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McWhite CD, Sae-Lee W, Yuan Y, Mallam AL, Gort-Freitas NA, Ramundo S, Onishi M, Marcotte EM. Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Mol Syst Biol 2024; 20:933-951. [PMID: 38918600 DOI: 10.1038/s44320-024-00048-3] [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: 02/01/2023] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans, Arabidopsis, and the green alga Chlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where the loss of a domain may accompany complex formation.
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Affiliation(s)
- Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yaning Yuan
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Anna L Mallam
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Silvia Ramundo
- Gregor Mendel Institute of Molecular Plant Biology, 1030, Wien, Austria
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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2
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Bannell TAK, Cockburn JJB. The molecular structure and function of fibrocystin, the key gene product implicated in autosomal recessive polycystic kidney disease (ARPKD). Ann Hum Genet 2024; 88:58-75. [PMID: 37905714 DOI: 10.1111/ahg.12535] [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: 07/11/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Autosomal recessive polycystic kidney disease is an early onset inherited hepatorenal disorder affecting around 1 in 20,000 births with no approved specific therapies. The disease is almost always caused by variations in the polycystic kidney and hepatic disease 1 gene, which encodes fibrocystin (FC), a very large, single-pass transmembrane glycoprotein found in primary cilia, urine and urinary exosomes. By comparison to proteins involved in autosomal dominant PKD, our structural and molecular understanding of FC has lagged far behind such that there are no published experimentally determined structures of any part of the protein. Bioinformatics analyses predict that the ectodomain contains a long chain of immunoglobulin-like plexin-transcription factor domains, a protective antigen 14 domain, a tandem G8-TMEM2 homology region and a sperm protein, enterokinase and agrin domain. Here we review current knowledge on the molecular function of the protein from a structural perspective.
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Affiliation(s)
- Travis A K Bannell
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joseph J B Cockburn
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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3
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Harafuji N, Yang C, Wu M, Thiruvengadam G, Gordish-Dressman H, Thompson RG, Bell PD, Rosenberg AZ, Dafinger C, Liebau MC, Bebok Z, Caldovic L, Guay-Woodford LM. Differential regulation of MYC expression by PKHD1/Pkhd1 in human and mouse kidneys: phenotypic implications for recessive polycystic kidney disease. Front Cell Dev Biol 2023; 11:1270980. [PMID: 38125876 PMCID: PMC10731465 DOI: 10.3389/fcell.2023.1270980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/30/2023] [Indexed: 12/23/2023] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD; MIM#263200) is a severe, hereditary, hepato-renal fibrocystic disorder that leads to early childhood morbidity and mortality. Typical forms of ARPKD are caused by pathogenic variants in the PKHD1 gene, which encodes the fibrocystin/polyductin (FPC) protein. MYC overexpression has been proposed as a driver of renal cystogenesis, but little is known about MYC expression in recessive PKD. In the current study, we provide the first evidence that MYC is overexpressed in kidneys from ARPKD patients and confirm that MYC is upregulated in cystic kidneys from cpk mutant mice. In contrast, renal MYC expression levels were not altered in several Pkhd1 mutant mice that lack a significant cystic kidney phenotype. We leveraged previous observations that the carboxy-terminus of mouse FPC (FPC-CTD) is proteolytically cleaved through Notch-like processing, translocates to the nucleus, and binds to double stranded DNA, to examine whether the FPC-CTD plays a role in regulating MYC/Myc transcription. Using immunofluorescence, reporter gene assays, and ChIP, we demonstrate that both human and mouse FPC-CTD can localize to the nucleus, bind to the MYC/Myc P1 promoter, and activate MYC/Myc expression. Interestingly, we observed species-specific differences in FPC-CTD intracellular trafficking. Furthermore, our informatic analyses revealed limited sequence identity of FPC-CTD across vertebrate phyla and database queries identified temporal differences in PKHD1/Pkhd1 and CYS1/Cys1 expression patterns in mouse and human kidneys. Given that cystin, the Cys1 gene product, is a negative regulator of Myc transcription, these temporal differences in gene expression could contribute to the relative renoprotection from cystogenesis in Pkhd1-deficient mice. Taken together, our findings provide new mechanistic insights into differential mFPC-CTD and hFPC-CTD regulation of MYC expression in renal epithelial cells, which may illuminate the basis for the phenotypic disparities between human patients with PKHD1 pathogenic variants and Pkhd1-mutant mice.
