krizova
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Alzbeta Dostalkova
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Michaela Rumlova
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Karel Vondrak
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Filip Fencl
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jakub Zieg
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Ondrej Soucek
- Vera Vavrova Lab/VIAL, Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague, Czech Republic
| |
Collapse
|
13
|
Yang YW, Poudel B, Frederick J, Dhillon P, Shrestha R, Ma Z, Wu J, Okamoto K, Kopp JB, Booten SL, Gattis D, Watt AT, Palmer M, Aghajan M, Susztak K. Antisense oligonucleotides ameliorate kidney dysfunction in podocyte specific APOL1 risk variant mice. Mol Ther 2022; 30:2491-2504. [PMID: 35450819 DOI: 10.1016/j.ymthe.2022.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/23/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022] Open
Abstract
Coding variants (named G1 and G2) in Apolipoprotein L1 (APOL1) can explain the most excess risk of kidney disease observed in African Americans. It has been proposed that risk variant APOL1 dose, such as increased risk variant APOL1 level serves as a trigger (second hit) for disease development. The goal of this study was to determine whether lowering risk variant APOL1 levels protects from disease development in podocyte specific transgenic mouse disease model. We administered antisense oligonucleotides (ASO) targeting APOL1 to podocyte specific G2APOL1 mice and observed efficient reduction of APOL1 levels. APOL1 ASO1, which more efficiently lowered APOL1 transcript levels, protected mice from albuminuria, glomerulosclerosis, tubulointerstitial fibrosis, and renal failure. The administration of APOL1 ASO1 was effective even for established disease in the NEFTA-rtTA/TRE-G2APOL1 (NEFTA/G2APOL1) mice. We observed a strong correlation between APOL1 transcript level and disease severity. We concluded that an APOL1 ASO1 may be an effective therapeutic approach for APOL1-associated glomerular disease.
Collapse
Affiliation(s)
- Ya-Wen Yang
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA; Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Bibek Poudel
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia Frederick
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Poonam Dhillon
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rojesh Shrestha
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Junnan Wu
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Koji Okamoto
- Kidney Disease Section, NIDDK, NIH, Bethesda, MD, USA
| | | | | | | | | | - Matthew Palmer
- Department of Pathology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Katalin Susztak
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
14
|
NUP133 Controls Nuclear Pore Assembly, Transcriptome Composition, and Cytoskeleton Regulation in Podocytes. Cells 2022; 11:cells11081259. [PMID: 35455939 PMCID: PMC9025798 DOI: 10.3390/cells11081259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) frequently leads to end-stage renal disease, ultimately requiring kidney replacement therapies. SRNS is often caused by hereditary monogenic mutations, specifically affecting specialized epithelial cells (podocytes) of the glomerular filtration barrier. Mutations in several components of the nuclear pore complex, including NUP133 and NUP107, have been recently identified to cause hereditary SRNS. However, underlying pathomechanisms, eliciting podocyte-specific manifestations of these nucleoporopathies, remained largely elusive. Here, we generated an in vitro model of NUP133-linked nucleoporopathies using CRISPR/Cas9-mediated genome editing in human podocytes. Transcriptome, nuclear pore assembly, and cytoskeleton regulation of NUP133 loss-of-function, mutant, and wild-type podocytes were analyzed. Loss of NUP133 translated into a disruption of the nuclear pore, alterations of the podocyte-specific transcriptome, and impaired cellular protrusion generation. Surprisingly, comparative analysis of the described SRNS-related NUP133 mutations revealed only mild defects. Am impaired protein interaction in the Y-complex and decrease of NUP133 protein levels might be the primary and unifying consequence of mutant variants, leading to a partial loss-of-function phenotype and disease manifestation in susceptible cell types, such as podocytes.
Collapse
|
15
|
Koehler S, Odenthal J, Ludwig V, Jess DU, Höhne M, Jüngst C, Grawe F, Helmstädter M, Janku JL, Bergmann C, Hoyer PF, Hagmann HHH, Walz G, Bloch W, Niessen C, Schermer B, Wodarz A, Denholm B, Benzing T, Iden S, Brinkkoetter PT. Scaffold polarity proteins Par3A and Par3B share redundant functions while Par3B acts independent of atypical protein kinase C/Par6 in podocytes to maintain the kidney filtration barrier. Kidney Int 2021; 101:733-751. [PMID: 34929254 DOI: 10.1016/j.kint.2021.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
Glomerular diseases are a major cause for chronic kidney disorders. In most cases podocyte injury is causative for disease development. Cytoskeletal rearrangements and morphological changes are hallmark features of podocyte injury and result in dedifferentiation and loss of podocytes. Here, we establish a link between the Par3 polarity complex and actin regulators necessary to establish and maintain podocyte architecture by utilizing mouse and Drosophila models to characterize the functional role of Par3A and Par3B and its fly homologue Bazooka in vivo. Only simultaneous inactivation of both Par3 proteins caused a severe disease phenotype. Rescue experiments in Drosophila nephrocytes revealed atypical protein kinase C (aPKC)-Par6 dependent and independent effects. While Par3A primarily acts via aPKC-Par6, Par3B function was independent of Par6. Actin-associated synaptopodin protein levels were found to be significantly upregulated upon loss of Par3A/B in mouse podocytes. Tropomyosin2, which shares functional similarities with synaptopodin, was also elevated in Bazooka depleted nephrocytes. The simultaneous depletion of Bazooka and Tropomyosin2 resulted in a partial rescue of the Bazooka knockdown phenotype and prevented increased Rho1, a member of a GTPase protein family regulating the cytoskeleton. The latter contribute to the nephrocyte phenotype observed upon loss of Bazooka. Thus, we demonstrate that Par3 proteins share a high functional redundancy but also have specific functions. Par3A acts in an aPKC-Par6 dependent way and regulates RhoA-GTP levels, while Par3B exploits Par6 independent functions influencing synaptopodin localization. Hence, Par3A and Par3B link elements of polarity signaling and actin regulators to maintain podocyte architecture.
Collapse
Affiliation(s)
- Sybille Koehler
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Johanna Odenthal
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Vivian Ludwig
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - David Unnersjö Jess
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ferdi Grawe
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Molecular Cell Biology, Institute I for Anatomy, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Helmstädter
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Johanna L Janku
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany; Department of Medicine, Nephrology, University Hospital Freiburg, Germany
| | - Peter F Hoyer
- Klinik für Kinderheilkunde 2, Zentrum für Kinder- und Jugendmedizin, Universitätsklinikum Essen, Essen, Germany
| | - H H Henning Hagmann
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Gerd Walz
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Carien Niessen
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Department of Dermatology, University Hospital of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Andreas Wodarz
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Molecular Cell Biology, Institute I for Anatomy, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Barry Denholm
- Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Thomas Benzing
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sandra Iden
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute for Cell and Developmental Biology, Saarland University, Homburg/Saar, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| |
Collapse
|
16
|
Chung H, Komada T, Lau A, Chappellaz M, Platnich JM, de Koning HD, Petri B, Luque Y, Walker S, Benediktsson H, Mesnard L, Chun J, Muruve DA. AIM2 Suppresses Inflammation and Epithelial Cell Proliferation during Glomerulonephritis. THE JOURNAL OF IMMUNOLOGY 2021; 207:2799-2812. [PMID: 34740957 DOI: 10.4049/jimmunol.2100483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 11/19/2022]
Abstract
Absent in melanoma-2 (AIM2) is an inflammasome-forming innate immune sensor for dsDNA but also exhibits inflammasome-independent functions such as restricting cellular proliferation. AIM2 is expressed in the kidney, but its localization and function are not fully characterized. In normal human glomeruli, AIM2 localized to podocytes. In patients with glomerulonephritis, AIM2 expression increased in CD44+-activated parietal epithelial cells within glomerular crescents. To explore AIM2 effects in glomerular disease, studies in Aim2 -/- mice were performed. Aim2-/- glomeruli showed reduced expression of Wilm tumor gene-1 (WT1), WT1-driven podocyte genes, and increased proliferation in outgrowth assays. In a nephrotoxic serum (NTS)-induced glomerulonephritis model, Aim2-/- (B6) mice exhibited more severe glomerular crescent formation, tubular injury, inflammation, and proteinuria compared with wild-type controls. Inflammasome activation markers were absent in both Aim2 -/- and wild-type kidneys, despite an increased inflammatory transcriptomic signature in Aim2 -/- mice. Aim2 -/- mice also demonstrated dysregulated cellular proliferation and an increase in CD44+ parietal epithelial cells during glomerulonephritis. The augmented inflammation and epithelial cell proliferation in Aim2 -/- (B6) mice was not due to genetic background, as Aim2 -/- (B6.129) mice demonstrated a similar phenotype during NTS glomerulonephritis. The AIM2-like receptor (ALR) locus was necessary for the inflammatory glomerulonephritis phenotype observed in Aim2 -/- mice, as NTS-treated ALR -/- mice displayed equal levels of injury as wild-type controls. Podocyte outgrowth from ALR -/- glomeruli was still increased, however, confirming that the ALR locus is dispensable for AIM2 effects on epithelial cell proliferation. These results identify a noncanonical role for AIM2 in suppressing inflammation and epithelial cell proliferation during glomerulonephritis.
Collapse
Affiliation(s)
- Hyunjae Chung
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Takanori Komada
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Arthur Lau
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mona Chappellaz
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jaye M Platnich
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Heleen D de Koning
- Department of Dermatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Björn Petri
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Yosu Luque
- Soins Intensifs Néphrologiques et Rein Aigu (SINRA), Département de Néphrologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Inserm UMR_S1155, Sorbonne Université, Paris, France; and
| | - Simon Walker
- Department of Pathology and Laboratory Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Hallgrimur Benediktsson
- Department of Pathology and Laboratory Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu (SINRA), Département de Néphrologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Inserm UMR_S1155, Sorbonne Université, Paris, France; and
| | - Justin Chun
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Daniel A Muruve
- Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada;
| |
Collapse
|
17
|
Agarwal S, Sudhini YR, Polat OK, Reiser J, Altintas MM. Renal cell markers: lighthouses for managing renal diseases. Am J Physiol Renal Physiol 2021; 321:F715-F739. [PMID: 34632812 DOI: 10.1152/ajprenal.00182.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Kidneys, one of the vital organs in our body, are responsible for maintaining whole body homeostasis. The complexity of renal function (e.g., filtration, reabsorption, fluid and electrolyte regulation, and urine production) demands diversity not only at the level of cell types but also in their overall distribution and structural framework within the kidney. To gain an in depth molecular-level understanding of the renal system, it is imperative to discern the components of kidney and the types of cells residing in each of the subregions. Recent developments in labeling, tracing, and imaging techniques have enabled us to mark, monitor, and identify these cells in vivo with high efficiency in a minimally invasive manner. In this review, we summarize different cell types, specific markers that are uniquely associated with those cell types, and their distribution in the kidney, which altogether make kidneys so special and different. Cellular sorting based on the presence of certain proteins on the cell surface allowed for the assignment of multiple markers for each cell type. However, different studies using different techniques have found contradictions in cell type-specific markers. Thus, the term "cell marker" might be imprecise and suboptimal, leading to uncertainty when interpreting the data. Therefore, we strongly believe that there is an unmet need to define the best cell markers for a cell type. Although the compendium of renal-selective marker proteins presented in this review is a resource that may be useful to researchers, we acknowledge that the list may not be necessarily exhaustive.
Collapse
Affiliation(s)
- Shivangi Agarwal
- Department of Internal Medicine, Rush University, Chicago, Illinois
| | | | - Onur K Polat
- Department of Internal Medicine, Rush University, Chicago, Illinois
| | - Jochen Reiser
- Department of Internal Medicine, Rush University, Chicago, Illinois
| | | |
Collapse
|
18
|
Waehle V, Ungricht R, Hoppe PS, Betschinger J. The tumor suppressor WT1 drives progenitor cell progression and epithelialization to prevent Wilms tumorigenesis in human kidney organoids. Stem Cell Reports 2021; 16:2107-2117. [PMID: 34450039 PMCID: PMC8452534 DOI: 10.1016/j.stemcr.2021.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 12/04/2022] Open
Abstract
Wilms tumor is the most widespread kidney cancer in children and frequently associated with homozygous loss of the tumor suppressor WT1. Pediatric tumorigenesis is largely inaccessible in humans. Here, we develop a human kidney organoid model for Wilms tumor formation and show that deletion of WT1 during organoid development induces overgrowth of kidney progenitor cells at the expense of differentiating glomeruli and tubules. Functional and gene expression analyses demonstrate that absence of WT1 halts progenitor cell progression at a pre-epithelialized cell state and recapitulates the transcriptional changes detected in a subgroup of Wilms tumor patients with ectopic myogenesis. By "transplanting" WT1 mutant cells into wild-type kidney organoids, we find that their propagation requires an untransformed microenvironment. This work defines the role of WT1 in kidney progenitor cell progression and tumor suppression, and establishes human kidney organoids as a phenotypic model for pediatric tumorigenesis.
Collapse
Affiliation(s)
- Verena Waehle
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Rosemarie Ungricht
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Philipp S Hoppe
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| |
Collapse
|
19
|
Mysh M, Poulton JS. The Basolateral Polarity Module Promotes Slit Diaphragm Formation in Drosophila Nephrocytes, a Model of Vertebrate Podocytes. J Am Soc Nephrol 2021; 32:1409-1424. [PMID: 33795424 PMCID: PMC8259641 DOI: 10.1681/asn.2020071050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/12/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Podocyte slit diaphragms (SDs) are intercellular junctions that function as size-selective filters, excluding most proteins from urine. Abnormalities in SDs cause proteinuria and nephrotic syndrome. Podocytes exhibit apicobasal polarity, which can affect fundamental aspects of cell biology, including morphology, intercellular junction formation, and asymmetric protein distribution along the plasma membrane. Apical polarity protein mutations cause nephrotic syndrome, and data suggest apical polarity proteins regulate SD formation. However, there is no evidence that basolateral polarity proteins regulate SDs. Thus, the role of apicobasal polarity in podocytes remains unclear. METHODS Genetic manipulations and transgenic reporters determined the effects of disrupting apicobasal polarity proteins in Drosophila nephrocytes, which have SDs similar to those of mammalian podocytes. Confocal and electron microscopy were used to characterize SD integrity after loss of basolateral polarity proteins, and genetic-interaction studies illuminated relationships among apicobasal polarity proteins. RESULTS The study identified four novel regulators of nephrocyte SDs: Dlg, Lgl, Scrib, and Par-1. These proteins comprise the basolateral polarity module and its effector kinase. The data suggest these proteins work together, with apical polarity proteins, to regulate SDs by promoting normal endocytosis and trafficking of SD proteins. CONCLUSIONS Given the recognized importance of apical polarity proteins and SD protein trafficking in podocytopathies, the findings connecting basolateral polarity proteins to these processes significantly advance our understanding of SD regulation.
Collapse
Affiliation(s)
- Michael Mysh
- Department of Biology, UNC Kidney Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John S. Poulton
- Division of Nephrology and Hypertension, Department of Medicine, UNC Kidney Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
20
|
Yang J, Zhang D, Motojima M, Kume T, Hou Q, Pan Y, Duan A, Zhang M, Jiang S, Hou J, Shi J, Qin Z, Liu Z. Super-Enhancer-Associated Transcription Factors Maintain Transcriptional Regulation in Mature Podocytes. J Am Soc Nephrol 2021; 32:1323-1337. [PMID: 33771836 PMCID: PMC8259645 DOI: 10.1681/asn.2020081177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/30/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Transcriptional programs control cell fate, and identifying their components is critical for understanding diseases caused by cell lesion, such as podocytopathy. Although many transcription factors (TFs) are necessary for cell-state maintenance in glomeruli, their roles in transcriptional regulation are not well understood. METHODS The distribution of H3K27ac histones in human glomerulus cells was analyzed to identify superenhancer-associated TFs, and ChIP-seq and transcriptomics were performed to elucidate the regulatory roles of the TFs. Transgenic animal models of disease were further investigated to confirm the roles of specific TFs in podocyte maintenance. RESULTS Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B. Integration of transcriptome and cistrome data of FOXC1/2 in mice resolved transcriptional regulation in podocyte maintenance. FOXC1/2 regulated differentiation-associated transcription in mature podocytes. In both humans and animal models, mature podocyte injury was accompanied by deregulation of FOXC1/2 expression, and FOXC1/2 overexpression could protect podocytes in zebrafish. CONCLUSIONS FOXC1/2 maintain podocyte differentiation through transcriptional stabilization. The genome-wide chromatin resources support further investigation of TFs' regulatory roles in glomeruli transcription programs.
Collapse
Affiliation(s)
- Jingping Yang
- Medical School of Nanjing University, Nanjing, China,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Difei Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Tsutomu Kume
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Qing Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yu Pan
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Aiping Duan
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Song Jiang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jinhua Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jingsong Shi
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Zhihong Liu
- Medical School of Nanjing University, Nanjing, China,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| |
Collapse
|
21
|
Nagano C, Takaoka Y, Kamei K, Hamada R, Ichikawa D, Tanaka K, Aoto Y, Ishiko S, Rossanti R, Sakakibara N, Okada E, Horinouchi T, Yamamura T, Tsuji Y, Noguchi Y, Ishimori S, Nagase H, Ninchoji T, Iijima K, Nozu K. Genotype-Phenotype Correlation in WT1 Exon 8 to 9 Missense Variants. Kidney Int Rep 2021; 6:2114-2121. [PMID: 34386660 PMCID: PMC8343804 DOI: 10.1016/j.ekir.2021.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/05/2022] Open
Abstract
Introduction WT1 missense mutation in exon 8 or 9 causes infantile nephrotic syndrome with early progression to end-stage kidney disease (ESKD), Wilms tumor, and 46,XY female. However, some patients with missense mutations in exon 8 or 9 progress to ESKD in their teens or later. Therefore, we conducted a systematic review and functional analysis of WT1 transcriptional activity. Methods We conducted a systematic review of 174 cases with WT1 exon 8 or 9 missense variants from our cohort (n=13) and previous reports (n=161). Of these cases, mild and severe genotypes were selected for further in vitro functional analysis using luciferase assay. Results The median age of developing ESKD was 1.17 years. A comparative study was conducted among three WT1 genotype classes: mutations of the DNA-binding site (DBS group), mutations outside the DNA-binding site but at sites important for zinc finger structure formation by 2 cysteines and 2 histidines (C2H2 group), and mutations leading to other amino acid changes (Others group). The DBS group showed the severest phenotype and the C2H2 group was intermediate, whereas the Others group showed the mildest phenotype (developing ESKD at 0.90, 2.00, and 3.92 years, respectively, with significant differences). In vitro functional analysis showed dominant-negative effects for all variants; in addition, the DBS and C2H2 mutations were associated with significantly lower WT1 transcriptional activity than the other mutations. Conclusion Not only the DNA-binding site but also C2H2 zinc finger structure sites are important for maintaining WT1 transcriptional activity, and their mutation causes severe clinical symptoms.