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Affiliation(s)
- Naoe Harafuji
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Chaozhe Yang
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Maoqing Wu
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Girija Thiruvengadam
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | | | - R. Griffin Thompson
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - P. Darwin Bell
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Claudia Dafinger
- Department of Pediatrics and Center for Molecular Medicine, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Max C. Liebau
- Department of Pediatrics, Center for Family Health, Center for Rare Diseases and Center for Molecular Medicine, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Zsuzsanna Bebok
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States
- Department of Genomics and Precision Medicine, School of Medical and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lisa M. Guay-Woodford
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States
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4
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Walker RV, Yao Q, Xu H, Maranto A, Swaney KF, Ramachandran S, Li R, Cassina L, Polster BM, Outeda P, Boletta A, Watnick T, Qian F. Fibrocystin/Polyductin releases a C-terminal fragment that translocates into mitochondria and suppresses cystogenesis. Nat Commun 2023; 14:6513. [PMID: 37845212 PMCID: PMC10579373 DOI: 10.1038/s41467-023-42196-4] [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: 08/31/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Fibrocystin/Polyductin (FPC), encoded by PKHD1, is associated with autosomal recessive polycystic kidney disease (ARPKD), yet its precise role in cystogenesis remains unclear. Here we show that FPC undergoes complex proteolytic processing in developing kidneys, generating three soluble C-terminal fragments (ICDs). Notably, ICD15, contains a novel mitochondrial targeting sequence at its N-terminus, facilitating its translocation into mitochondria. This enhances mitochondrial respiration in renal epithelial cells, partially restoring impaired mitochondrial function caused by FPC loss. FPC inactivation leads to abnormal ultrastructural morphology of mitochondria in kidney tubules without cyst formation. Moreover, FPC inactivation significantly exacerbates renal cystogenesis and triggers severe pancreatic cystogenesis in a Pkd1 mouse mutant Pkd1V/V in which cleavage of Pkd1-encoded Polycystin-1 at the GPCR Proteolysis Site is blocked. Deleting ICD15 enhances renal cystogenesis without inducing pancreatic cysts in Pkd1V/V mice. These findings reveal a direct link between FPC and a mitochondrial pathway through ICD15 cleavage, crucial for cystogenesis mechanisms.
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Affiliation(s)
- Rebecca V Walker
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qin Yao
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Hangxue Xu
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anthony Maranto
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kristen F Swaney
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sreekumar Ramachandran
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rong Li
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore
| | - Laura Cassina
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma, and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patricia Outeda
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alessandra Boletta
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Terry Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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5
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Martinez Lyons A, Boulter L. NOTCH signalling - a core regulator of bile duct disease? Dis Model Mech 2023; 16:dmm050231. [PMID: 37605966 PMCID: PMC10461466 DOI: 10.1242/dmm.050231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023] Open
Abstract
The Notch signalling pathway is an evolutionarily conserved mechanism of cell-cell communication that mediates cellular proliferation, fate determination and maintenance of stem/progenitor cell populations across tissues. Although it was originally identified as a critical regulator of embryonic liver development, NOTCH signalling activation has been associated with the pathogenesis of a number of paediatric and adult liver diseases. It remains unclear, however, what role NOTCH actually plays in these pathophysiological processes and whether NOTCH activity represents the reactivation of a conserved developmental programme that is essential for adult tissue repair. In this Review, we explore the concepts that NOTCH signalling reactivation in the biliary epithelium is a reiterative and essential response to bile duct damage and that, in disease contexts in which biliary epithelial cells need to be regenerated, NOTCH signalling supports ductular regrowth. Furthermore, we evaluate the recent literature on NOTCH signalling as a critical factor in progenitor-mediated hepatocyte regeneration, which indicates that the mitogenic role for NOTCH signalling in biliary epithelial cell proliferation has also been co-opted to support other forms of epithelial regeneration in the adult liver.
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Affiliation(s)
| | - Luke Boulter
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
- CRUK Scottish Centre, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
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6
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Clearman KR, Haycraft CJ, Croyle MJ, Collawn JF, Yoder BK. Functions of the primary cilium in the kidney and its connection with renal diseases. Curr Top Dev Biol 2023; 155:39-94. [PMID: 38043952 DOI: 10.1016/bs.ctdb.2023.07.001] [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] [Indexed: 12/05/2023]
Abstract
The nonmotile primary cilium is a sensory structure found on most mammalian cell types that integrates multiple signaling pathways involved in tissue development and postnatal function. As such, mutations disrupting cilia activities cause a group of disorders referred to as ciliopathies. These disorders exhibit a wide spectrum of phenotypes impacting nearly every tissue. In the kidney, primary cilia dysfunction caused by mutations in polycystin 1 (Pkd1), polycystin 2 (Pkd2), or polycystic kidney and hepatic disease 1 (Pkhd1), result in polycystic kidney disease (PKD), a progressive disorder causing renal functional decline and end-stage renal disease. PKD affects nearly 1 in 1000 individuals and as there is no cure for PKD, patients frequently require dialysis or renal transplantation. Pkd1, Pkd2, and Pkhd1 encode membrane proteins that all localize in the cilium. Pkd1 and Pkd2 function as a nonselective cation channel complex while Pkhd1 protein function remains uncertain. Data indicate that the cilium may act as a mechanosensor to detect fluid movement through renal tubules. Other functions proposed for the cilium and PKD proteins in cyst development involve regulation of cell cycle and oriented division, regulation of renal inflammation and repair processes, maintenance of epithelial cell differentiation, and regulation of mitochondrial structure and metabolism. However, how loss of cilia or cilia function leads to cyst development remains elusive. Studies directed at understanding the roles of Pkd1, Pkd2, and Pkhd1 in the cilium and other locations within the cell will be important for developing therapeutic strategies to slow cyst progression.
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Affiliation(s)
- Kelsey R Clearman
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J Haycraft
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J Croyle
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.
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7
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Zhang YJ, Yang C, Wang W, Harafuji N, Stasiak P, Bell PD, Caldovic L, Sztul E, Guay-Woodford LM, Bebok Z. Cystin is required for maintaining fibrocystin (FPC) levels and safeguarding proteome integrity in mouse renal epithelial cells: A mechanistic connection between the kidney defects in cpk mice and human ARPKD. FASEB J 2023; 37:e23008. [PMID: 37318790 DOI: 10.1096/fj.202300100r] [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: 01/20/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is caused primarily by mutations in PKHD1, encoding fibrocystin (FPC), but Pkhd1 mutant mice failed to reproduce the human phenotype. In contrast, the renal lesion in congenital polycystic kidney (cpk) mice, with a mutation in Cys1 and cystin protein loss, closely phenocopies ARPKD. Although the nonhomologous mutation diminished the translational relevance of the cpk model, recent identification of patients with CYS1 mutations and ARPKD prompted the investigations described herein. We examined cystin and FPC expression in mouse models (cpk, rescued-cpk (r-cpk), Pkhd1 mutants) and mouse cortical collecting duct (CCD) cell lines (wild type (wt), cpk). We found that cystin deficiency caused FPC loss in both cpk kidneys and CCD cells. FPC levels increased in r-cpk kidneys and siRNA of Cys1 in wt cells reduced FPC. However, FPC deficiency in Pkhd1 mutants did not affect cystin levels. Cystin deficiency and associated FPC loss impacted the architecture of the primary cilium, but not ciliogenesis. No reduction in Pkhd1 mRNA levels in cpk kidneys and CCD cells suggested posttranslational FPC loss. Studies of cellular protein degradation systems suggested selective autophagy as a mechanism. In support of the previously described function of FPC in E3 ubiquitin ligase complexes, we demonstrated reduced polyubiquitination and elevated levels of functional epithelial sodium channel in cpk cells. Therefore, our studies expand the function of cystin in mice to include inhibition of Myc expression via interaction with necdin and maintenance of FPC as functional component of the NEDD4 E3 ligase complexes. Loss of FPC from E3 ligases may alter the cellular proteome, contributing to cystogenesis through multiple, yet to be defined, mechanisms.