Collapse
Affiliation(s)
- China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yutaka Takaoka
- Division of Medical Informatics and Bioinformatics, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Daisuke Ichikawa
- Division of Nephrology and Hypertension, St. Marianna University Graduate School of Medicine, Kawasaki City, Kanagawa, Japan
| | - Kazuki Tanaka
- Department of Nephrology, Aichi Children's Health and Medical Center, Obu, Aichi, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yurika Tsuji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yuko Noguchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| |
Collapse
|
22
|
Imeri F, Stepanovska Tanturovska B, Schwalm S, Saha S, Zeng-Brouwers J, Pavenstädt H, Pfeilschifter J, Schaefer L, Huwiler A. Loss of sphingosine kinase 2 enhances Wilm's tumor suppressor gene 1 and nephrin expression in podocytes and protects from streptozotocin-induced podocytopathy and albuminuria in mice. Matrix Biol 2021; 98:32-48. [PMID: 34015468 DOI: 10.1016/j.matbio.2021.05.003] [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: 01/26/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
The sphingosine 1-phosphate (S1P) is a bioactive sphingolipid that is now appreciated as key regulatory factor for various cellular functions in the kidney, including matrix remodeling. It is generated by two sphingosine kinases (Sphk), Sphk1 and Sphk2, which are ubiquitously expressed, but have distinct enzymatic activities and subcellular localizations. In this study, we have investigated the role of Sphk2 in podocyte function and its contribution to diabetic nephropathy. We show that streptozotocin (STZ)-induced nephropathy and albuminuria in mice is prevented by genetic depletion of Sphk2. This protection correlated with an increased protein expression of the transcription factor Wilm's tumor suppressor gene 1 (WT1) and its target gene nephrin, and a reduced macrophage infiltration in immunohistochemical renal sections of STZ-treated Sphk2-/- mice compared to STZ-treated wildtype mice. To investigate changes on the cellular level, we used an immortalized human podocyte cell line and generated a stable knockdown of Sphk2 (Sphk2-kd) by a lentiviral transduction method. These Sphk2-kd cells accumulated sphingosine as a consequence of the knockdown, and showed enhanced nephrin and WT1 mRNA and protein expressions similar to the finding in Sphk2 knockout mice. Treatment of wildtype podocytes with the highly selective Sphk2 inhibitor SLM6031434 caused a similar upregulation of nephrin and WT1 expression. Furthermore, exposing cells to the profibrotic mediator transforming growth factor β (TGFβ) resulted on the one side in reduced nephrin and WT1 expression, but on the other side, in upregulation of various profibrotic marker proteins, including connective tissue growth factor (CTGF), fibronectin (FN) and plasminogen activator inhibitor (PAI) 1. All these effects were reverted by Sphk2-kd and SLM6031434. Mechanistically, the protection by Sphk2-kd may depend on accumulated sphingosine and inhibited PKC activity, since treatment of cells with exogenous sphingosine not only reduced the phosphorylation pattern of PKC substrates, but also increased WT1 protein expression. Moreover, the selective stable knockdown of PKCδ increased WT1 expression, suggesting the involvement of this PKC isoenzyme in WT1 regulation. The glucocorticoid dexamethasone, which is a treatment option in many glomerular diseases and is known to mediate a nephroprotection, not only downregulated Sphk2 and enhanced cellular sphingosine, but also enhanced WT1 and nephrin expressions, thus, suggesting that parts of the nephroprotective effect of dexamethasone is mediated by Sphk2 downregulation. Altogether, our data demonstrated that loss of Sphk2 is protective in diabetes-induced podocytopathy and can prevent proteinuria, which is a hallmark of many glomerular diseases. Thus, Sphk2 could serve as a new attractive pharmacological target to treat proteinuric kidney diseases.
Collapse
Affiliation(s)
- Faik Imeri
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, Bern CH-3010, Switzerland
| | | | - Stephanie Schwalm
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main D-60590, Germany
| | - Sarbari Saha
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main D-60590, Germany
| | - Jinyang Zeng-Brouwers
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main D-60590, Germany
| | - Herrmann Pavenstädt
- Medizinische Klinik D, University Hospital Münster, Münster D-48149, Germany
| | - Josef Pfeilschifter
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main D-60590, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main D-60590, Germany.
| | - Andrea Huwiler
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, Bern CH-3010, Switzerland.
| |
Collapse
|
23
|
He X, Luo X, Dong J, Deng X, Liu F, Wei G. Long Non-Coding RNA XIST Promotes Wilms Tumor Progression Through the miR-194-5p/YAP Axis. Cancer Manag Res 2021; 13:3171-3180. [PMID: 33883934 PMCID: PMC8055356 DOI: 10.2147/cmar.s297842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/22/2021] [Indexed: 01/13/2023] Open
Abstract
Purpose Although the long non-coding RNA (lncRNA) X inactive-specific transcript (XIST) has been reported to have an anti-tumor effect in multiple malignant tumors, its role in Wilms tumor (WT) progression has not been characterized. Thus, we investigated the underlying mechanism by which XIST regulates WT progression. Patients and Methods We performed microarray analysis and real-time quantitative PCR (RT-qPCR) to detect the expression levels of XIST lncRNA, microRNA-194-5p (miR-194-5p), and YAP (yes-associated protein in Hippo pathway) in tumor and matched adjacent normal tissues and blood collected from 49 WT patients. We also conducted bioinformatics analyses to identify differentially expressed genes. We measured the effects of XIST overexpression and knockdown on cell proliferation, apoptosis, migration, and invasion, and its association with the miR-194-5p/YAP pathway in the rhabdoid G401cell line using flow cytometry, transwell assays, immunohistochemistry, Western blot analysis, and the dual luciferase reporter gene assay. Results We found that XIST lncRNA levels were increased in blood and tissue samples of WT patients, and this upregulation was significantly correlated with TNM staging and shorter survival time. Notably, we found that XIST upregulation correlated with miR-194-5p downregulation and YAP upregulation in WT tissues, suggesting that XIST regulates the miR-194-5p/YAP pathway. Conversely, XIST downregulation inhibited WT cell proliferation, migration, and invasion and induced apoptosis. Our study revealed the oncogenic role of the lncRNA XIST in WT and demonstrated its role as a competitive endogenous RNA that regulates the miR-194-5p/YAP pathway. Conclusion Our study demonstrates XIST’s potential as a clinical prognostic biomarker and therapeutic target for WT.
Collapse
Affiliation(s)
- Xingyue He
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China
| | - Xin Luo
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Chongqing Key Laboratory of Pediatrics, Chongqing, People's Republic of China
| | - Junjun Dong
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China
| | - Xing Deng
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China
| | - Feng Liu
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China.,Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Chongqing Key Laboratory of Pediatrics, Chongqing, People's Republic of China
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China.,Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Chongqing Key Laboratory of Pediatrics, Chongqing, People's Republic of China
| |
Collapse
|
24
|
Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes. Nat Commun 2021; 12:2141. [PMID: 33837218 PMCID: PMC8035407 DOI: 10.1038/s41467-021-22331-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/04/2021] [Indexed: 01/06/2023] Open
Abstract
Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies. The molecular identity of renal glomerular cells is poorly characterized and rodent glomerulopathy models translate poorly to humans. Here, the authors show molecular signatures of glomerulus-associated cells using single cell RNA sequencing and highlight differences between mouse and human cells.
Collapse
|
25
|
Talyan S, Filipów S, Ignarski M, Smieszek M, Chen H, Kühne L, Butt L, Göbel H, Hoyer-Allo KJR, Koehler FC, Altmüller J, Brinkkötter P, Schermer B, Benzing T, Kann M, Müller RU, Dieterich C. CALINCA-A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease. Cells 2021; 10:692. [PMID: 33804736 PMCID: PMC8003990 DOI: 10.3390/cells10030692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
Diseases of the renal filtration unit-the glomerulus-are the most common cause of chronic kidney disease. Podocytes are the pivotal cell type for the function of this filter and focal-segmental glomerulosclerosis (FSGS) is a classic example of a podocytopathy leading to proteinuria and glomerular scarring. Currently, no targeted treatment of FSGS is available. This lack of therapeutic strategies is explained by a limited understanding of the defects in podocyte cell biology leading to FSGS. To date, most studies in the field have focused on protein-coding genes and their gene products. However, more than 80% of all transcripts produced by mammalian cells are actually non-coding. Here, long non-coding RNAs (lncRNAs) are a relatively novel class of transcripts and have not been systematically studied in FSGS to date. The appropriate tools to facilitate lncRNA research for the renal scientific community are urgently required due to a row of challenges compared to classical analysis pipelines optimized for coding RNA expression analysis. Here, we present the bioinformatic pipeline CALINCA as a solution for this problem. CALINCA automatically analyzes datasets from murine FSGS models and quantifies both annotated and de novo assembled lncRNAs. In addition, the tool provides in-depth information on podocyte specificity of these lncRNAs, as well as evolutionary conservation and expression in human datasets making this pipeline a crucial basis to lncRNA studies in FSGS.
Collapse
Affiliation(s)
- Sweta Talyan
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany;
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany;
| | - Samantha Filipów
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Magdalena Smieszek
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany;
| | - He Chen
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Lucas Kühne
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Linus Butt
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Heike Göbel
- Institute for Pathology, Diagnostic and Experimental Nephropathology Unit, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany;
| | - K. Johanna R. Hoyer-Allo
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Felix C. Koehler
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany;
| | - Paul Brinkkötter
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Martin Kann
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany; (S.F.); (M.I.); (H.C.); (L.K.); (L.B.); (K.J.R.H.-A.); (F.C.K.); (P.B.); (B.S.); (T.B.); (M.K.)
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Christoph Dieterich
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany;
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany;
| |
Collapse
|
26
|
Okabe M, Yamamoto K, Miyazaki Y, Motojima M, Ohtsuka M, Pastan I, Yokoo T, Matsusaka T. Indirect podocyte injury manifested in a partial podocytectomy mouse model. Am J Physiol Renal Physiol 2021; 320:F922-F933. [PMID: 33719575 DOI: 10.1152/ajprenal.00602.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In progressive glomerular diseases, segmental podocyte injury often expands, leading to global glomerulosclerosis by unclear mechanisms. To study the expansion of podocyte injury, we established a new mosaic mouse model in which a fraction of podocytes express human (h)CD25 and can be injured by the immunotoxin LMB2. hCD25+ and hCD25- podocytes were designed to express tdTomato and enhanced green fluorescent protein (EGFP), respectively, which enabled cell sorting analysis of podocytes. After the injection of LMB2, mosaic mice developed proteinuria and glomerulosclerosis. Not only tdTomato+ podocytes but also EGFP+ podocytes were decreased in number and showed damage, as evidenced by a decrease in nephrin and an increase in desmin at both protein and RNA levels. Transcriptomics analysis found a decrease in the glucocorticoid-induced transcript 1 gene and an increase in the thrombospondin 4, heparin-binding EGF-like growth factor, and transforming growth factor-β genes in EGFP+ podocytes; these genes may be candidate mediators of secondary podocyte damage. Pathway analysis suggested that focal adhesion, integrin-mediated cell adhesion, and focal adhesion-phosphatidylinositol 3-kinase-Akt-mammalian target of rapamycin signaling are involved in secondary podocyte injury. Finally, treatment of mosaic mice with angiotensin II receptor blocker markedly ameliorated secondary podocyte injury. This mosaic podocyte injury model has distinctly demonstrated that damaged podocytes cause secondary podocyte damage, which may be a promising therapeutic target in progressive kidney diseases.NEW & NOTEWORTHY This novel mosaic model has demonstrated that when a fraction of podocytes is injured, other podocytes are subjected to secondary injury. This spreading of injury may occur ubiquitously irrespective of the primary cause of podocyte injury, leading to end-stage renal failure. Understanding the molecular mechanism of secondary podocyte injury and its prevention is important for the treatment of progressive kidney diseases. This model will be a powerful tool for studying the indirect podocyte injury.
Collapse
Affiliation(s)
- Masahiro Okabe
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kazuyoshi Yamamoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Yoichi Miyazaki
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masato Ohtsuka
- Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan.,Institute of Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Taiji Matsusaka
- Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan.,Institute of Medical Science, Tokai University School of Medicine, Isehara, Japan
| |
Collapse
|
27
|
Rogg M, Maier JI, Dotzauer R, Artelt N, Kretz O, Helmstädter M, Abed A, Sammarco A, Sigle A, Sellung D, Dinse P, Reiche K, Yasuda-Yamahara M, Biniossek ML, Walz G, Werner M, Endlich N, Schilling O, Huber TB, Schell C. SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. J Am Soc Nephrol 2021; 32:563-579. [PMID: 33514561 PMCID: PMC7920176 DOI: 10.1681/asn.2020081126] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/15/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Previous research demonstrated that small Rho GTPases, modulators of the actin cytoskeleton, are drivers of podocyte foot-process effacement in glomerular diseases, such as FSGS. However, a comprehensive understanding of the regulatory networks of small Rho GTPases in podocytes is lacking. METHODS We conducted an analysis of podocyte transcriptome and proteome datasets for Rho GTPases; mapped in vivo, podocyte-specific Rho GTPase affinity networks; and examined conditional knockout mice and murine disease models targeting Srgap1. To evaluate podocyte foot-process morphology, we used super-resolution microscopy and electron microscopy; in situ proximity ligation assays were used to determine the subcellular localization of the small GTPase-activating protein SRGAP1. We performed functional analysis of CRISPR/Cas9-generated SRGAP1 knockout podocytes in two-dimensional and three-dimensional cultures and quantitative interaction proteomics. RESULTS We demonstrated SRGAP1 localization to podocyte foot processes in vivo and to cellular protrusions in vitro. Srgap1fl/fl*Six2Cre but not Srgap1fl/fl*hNPHS2Cre knockout mice developed an FSGS-like phenotype at adulthood. Podocyte-specific deletion of Srgap1 by hNPHS2Cre resulted in increased susceptibility to doxorubicin-induced nephropathy. Detailed analysis demonstrated significant effacement of podocyte foot processes. Furthermore, SRGAP1-knockout podocytes showed excessive protrusion formation and disinhibition of the small Rho GTPase machinery in vitro. Evaluation of a SRGAP1-dependent interactome revealed the involvement of SRGAP1 with protrusive and contractile actin networks. Analysis of glomerular biopsy specimens translated these findings toward human disease by displaying a pronounced redistribution of SRGAP1 in FSGS. CONCLUSIONS SRGAP1, a podocyte-specific RhoGAP, controls podocyte foot-process architecture by limiting the activity of protrusive, branched actin networks. Therefore, elucidating the complex regulatory small Rho GTPase affinity network points to novel targets for potentially precise intervention in glomerular diseases.
Collapse
Affiliation(s)
- Manuel Rogg
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany,Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Jasmin I. Maier
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Robert Dotzauer
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Nadine Artelt
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Helmstädter
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Ahmed Abed
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Alena Sammarco
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - August Sigle
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany,Department of Urology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Dominik Sellung
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany,Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany
| | - Patrick Dinse
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Karoline Reiche
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Mako Yasuda-Yamahara
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany,Department of Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Martin L. Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Gerd Walz
- Department of Medicine IV, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Tobias B. Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schell
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany,Berta-Ottenstein Program, Medical Faculty, Medical Center – University of Freiburg, Freiburg, Germany
| |
Collapse
|
28
|
Lepa C, Hoppe S, Stöber A, Skryabin BV, Sievers LK, Heitplatz B, Ciarimboli G, Neugebauer U, Lindenmeyer MT, Cohen CD, Drexler HC, Boor P, Weide T, Pavenstädt H, George B. TrkC Is Essential for Nephron Function and Trans-Activates Igf1R Signaling. J Am Soc Nephrol 2021; 32:357-374. [PMID: 33380522 PMCID: PMC8054883 DOI: 10.1681/asn.2020040424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/03/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Injury to kidney podocytes often results in chronic glomerular disease and consecutive nephron malfunction. For most glomerular diseases, targeted therapies are lacking. Thus, it is important to identify novel signaling pathways contributing to glomerular disease. Neurotrophic tyrosine kinase receptor 3 (TrkC) is expressed in podocytes and the protein transmits signals to the podocyte actin cytoskeleton. METHODS Nephron-specific TrkC knockout (TrkC-KO) and nephron-specific TrkC-overexpressing (TrkC-OE) mice were generated to dissect the role of TrkC in nephron development and maintenance. RESULTS Both TrkC-KO and TrkC-OE mice exhibited enlarged glomeruli, mesangial proliferation, basement membrane thickening, albuminuria, podocyte loss, and aspects of FSGS during aging. Igf1 receptor (Igf1R)-associated gene expression was dysregulated in TrkC-KO mouse glomeruli. Phosphoproteins associated with insulin, erb-b2 receptor tyrosine kinase (Erbb), and Toll-like receptor signaling were enriched in lysates of podocytes treated with the TrkC ligand neurotrophin-3 (Nt-3). Activation of TrkC by Nt-3 resulted in phosphorylation of the Igf1R on activating tyrosine residues in podocytes. Igf1R phosphorylation was increased in TrkC-OE mouse kidneys while it was decreased in TrkC-KO kidneys. Furthermore, TrkC expression was elevated in glomerular tissue of patients with diabetic kidney disease compared with control glomerular tissue. CONCLUSIONS Our results show that TrkC is essential for maintaining glomerular integrity. Furthermore, TrkC modulates Igf-related signaling in podocytes.