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Affiliation(s)
- Yiming J Zhang
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Chaozhe Yang
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Wei Wang
- Cystic Fibrosis Research Center, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Naoe Harafuji
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Piotr Stasiak
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - P Darwin Bell
- Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ljubica Caldovic
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Elizabeth Sztul
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Lisa M Guay-Woodford
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Zsuzsanna Bebok
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
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8
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Heidari M, Gharshasbi H, Isazadeh A, Soleyman-Nejad M, Taskhiri MH, Shapouri J, Bolhassani M, Sadighi N, Heidari M. Identification of Two Novel Mutations in PKHD1 Gene from Two Families with Polycystic Kidney Disease by Whole Exome Sequencing. Curr Genomics 2021; 22:232-236. [PMID: 34975292 PMCID: PMC8640847 DOI: 10.2174/1389202922666210219111810] [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: 12/27/2019] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 11/25/2022] Open
Abstract
Background Polycystic kidney disease (PKD) is an autosomal recessive disorder resulting from mutations in the PKHD1 gene on chromosome 6 (6p12), a large gene spanning 470 kb of genomic DNA. Objective The aim of the present study was to report newly identified mutations in the PKHD1 gene in two Iranian families with PKD. Materials and Methods Genetic alterations of a 3-month-old boy and a 27-year-old girl with PKD were evaluated using whole-exome sequencing. The PCR direct sequencing was performed to analyse the co-segregation of the variants with the disease in the family. Finally, the molecular function of the identified novel mutations was evaluated by in silico study. Results In the 3 month-old boy, a novel homozygous frameshift mutation was detected in the PKHD1 gene, which can cause PKD. Moreover, we identified three novel heterozygous missense mutations in ATIC, VPS13B, and TP53RK genes. In the 27-year-old woman, with two recurrent abortions history and two infant mortalities at early weeks due to metabolic and/or renal disease, we detected a novel missense mutation on PKHD1 gene and a novel mutation in ETFDH gene. Conclusion In general, we have identified two novel mutations in the PKHD1 gene. These molecular findings can help accurately correlate genotype and phenotype in families with such disease in order to reduce patient births through preoperative genetic diagnosis or better management of disorders.
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Affiliation(s)
- Masoud Heidari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Hamid Gharshasbi
- Department of Genetics, Tabriz Branch Islamic Azad University, Tabriz, Iran
| | - Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Javad Shapouri
- Pediatric Clinical Research and Development Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Nahid Sadighi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mansour Heidari
- Department of Medical Genetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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9
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Molecular Pathophysiology of Autosomal Recessive Polycystic Kidney Disease. Int J Mol Sci 2021; 22:ijms22126523. [PMID: 34204582 PMCID: PMC8235086 DOI: 10.3390/ijms22126523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a rare disorder and one of the most severe forms of polycystic kidney disease, leading to end-stage renal disease (ESRD) in childhood. PKHD1 is the gene that is responsible for the vast majority of ARPKD. However, some cases have been related to a new gene that was recently identified (DZIP1L gene), as well as several ciliary genes that can mimic a ARPKD-like phenotypic spectrum. In addition, a number of molecular pathways involved in the ARPKD pathogenesis and progression were elucidated using cellular and animal models. However, the function of the ARPKD proteins and the molecular mechanism of the disease currently remain incompletely understood. Here, we review the clinics, treatment, genetics, and molecular basis of ARPKD, highlighting the most recent findings in the field.
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10
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Lasagni A, Cadamuro M, Morana G, Fabris L, Strazzabosco M. Fibrocystic liver disease: novel concepts and translational perspectives. Transl Gastroenterol Hepatol 2021; 6:26. [PMID: 33824930 DOI: 10.21037/tgh-2020-04] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Fibrocystic liver diseases (FLDs) comprise a heterogeneous group of rare diseases of the biliary tree, having in common an abnormal development of the embryonic ductal plate caused by genetically-determined dysfunctions of proteins expressed in the primary cilia of cholangiocytes (and therefore grouped among the "ciliopathies"). The ductal dysgenesis may affect the biliary system at multiple levels, from the small intrahepatic bile ducts [congenital hepatic fibrosis (CHF)], to the larger intrahepatic bile ducts [Caroli disease (CD), or Caroli syndrome (CS), when CD coexists with CHF], leading to biliary microhamartomas and segmental bile duct dilations. Biliary changes are accompanied by progressive deposition of abundant peribiliary fibrosis. Peribiliary fibrosis and biliary cysts are the fundamental lesions of FLDs and are responsible for the main clinical manifestations, such as portal hypertension, recurrent cholangitis, cholestasis, sepsis and eventually cholangiocarcinoma. Furthermore, FLDs often associate with a spectrum of disorders affecting primarily the kidney. Among them, the autosomal recessive polycystic kidney disease (ARPKD) is the most frequent, and the renal function impairment is central in disease progression. CHF, CD/CS, and ARPKD are caused by a number of mutations in polycystic kidney hepatic disease 1 (PKHD1), a gene that encodes for fibrocystin/polyductin, a protein of unclear function, but supposedly involved in planar cell polarity and other fundamental cell functions. Targeted medical therapy is not available yet and thus the current treatment aims at controlling the complications. Interventional radiology or surgical treatments, including liver transplantation, are used in selected cases.