Collapse
Affiliation(s)
- Carolin Lepa
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Sascha Hoppe
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Antje Stöber
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Boris V. Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), Westfälische-Wilhelms-University, Münster, Germany
| | | | - Barbara Heitplatz
- Gerhard-Domagk Institute for Pathology, University Hospital Münster, Münster, Germany
| | | | - Ute Neugebauer
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Maja T. Lindenmeyer
- III. Medizinische Klinik und Poliklinik, University Hospital Hamburg-Eppendorf, Germany
| | - Clemens D. Cohen
- Klinik für Nieren-, Hochdruck- und Rheumaerkrankungen, München Klinik Harlaching, Germany
| | - Hannes C.A. Drexler
- Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Thomas Weide
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | | | - Britta George
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| |
Collapse
|
29
|
Fabretti F, Tschernoster N, Erger F, Hedergott A, Buescher AK, Dafinger C, Reusch B, Köntges VK, Kohl S, Bartram MP, Weber LT, Thiele H, Altmueller J, Schermer B, Beck BB, Habbig S. Expanding the Spectrum of FAT1 Nephropathies by Novel Mutations That Affect Hippo Signaling. Kidney Int Rep 2021; 6:1368-1378. [PMID: 34013115 PMCID: PMC8116753 DOI: 10.1016/j.ekir.2021.01.023] [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: 10/19/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/19/2023] Open
Abstract
Introduction Disease-causing mutations in the protocadherin FAT1 have been recently described both in patients with a glomerulotubular nephropathy and in patients with a syndromic nephropathy. Methods We identified 4 patients with FAT1-associated disease, performed clinical and genetic characterization, and compared our findings to the previously published patients. Patient-derived primary urinary epithelial cells were analyzed by quantitative polymerase chain reaction (qPCR) and immunoblotting to identify possible alterations in Hippo signaling. Results Here we expand the spectrum of FAT1-associated disease with the identification of novel FAT1 mutations in 4 patients from 3 families (homozygous truncating variants in 3, compound heterozygous missense variants in 1 patient). All patients show an ophthalmologic phenotype together with heterogeneous renal phenotypes ranging from normal renal function to early-onset end-stage kidney failure. Molecular analysis of primary urine-derived urinary renal epithelial cells revealed alterations in the Hippo signaling cascade with a decreased phosphorylation of both the core kinase MST and the downstream effector YAP. Consistently, we found a transcriptional upregulation of bona fide YAP target genes. Conclusion A comprehensive review of the here identified patients and those previously published indicates a highly diverse phenotype in patients with missense mutations but a more uniform and better recognizable phenotype in the patients with truncating mutations. Altered Hippo signaling and de-repressed YAP activity might be novel contributing factors to the pathomechanism in FAT1-associated renal disease.
Collapse
Affiliation(s)
- Francesca Fabretti
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nikolai Tschernoster
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Florian Erger
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Andrea Hedergott
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anja K Buescher
- Children's Hospital, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Claudia Dafinger
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Bjoern Reusch
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Vincent K Köntges
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Stefan Kohl
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Malte P Bartram
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Lutz Thorsten Weber
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Bodo B Beck
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sandra Habbig
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| |
Collapse
|
30
|
Generation of Monogenic Candidate Genes for Human Nephrotic Syndrome Using 3 Independent Approaches. Kidney Int Rep 2020; 6:460-471. [PMID: 33615071 PMCID: PMC7879125 DOI: 10.1016/j.ekir.2020.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/22/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction Steroid-resistant nephrotic syndrome (SRNS) is the second most common cause of chronic kidney disease during childhood. Identification of 63 monogenic human genes has delineated 12 distinct pathogenic pathways. Methods Here, we generated 2 independent sets of nephrotic syndrome (NS) candidate genes to augment the discovery of additional monogenic causes based on whole-exome sequencing (WES) data from 1382 families with NS. Results We first identified 63 known monogenic causes of NS in mice from public databases and scientific publications, and 12 of these genes overlapped with the 63 known human monogenic SRNS genes. Second, we used a set of 64 genes that are regulated by the transcription factor Wilms tumor 1 (WT1), which causes SRNS if mutated. Thirteen of these WT1-regulated genes overlapped with human or murine NS genes. Finally, we overlapped these lists of murine and WT1 candidate genes with our list of 120 candidate genes generated from WES in 1382 NS families, to identify novel candidate genes for monogenic human SRNS. Using this approach, we identified 7 overlapping genes, of which 3 genes were shared by all datasets, including SYNPO. We show that loss-of-function of SYNPO leads to decreased CDC42 activity and reduced podocyte migration rate, both of which are rescued by overexpression of wild-type complementary DNA (cDNA), but not by cDNA representing the patient mutation. Conclusion Thus, we identified 3 novel candidate genes for human SRNS using 3 independent, nonoverlapping hypotheses, and generated functional evidence for SYNPO as a novel potential monogenic cause of NS.
Collapse
|
31
|
Wang Y, Pedigo CE, Inoue K, Tian X, Cross E, Ebenezer K, Li W, Wang Z, Shin JW, Schwartze E, Groener M, Ishibe S. Murine Epsins Play an Integral Role in Podocyte Function. J Am Soc Nephrol 2020; 31:2870-2886. [PMID: 33051360 PMCID: PMC7790213 DOI: 10.1681/asn.2020050691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/30/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Epsins, a family of evolutionarily conserved membrane proteins, play an essential role in endocytosis and signaling in podocytes. METHODS Podocyte-specific Epn1, Epn2, Epn3 triple-knockout mice were generated to examine downstream regulation of serum response factor (SRF) by cell division control protein 42 homolog (Cdc42). RESULTS Podocyte-specific loss of epsins resulted in increased albuminuria and foot process effacement. Primary podocytes isolated from these knockout mice exhibited abnormalities in cell adhesion and spreading, which may be attributed to reduced activation of cell division control protein Cdc42 and SRF, resulting in diminished β1 integrin expression. In addition, podocyte-specific loss of Srf resulted in severe albuminuria and foot process effacement, and defects in cell adhesion and spreading, along with decreased β1 integrin expression. CONCLUSIONS Epsins play an indispensable role in maintaining properly functioning podocytes through the regulation of Cdc42 and SRF-dependent β1 integrin expression.
Collapse
Affiliation(s)
- Ying Wang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
- Centre for Evidence-Based Chinese Medicine, Beijing University of Chinese Medicine, Chaoyang District, Beijing, 100029, China
| | - Christopher E Pedigo
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Kazunori Inoue
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Xuefei Tian
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Elizabeth Cross
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Karen Ebenezer
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Wei Li
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Zhen Wang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Jee Won Shin
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Eike Schwartze
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Marwin Groener
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Shuta Ishibe
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| |
Collapse
|
32
|
The Protective Effect of Shen Qi Wan on Adenine-Induced Podocyte Injury. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:5803192. [PMID: 33273954 PMCID: PMC7700022 DOI: 10.1155/2020/5803192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/21/2020] [Accepted: 11/05/2020] [Indexed: 11/22/2022]
Abstract
Podocytes are a special type of differentiated epithelial cells that maintain the glomerular filtration barrier in the kidney. Injury or damages in podocytes can cause kidney-related disorders, like CKD. The injury or dysfunction of podocytes can occur by different metabolic disorders. Due to the severity and complexity of podocyte injuries, this state is considered as a serious health issue worldwide. Here, we examined and addressed the efficacy of an alternative Chinese medicine, Shen Qi Wan (SQW), on podocyte-related kidney injury. We evaluated the role and mechanism of action of SQW in podocyte injury. We observed that SQW significantly reduced 24-hour urinary protein and blood urea nitrogen levels and alleviated the pathological damage caused by adenine. Moreover, SQW significantly decreased the expression of nephrin and increased the expression of WT1 and AQP1 in the kidney of mice treated with adenine. We observed that SQW did not effectively reduce the high level of proteinuria in AQP1−/− mice indicating the prominent role of AQP1 in the SQW-ameliorating pathway. Transmission electron microscopy (TEM) images indicated the food processes effacement in AQP1−/− mice were not lessened by SQW. In conclusion, podocyte injury could alter the pathological nature of the kidney, and SQW administration relieves the nature of pathogenesis by activating AQP1.
Collapse
|
33
|
He C, Qin H, Tang H, Yang D, Li Y, Huang Z, Zhang D, Lv C. Comprehensive bioinformatics analysis of the TP53 signaling pathway in Wilms' tumor. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1228. [PMID: 33178760 PMCID: PMC7607069 DOI: 10.21037/atm-20-6047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Differential expression of tumor protein 53 (TP53, or p53) has been observed in multiple cancers. However, the expression levels and prognostic role of TP53 signaling pathway genes in Wilms' tumor (WT) have yet to be fully explored. Methods The expression levels of TP53 signaling pathway genes including TP53, mouse double minute 2 (MDM2), mouse double minute 4 (MDM4), cyclin-dependent kinase 2A (CDKN2A), cyclin-dependent kinase 2B (CDKN2B), and tumor suppressor p53-binding protein 1 (TP53BP1) in WT were analyzed using the Oncomine database. Aberration types, co-mutations, mutation locations, signaling pathways, and the prognostic role of TP53 in WT were investigated using cBioPortal. MicroRNA (miRNA) and transcription factor (TF) targets were identified with miRTarBase, miWalk, and ChIP-X Enrichment Analysis 3 (CheA3), respectively. A protein-protein network was constructed using GeneMANIA. The expression of TP53 signaling genes were confirmed in WT samples and normal kidney tissues using the Human Protein Atlas (HPA). Cancer Therapeutics Response Portal (CTRP) was used to analyze the small molecules potentially targeting TP53. Results TP53 was significantly expressed in the Cutcliffe Renal (P=0.010), but not in the Yusenko Renal (P=0.094). Meanwhile, MDM2 was significantly overexpressed in the Yusenko Renal (P=0.058), but not in the Cutcliffe Renal (P=0.058). The expression levels of MDM4 no significant difference between the tumor and normal tissue samples. The most common TP53 alteration was missense and the proportion of TP53 pathway-related mutations was 2.3%. Co-expressed genes included ZNF609 (zinc finger protein 609), WRAP53 (WD40-encoding RNA antisense to p53), CNOT2 (CC chemokine receptor 4-negative regulator of transcription 2), and CDH13 (cadherin 13). TP53 alterations indicated poor prognosis of WT (P=1.051e-4). The regulators of the TP53 pathway included miR-485-5p and TFs NR2F2 and KDM5B. The functions of TP53 signaling pathway were signal transduction in response to DNA damage and regulate the cell cycle. The small molecules targeting TP53 included PRIMA-1, RITA, SJ-172550, and SCH-529074. Conclusions TP53 was found to be differentially expressed in WT tissues. TP53 mutations indicated poor outcomes of WT. Therefore, pifithrin-mu, PRIMA-1, RITA, SJ-172550, and SCH-529074 could be used in combination with traditional chemotherapy to treat WT.
Collapse
Affiliation(s)
- Changjing He
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Huatao Qin
- Department of Nursing, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Haizhou Tang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Di Yang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yufeng Li
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhenwen Huang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Donghu Zhang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Changheng Lv
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| |
Collapse
|
34
|
Chen Q, Chen J, Wang C, Chen X, Liu J, Zhou L, Liu Y. MicroRNA-466o-3p mediates β-catenin-induced podocyte injury by targeting Wilms tumor 1. FASEB J 2020; 34:14424-14439. [PMID: 32888352 DOI: 10.1096/fj.202000464r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022]
Abstract
Podocytes are highly specialized cells that play an essential role in maintaining the integrity and function of the glomerular filtration barrier. Wilms tumor 1 (WT1) and β-catenin are two master regulators that play opposing roles in podocyte biology and mutually antagonize each other. However, exactly how β-catenin inhibits WT1 remains incompletely understood. In this study, we demonstrated the role of miR-466o-3p in mediating β-catenin-triggered podocyte injury by targeting WT1. The expression of miR-466o-3p was upregulated in cultured podocytes after β-catenin activation and in glomerular podocytes in adriamycin (ADR) nephropathy, remnant kidney after 5/6 renal ablation, and diabetic kidney disease. Bioinformatics analysis and luciferase reporter assay confirmed that miR-466o-3p directly targeted WT1 mRNA. Furthermore, overexpression of miR-466o-3p downregulated WT1 protein and promoted podocyte injury in vitro. Conversely, inhibition of miR-466o-3p alleviated β-catenin-induced podocyte dysfunction. In mouse model of ADR nephropathy, overexpression of miR-466o-3p inhibited WT1, aggravated podocytes injury and deteriorated proteinuria. In contrast, inhibition of renal miR-466o-3p by antagomiR, either prior to or after ADR injection, substantially restored WT1, alleviated podocytes injury and reduced renal fibrosis. These studies reveal a critical role for miR-466o-3p, a novel microRNA that has not been characterized previously, in mediating β-catenin-triggered WT1 inhibition. Our findings also uncover a new pathogenic mechanism by which β-catenin promotes podocyte injury and proteinuria in glomerular diseases.
Collapse
Affiliation(s)
- Qiyan Chen
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiongcheng Chen
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chunhong Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaowen Chen
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lili Zhou
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Youhua Liu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
35
|
Ettou S, Jung YL, Miyoshi T, Jain D, Hiratsuka K, Schumacher V, Taglienti ME, Morizane R, Park PJ, Kreidberg JA. Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury. SCIENCE ADVANCES 2020; 6:eabb5460. [PMID: 32754639 PMCID: PMC7380960 DOI: 10.1126/sciadv.abb5460] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
In the context of human disease, the mechanisms whereby transcription factors reprogram gene expression in reparative responses to injury are not well understood. We have studied the mechanisms of transcriptional reprogramming in disease using murine kidney podocytes as a model for tissue injury. Podocytes are a crucial component of glomeruli, the filtration units of each nephron. Podocyte injury is the initial event in many processes that lead to end-stage kidney disease. Wilms tumor-1 (WT1) is a master regulator of gene expression in podocytes, binding nearly all genes known to be crucial for maintenance of the glomerular filtration barrier. Using murine models and human kidney organoids, we investigated WT1-mediated transcriptional reprogramming during the course of podocyte injury. Reprogramming the transcriptome involved highly dynamic changes in the binding of WT1 to target genes during a reparative injury response, affecting chromatin state and expression levels of target genes.
Collapse
Affiliation(s)
- Sandrine Ettou
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Youngsook L. Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Tomoya Miyoshi
- Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
- Renal Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ken Hiratsuka
- Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
- Renal Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Valerie Schumacher
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E. Taglienti
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Ryuji Morizane
- Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
- Renal Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jordan A. Kreidberg
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| |
Collapse
|
36
|
Koehler S, Kuczkowski A, Kuehne L, Jüngst C, Hoehne M, Grahammer F, Eddy S, Kretzler M, Beck BB, Höhfeld J, Schermer B, Benzing T, Brinkkoetter PT, Rinschen MM. Proteome Analysis of Isolated Podocytes Reveals Stress Responses in Glomerular Sclerosis. J Am Soc Nephrol 2020; 31:544-559. [PMID: 32047005 DOI: 10.1681/asn.2019030312] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Understanding podocyte-specific responses to injury at a systems level is difficult because injury leads to podocyte loss or an increase of extracellular matrix, altering glomerular cellular composition. Finding a window into early podocyte injury might help identify molecular pathways involved in the podocyte stress response. METHODS We developed an approach to apply proteome analysis to very small samples of purified podocyte fractions. To examine podocytes in early disease states in FSGS mouse models, we used podocyte fractions isolated from individual mice after chemical induction of glomerular disease (with Doxorubicin or LPS). We also applied single-glomerular proteome analysis to tissue from patients with FSGS. RESULTS Transcriptome and proteome analysis of glomeruli from patients with FSGS revealed an underrepresentation of podocyte-specific genes and proteins in late-stage disease. Proteome analysis of purified podocyte fractions from FSGS mouse models showed an early stress response that includes perturbations of metabolic, mechanical, and proteostasis proteins. Additional analysis revealed a high correlation between the amount of proteinuria and expression levels of the mechanosensor protein Filamin-B. Increased expression of Filamin-B in podocytes in biopsy samples from patients with FSGS, in single glomeruli from proteinuric rats, and in podocytes undergoing mechanical stress suggests that this protein has a role in detrimental stress responses. In Drosophila, nephrocytes with reduced filamin homolog Cher displayed altered filtration capacity, but exhibited no change in slit diaphragm structure. CONCLUSIONS We identified conserved mechanisms of the podocyte stress response through ultrasensitive proteome analysis of human glomerular FSGS tissue and purified native mouse podocytes during early disease stages. This approach enables systematic comparisons of large-scale proteomics data and phenotype-to-protein correlation.
Collapse
Affiliation(s)
- Sybille Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alexander Kuczkowski
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Lucas Kuehne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Martin Hoehne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Hamburg, Germany
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, and
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, and.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Bodo B Beck
- Department of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Jörg Höhfeld
- Cell Biology, University of Bonn, Bonn, Germany; and
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California
| |
Collapse
|
37
|
Rodriguez S, Little HC, Daneshpajouhnejad P, Shepard BD, Tan SY, Wolfe A, Cheema MU, Jandu S, Woodward OM, Talbot CC, Berkowitz DE, Rosenberg AZ, Pluznick JL, Wong GW. Late-onset renal hypertrophy and dysfunction in mice lacking CTRP1. FASEB J 2020; 34:2657-2676. [PMID: 31908037 PMCID: PMC7739198 DOI: 10.1096/fj.201900558rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022]
Abstract
Local and systemic factors that influence renal structure and function in aging are not well understood. The secretory protein C1q/TNF-related protein 1 (CTRP1) regulates systemic metabolism and cardiovascular function. We provide evidence here that CTRP1 also modulates renal physiology in an age- and sex-dependent manner. In mice lacking CTRP1, we observed significantly increased kidney weight and glomerular hypertrophy in aged male but not female or young mice. Although glomerular filtration rate, plasma renin and aldosterone levels, and renal response to water restriction did not differ between genotypes, CTRP1-deficient male mice had elevated blood pressure. Echocardiogram and pulse wave velocity measurements indicated normal heart function and vascular stiffness in CTRP1-deficient animals, and increased blood pressure was not due to greater salt retention. Paradoxically, CTRP1-deficient mice had elevated urinary sodium and potassium excretion, partially resulting from reduced expression of genes involved in renal sodium and potassium reabsorption. Despite renal hypertrophy, markers of inflammation, fibrosis, and oxidative stress were reduced in CTRP1-deficient mice. RNA sequencing revealed alterations and enrichments of genes in metabolic processes in CTRP1-deficient animals. These results highlight novel contributions of CTRP1 to aging-associated changes in renal physiology.