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Affiliation(s)
- Alberto Lasagni
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Giovanni Morana
- Division of Radiology, Treviso Regional Hospital, Treviso, Italy
| | - Luca Fabris
- Department of Molecular Medicine, University of Padua, Padua, Italy.,Liver Center and Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Mario Strazzabosco
- Liver Center and Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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11
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Dafinger C, Mandel AM, Braun A, Göbel H, Burgmaier K, Massella L, Mastrangelo A, Dötsch J, Benzing T, Weimbs T, Schermer B, Liebau MC. The carboxy-terminus of the human ARPKD protein fibrocystin can control STAT3 signalling by regulating SRC-activation. J Cell Mol Med 2020; 24:14633-14638. [PMID: 33112055 PMCID: PMC7754027 DOI: 10.1111/jcmm.16014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 12/04/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is mainly caused by variants in the PKHD1 gene, encoding fibrocystin (FC), a large transmembrane protein of incompletely understood cellular function. Here, we show that a C‐terminal fragment of human FC can suppress a signalling module of the kinase SRC and signal transducer and activator of transcription 3 (STAT3). Consistently, we identified truncating genetic variants specifically affecting the cytoplasmic tail in ARPKD patients, found SRC and the cytoplasmic tail of fibrocystin in a joint dynamic protein complex and observed increased activation of both SRC and STAT3 in cyst‐lining renal epithelial cells of ARPKD patients.
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Affiliation(s)
- Claudia Dafinger
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Amrei M Mandel
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alina Braun
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Heike Göbel
- Institute of Pathology, Faculty of Medicine, University Hospital Cologne and University of Cologne, Cologne, Germany
| | - Kathrin Burgmaier
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Laura Massella
- Nephrology and Dialysis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Mastrangelo
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Jörg Dötsch
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Thomas Weimbs
- Molecular, Cellular, and Developmental Biology, and Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Max C Liebau
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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12
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Molinari E, Srivastava S, Dewhurst RM, Sayer JA. Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles. BMC Nephrol 2020; 21:435. [PMID: 33059616 PMCID: PMC7559414 DOI: 10.1186/s12882-020-02094-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background PKHD1 is the main genetic cause of autosomal recessive polycystic kidney disease (ARPKD), a hereditary hepato-renal fibrocystic disorder which is the most important cause of end-stage renal disease during early childhood. ARPKD can also present in adulthood with milder phenotypes. In this study, we describe a 24-year-old woman with atypical polycystic kidney, no family history of renal disease and no obvious extra-renal manifestations who was referred for genetic investigation. Methods We used a combination of next generation sequencing, Sanger sequencing and RNA and microscopy studies performed on urine-derived renal epithelial cells (URECs) to provide a genetic diagnosis of ARPKD. Results A next generation sequencing panel of cystic ciliopathy genes allowed the identification of two heterozygous sequence changes in PKHD1 (c.6900C > T; p.(Asn2300=) and c.7964A > C; p.(His2655Pro)). The pathogenicity of the synonymous PKHD1 variant is not clear and requires RNA studies, which cannot be carried out efficiently on RNA extracted from proband blood, due to the low expression levels of PKHD1 in lymphocytes. Using URECs as a source of kidney-specific RNA, we show that PKHD1 is alternatively spliced around exon 43, both in control and proband URECs. The variant p.(Asn2300=) shifts the expression ratio in favour of a shorter, out-of-frame transcript. To further study the phenotypic consequence of these variants, we investigated the ciliary phenotype of patient URECs, which were abnormally elongated and presented multiple blebs along the axoneme. Conclusions We confirm the power of URECs as a tool for functional studies on candidate variants in inherited renal disease, especially when the expression of the gene of interest is restricted to the kidney and we describe, for the first time, ciliary abnormalities in ARPKD patient cells.