Collapse
Affiliation(s)
- Susana Rodriguez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hannah C. Little
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Blythe D. Shepard
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefanie Y. Tan
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Wolfe
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Muhammad Umar Cheema
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sandeep Jandu
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Owen M. Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - C. Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dan E. Berkowitz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jennifer L. Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - G. William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
38
|
Paul P, Antonydhason V, Gopal J, Haga SW, Hasan N, Oh JW. Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. Int J Mol Sci 2020; 21:E961. [PMID: 32024005 PMCID: PMC7038205 DOI: 10.3390/ijms21030961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomics are highlighted in this review. The need for more attention and input from bioinformaticians is highlighted, so that progressive achievements and releases can be made. With just a handful of existing tools for renal and urinary proteomic research available, this review identifies a gap worth targeting by protein chemists and bioinformaticians. The probable causes for the lack of enthusiasm in this area are also speculated upon in this review. This is the first review that consolidates the bioinformatics applications specifically for renal and urinary proteomics.
Collapse
Affiliation(s)
- Piby Paul
- St. Jude Childrens Cancer Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Vimala Antonydhason
- Department of Microbiology and Immunology, Institute for Biomedicine, Gothenburg University, 413 90 Gothenburg, Sweden;
| | - Judy Gopal
- Department of Environmental Health Sciences, Konkuk University, Seoul 143-701, Korea;
| | - Steve W. Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung 804, Taiwan;
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| |
Collapse
|
39
|
Tran T, Lindström NO, Ransick A, De Sena Brandine G, Guo Q, Kim AD, Der B, Peti-Peterdi J, Smith AD, Thornton M, Grubbs B, McMahon JA, McMahon AP. In Vivo Developmental Trajectories of Human Podocyte Inform In Vitro Differentiation of Pluripotent Stem Cell-Derived Podocytes. Dev Cell 2020; 50:102-116.e6. [PMID: 31265809 DOI: 10.1016/j.devcel.2019.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/27/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022]
Abstract
The renal corpuscle of the kidney comprises a glomerular vasculature embraced by podocytes and supported by mesangial myofibroblasts, which ensure plasma filtration at the podocyte-generated slit diaphragm. With a spectrum of podocyte-expressed gene mutations causing chronic disease, an enhanced understanding of podocyte development and function to create relevant in vitro podocyte models is a clinical imperative. To characterize podocyte development, scRNA-seq was performed on human fetal kidneys, identifying distinct transcriptional signatures accompanying the differentiation of functional podocytes from progenitors. Interestingly, organoid-generated podocytes exhibited highly similar, progressive transcriptional profiles despite an absence of the vasculature, although abnormal gene expression was pinpointed in late podocytes. On transplantation into mice, organoid-derived podocytes recruited the host vasculature and partially corrected transcriptional profiles. Thus, human podocyte development is mostly intrinsically regulated and vascular interactions refine maturation. These studies support the application of organoid-derived podocytes to model disease and to restore or replace normal kidney functions.
Collapse
Affiliation(s)
- Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Guilherme De Sena Brandine
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Balint Der
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Janos Peti-Peterdi
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, CA 90089, USA
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, CA 90089, USA
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
40
|
BENZING THOMAS. MOLECULAR DESIGN OF THE KIDNEY FILTRATION BARRIER. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2020; 131:125-139. [PMID: 32675853 PMCID: PMC7358502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Kidneys are the central regulators of organismal homeostasis. These organs filter enormous amounts of fluid from plasma; excrete toxic waste products; maintain salt, water, and volume balance; coordinate blood pressure regulation; and maintain the acid-base equilibrium essential for life. Although it has been known for decades that renal glomeruli serve as the site of plasma ultrafiltration and urine production, both the molecular design and function of the kidney filtration barrier have remained elusive. Indeed, the past two decades have witnessed enormous breakthroughs in our fundamental understanding of kidney filtration and the critical role that podocytes, specialized terminally differentiated epithelial cells at the glomerular capillaries, fulfill in the function of the kidney filtration barrier. Here we discuss recent advances in this field that will change the way we think about plasma ultrafiltration in health and proteinuria as a manifestation of glomerular diseases.
Collapse
Affiliation(s)
- THOMAS BENZING
- Correspondence and reprint requests: Thomas Benzing, MD, Department II of Internal Medicine, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany+ 49 221 4784480, 49 221 4785959
| |
Collapse
|
41
|
Rinschen MM, Gödel M, Grahammer F, Zschiedrich S, Helmstädter M, Kretz O, Zarei M, Braun DA, Dittrich S, Pahmeyer C, Schroder P, Teetzen C, Gee H, Daouk G, Pohl M, Kuhn E, Schermer B, Küttner V, Boerries M, Busch H, Schiffer M, Bergmann C, Krüger M, Hildebrandt F, Dengjel J, Benzing T, Huber TB. A Multi-layered Quantitative In Vivo Expression Atlas of the Podocyte Unravels Kidney Disease Candidate Genes. Cell Rep 2019; 23:2495-2508. [PMID: 29791858 PMCID: PMC5986710 DOI: 10.1016/j.celrep.2018.04.059] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/07/2018] [Accepted: 04/15/2018] [Indexed: 12/31/2022] Open
Abstract
Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases. Here, we combine mass spectrometry-based proteomics with mRNA sequencing, bioinformatics, and hypothesis-driven studies to provide a comprehensive and quantitative map of mammalian podocytes that identifies unanticipated signaling pathways. Comparison of the in vivo datasets with proteomics data from podocyte cell cultures showed a limited value of available cell culture models. Moreover, in vivo stable isotope labeling by amino acids uncovered surprisingly rapid synthesis of mitochondrial proteins under steady-state conditions that was perturbed under autophagy-deficient, disease-susceptible conditions. Integration of acquired omics dimensions suggested FARP1 as a candidate essential for podocyte function, which could be substantiated by genetic analysis in humans and knockdown experiments in zebrafish. This work exemplifies how the integration of multi-omics datasets can identify a framework of cell-type-specific features relevant for organ health and disease. Deep proteome and transcriptome analyses of native podocytes unravel druggable targets Static and dynamic proteomics uncover features of podocyte identity and proteostasis Candidate genes for nephrotic syndrome were predicted based on multi-omic integration FARP1 is a previously unreported candidate gene for human proteinuric kidney disease
Collapse
Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany.
| | - Markus Gödel
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Stefan Zschiedrich
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Martin Helmstädter
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Mostafa Zarei
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany
| | - Daniela A Braun
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sebastian Dittrich
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Caroline Pahmeyer
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Patricia Schroder
- Department of Medicine/Nephrology, Hannover Medical School, 30625 Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA
| | - Carolin Teetzen
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - HeonYung Gee
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA; Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ghaleb Daouk
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Pohl
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Elisa Kuhn
- Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany
| | - Victoria Küttner
- Department for Neuroanatomy, University of Freiburg, 79104 Freiburg, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Department of Dermatology, Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany; German Cancer Consortium (DKTK), 79106 Freiburg, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany; Lübeck Institute for Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany
| | - Mario Schiffer
- Department of Medicine/Nephrology, Hannover Medical School, 30625 Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA
| | - Carsten Bergmann
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany
| | - Marcus Krüger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joern Dengjel
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany; Department of Dermatology, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; BIOSS Centre for Biological Signaling Studies, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany.
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
42
|
Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
Collapse
Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
43
|
Abstract
There are now many reports of human kidney organoids generated via the directed differentiation of human pluripotent stem cells (PSCs) based on an existing understanding of mammalian kidney organogenesis. Such kidney organoids potentially represent tractable tools for the study of normal human development and disease with improvements in scale, structure, and functional maturation potentially providing future options for renal regeneration. The utility of such organotypic models, however, will ultimately be determined by their developmental accuracy. While initially inferred from mouse models, recent transcriptional analyses of human fetal kidney have provided greater insight into nephrogenesis. In this review, we discuss how well human kidney organoids model the human fetal kidney and how the remaining differences challenge their utility.
Collapse
Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria 3052, Australia
- Department of Paediatrics, The University of Melbourne, Victoria 3052, Australia
| | - Alexander N Combes
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria 3052, Australia
| |
Collapse
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X. Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Nucleic Acids Res 2019; 46:3864-3877. [PMID: 29294058 PMCID: PMC5934627 DOI: 10.1093/nar/gkx1274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1-4). An alternative splicing of Wt1 can add three additional amino acids-lysine (K), threonine (T) and serine (S)-between ZF3 and ZF4. In the -KTS isoform, ZF2-4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type -KTS isoform ZF1-4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2-4, ZF1 can be positioned continuously in the DNA major groove forming a 'near-cognate' complex. Second, while ZF2-4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys-Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.
Collapse
Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu Zheng
- RGENE, Inc., 953 Indiana Street, San Francisco, CA 94107, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
46
|
Wang X, Adegoke EO, Ma M, Huang F, Zhang H, Adeniran SO, Zheng P, Zhang G. Influence of Wilms' tumor suppressor gene WT1 on bovine Sertoli cells polarity and tight junctions via non-canonical WNT signaling pathway. Theriogenology 2019; 138:84-93. [PMID: 31302435 DOI: 10.1016/j.theriogenology.2019.07.007] [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] [Received: 01/10/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
Sertoli cells (SCs) are polarized epithelial cells and provide a microenvironment for the development of germ cells (GCs). The Wilms' tumor suppressor gene WT1 which support spermatogenesis is expressed explicitly in SCs. This study investigated the effect of WT1 on the polarity and blood-testis barrier (BTB) formation of bovine SCs in order to provide theoretical and practical bases for the spermatogenic process in mammals. In this study, newborn calf SCs were used as research material, and the RNAi technique was used to knockdown the endogenous WT1. The results show that WT1 knockdown did not affect the proliferation ability of SCs, but down-regulated the expression of polarity-associated proteins (Par3, Par6b, and E-cadherin), junction-associated protein (occludin) and inhibits transcription of downstream genes (WNT4, JNK, αPKC, and CDC42) in non-canonical WNT signaling pathway. WT1 also altered ZO-1 and occludin protein distribution. Overexpression of WNT1 did not affect the expression of Par6b, E-cadherin, and occludin, whereas the non-canonical WNT signaling pathway inhibitors wnt-c59, CCG-1423, and GO-6983 down-regulated the expression of Par6b, E-cadherin, and occludin respectively. This study indicates that WT1 mediates the regulation of several proteins involved in bovine SCs polarity maintenance and intercellular tight junctions (TJ) by non-canonical WNT signaling pathway.
Collapse
Affiliation(s)
- Xue Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - E O Adegoke
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Mingjun Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Fushuo Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Han Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - S O Adeniran
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Peng Zheng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Guixue Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China.
| |
Collapse
|
47
|
Torban E, Braun F, Wanner N, Takano T, Goodyer PR, Lennon R, Ronco P, Cybulsky AV, Huber TB. From podocyte biology to novel cures for glomerular disease. Kidney Int 2019; 96:850-861. [PMID: 31420194 DOI: 10.1016/j.kint.2019.05.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 01/20/2023]
Abstract
The podocyte is a key component of the glomerular filtration barrier. Podocyte dysfunction is central to the underlying pathophysiology of many common glomerular diseases, including diabetic nephropathy, glomerulonephritis and genetic forms of nephrotic syndrome. Collectively, these conditions affect millions of people worldwide, and account for the majority of kidney diseases requiring dialysis and transplantation. The 12th International Podocyte Conference was held in Montreal, Canada from May 30 to June 2, 2018. The primary aim of this conference was to bring together nephrologists, clinician scientists, basic scientists and their trainees from all over the world to present their research and to establish networks with the common goal of developing new therapies for glomerular diseases based on the latest advances in podocyte biology. This review briefly highlights recent advances made in understanding podocyte structure and metabolism, experimental systems in which to study podocytes and glomerular disease, disease mediators, genetic and immune origins of glomerulopathies, and the development of novel therapeutic agents to protect podocyte and glomerular injury.
Collapse
Affiliation(s)
- Elena Torban
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada.
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Wanner
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomoko Takano
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - Paul R Goodyer
- Department of Pediatrics, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Pierre Ronco
- Sorbonne University, INSERM UMR_S 1155, and Nephrology and Dialysis Department, Hôpital Tenon, Paris France
| | - Andrey V Cybulsky
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| |
Collapse
|
48
|
Hamatani H, Sakairi T, Ikeuchi H, Kaneko Y, Maeshima A, Nojima Y, Hiromura K. TGF‐β1 alters DNA methylation levels in promoter and enhancer regions of the
WT1
gene in human podocytes. Nephrology (Carlton) 2019; 24:575-584. [DOI: 10.1111/nep.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Hiroko Hamatani
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| | - Toru Sakairi
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| | - Hidekazu Ikeuchi
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| | - Yoriaki Kaneko
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| | - Akito Maeshima
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| | - Yoshihisa Nojima
- Department of Rheumatology and NephrologyJapan Red Cross Maebashi Hospital Maebashi Japan
| | - Keiju Hiromura
- Department of Nephrology and RheumatologyGunma University Graduate School of Medicine Maebashi Japan
| |
Collapse
|
49
|
Dorval G, Kuzmuk V, Gribouval O, Welsh GI, Bierzynska A, Schmitt A, Miserey-Lenkei S, Koziell A, Haq S, Benmerah A, Mollet G, Boyer O, Saleem MA, Antignac C. TBC1D8B Loss-of-Function Mutations Lead to X-Linked Nephrotic Syndrome via Defective Trafficking Pathways. Am J Hum Genet 2019; 104:348-355. [PMID: 30661770 DOI: 10.1016/j.ajhg.2018.12.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) is characterized by high-range proteinuria and most often focal and segmental glomerulosclerosis (FSGS). Identification of mutations in genes causing SRNS has improved our understanding of disease mechanisms and highlighted defects in the podocyte, a highly specialized glomerular epithelial cell, as major factors in disease pathogenesis. By exome sequencing, we identified missense mutations in TBC1D8B in two families with an X-linked early-onset SRNS with FSGS. TBC1D8B is an uncharacterized Rab-GTPase-activating protein likely involved in endocytic and recycling pathways. Immunofluorescence studies revealed TBC1D8B presence in human glomeruli, and affected individual podocytes displayed architectural changes associated with migration defects commonly found in FSGS. In zebrafish we demonstrated that both knockdown and knockout of the unique TBC1D8B ortholog-induced proteinuria and that this phenotype was rescued by human TBC1D8B mRNA injection, but not by either of the two mutated mRNAs. We also showed an interaction between TBC1D8B and Rab11b, a key protein in vesicular recycling in cells. Interestingly, both internalization and recycling processes were dramatically decreased in affected individuals' podocytes and fibroblasts, confirming the crucial role of TBC1D8B in the cellular recycling processes, probably as a Rab11b GTPase-activating protein. Altogether, these results confirmed that pathogenic variations in TBC1D8B are involved in X-linked podocytopathy and points to alterations in recycling processes as a mechanism of SRNS.
Collapse
Affiliation(s)
- Guillaume Dorval
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France
| | - Valeryia Kuzmuk
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, UK
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France
| | - Gavin I Welsh
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, UK
| | - Agnieszka Bierzynska
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, UK
| | - Alain Schmitt
- Inserm, U1016, Institut Cochin, 75014 Paris, France; Cnrs, UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Stéphanie Miserey-Lenkei
- Institut Curie, PSL Research University, CNRS, UMR 144, Molecular Mechanisms of Intracellular Transport, 75005 Paris, France
| | - Ania Koziell
- Department of Children's Nephrology and Urology, Evelina London, London SE1 7EH, UK
| | - Shuman Haq
- Paediatric Nephrology, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France
| | - Géraldine Mollet
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France; Department of Pediatric Nephrology, Reference center for Hereditary Kidney Diseases (MARHEA), Necker Hospital, APHP, 75015 Paris, France
| | - Moin A Saleem
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, UK.
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, INSERM U1163, Paris Descartes University, 75015 Paris, France; Department of Genetics, Reference center for Hereditary Kidney Diseases (MARHEA), Necker Hospital, APHP,75015 Paris, France.
| |
Collapse
|
50
|
Okabe M, Motojima M, Miyazaki Y, Pastan I, Yokoo T, Matsusaka T. Global polysome analysis of normal and injured podocytes. Am J Physiol Renal Physiol 2018; 316:F241-F252. [PMID: 30379099 DOI: 10.1152/ajprenal.00115.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Podocyte injury is a key event for progressive renal failure. We have previously established a mouse model of inducible podocyte injury (NEP25) that progressively develops glomerulosclerosis after immunotoxin injection. We performed polysome analysis of intact and injured podocytes utilizing the NEP25 and RiboTag transgenic mice, in which a hemagglutinin tag is attached to ribosomal protein L22 selectively in podocytes. Podocyte-specific polysomes were successfully obtained by immunoprecipitation with an antihemagglutinin antibody from glomerular homogenate and analyzed using a microarray. Compared with glomerular cells, 353 genes were highly expressed and enriched in podocytes; these included important podocyte genes and also heretofore uncharacterized genes, such as Dach1 and Foxd2. Podocyte injury by immunotoxin induced many genes to be upregulated, including inflammation-related genes despite no infiltration of inflammatory cells in the glomeruli. MafF and Egr-1, which structurally have the potential to antagonize MafB and WT1, respectively, were rapidly and markedly increased in injured podocytes before MafB and WT1 were decreased. We demonstrated that Maff and Egr1 knockdown increased the MafB targets Nphs2 and Ptpro and the WT1 targets Ptpro, Nxph3, and Sulf1, respectively. This indicates that upregulated MafF and Egr-1 may promote deterioration of podocytes by antagonizing MafB and WT1. Our systematic microarray study of the heretofore undescribed behavior of podocyte genes may open new insights into the understanding of podocyte pathophysiology.
Collapse
Affiliation(s)
- Masahiro Okabe
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine , Tokyo , Japan.,Department of Basic Medicine, Tokai University School of Medicine , Isehara , Japan
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine , Isehara , Japan
| | - Yoichi Miyazaki
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine , Tokyo , Japan
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine , Tokyo , Japan
| | - Taiji Matsusaka
- Department of Basic Medicine, Tokai University School of Medicine , Isehara , Japan.,Institute of Medical Science, Tokai University School of Medicine , Isehara , Japan
| |
Collapse
|