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Affiliation(s)
- Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Shalabh Srivastava
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rebecca M Dewhurst
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. .,Renal Services, The Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK. .,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK.
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13
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Haumann S, Müller RU, Liebau MC. Metabolic Changes in Polycystic Kidney Disease as a Potential Target for Systemic Treatment. Int J Mol Sci 2020; 21:ijms21176093. [PMID: 32847032 PMCID: PMC7503958 DOI: 10.3390/ijms21176093] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/16/2022] Open
Abstract
Autosomal recessive and autosomal dominant polycystic kidney disease (ARPKD, ADPKD) are systemic disorders with pronounced hepatorenal phenotypes. While the main underlying genetic causes of both ARPKD and ADPKD have been well-known for years, the exact molecular mechanisms resulting in the observed clinical phenotypes in the different organs, remain incompletely understood. Recent research has identified cellular metabolic changes in PKD. These findings are of major relevance as there may be an immediate translation into clinical trials and potentially clinical practice. Here, we review important results in the field regarding metabolic changes in PKD and their modulation as a potential target of systemic treatment.
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Affiliation(s)
- Sophie Haumann
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany;
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany;
- CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, 50931 Cologne, Germany
| | - Max C. Liebau
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany;
- Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Correspondence: ; Tel.: +49-221-478-4359
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14
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Fibrocystin Is Essential to Cellular Control of Adhesion and Epithelial Morphogenesis. Int J Mol Sci 2020; 21:ijms21145140. [PMID: 32698519 PMCID: PMC7404311 DOI: 10.3390/ijms21145140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Mutations of the Pkhd1 gene cause autosomal recessive polycystic kidney disease (ARPKD). Pkhd1 encodes fibrocystin/polyductin (FPC), a ciliary type I membrane protein of largely unknown function, suggested to affect adhesion signaling of cells. Contributions of epithelial cell adhesion and contractility to the disease process are elusive. Here, we link loss of FPC to defective epithelial morphogenesis in 3D cell culture and altered cell contact formation. We study Pkhd1-silenced Madin-Darby Canine Kidney II (MDCKII) cells using an epithelial morphogenesis assay based on micropatterned glass coverslips. The assay allows analysis of cell adhesion, polarity and lumen formation of epithelial spheroids. Pkhd1 silencing critically affects the initial phase of the morphogenesis assay, leading to a reduction of correctly polarized spheroids by two thirds. Defects are characterized by altered cell adhesion and centrosome positioning of FPC-deficient cells in their 1-/2-cell stages. When myosin II inhibitor is applied to reduce cellular tension during the critical early phase of the assay, Pkhd1 silencing no longer inhibits formation of correctly polarized epithelia. We propose that altered sensing and cell interaction of FPC-deficient epithelial cells promote progressive epithelial defects in ARPKD.
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15
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Gallagher AR, Somlo S. Loss of Cilia Does Not Slow Liver Disease Progression in Mouse Models of Autosomal Recessive Polycystic Kidney Disease. ACTA ACUST UNITED AC 2020; 1:962-968. [PMID: 33829210 DOI: 10.34067/kid.0001022019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anna Rachel Gallagher
- Department of Internal Medicine (Nephrology), Yale School of Medicine, New Haven, Connecticut
| | - Stefan Somlo
- Department of Internal Medicine (Nephrology), Yale School of Medicine, New Haven, Connecticut.,Department of Genetics, Yale School of Medicine, New Haven, Connecticut
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16
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Güner G, Lichtenthaler SF. The substrate repertoire of γ-secretase/presenilin. Semin Cell Dev Biol 2020; 105:27-42. [PMID: 32616437 DOI: 10.1016/j.semcdb.2020.05.019] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 12/09/2022]
Abstract
The intramembrane protease γ-secretase is a hetero-tetrameric protein complex with presenilin as the catalytic subunit and cleaves its membrane protein substrates within their single transmembrane domains. γ-Secretase is well known for its role in Notch signalling and in Alzheimer's disease, where it catalyzes the formation of the pathogenic amyloid β (Aβ) peptide. However, in the 21 years since its discovery many more substrates and substrate candidates of γ-secretase were identified. Although the physiological relevance of the cleavage of many substrates remains to be studied in more detail, the substrates demonstrate a broad role for γ-secretase in embryonic development, adult tissue homeostasis, signal transduction and protein degradation. Consequently, chronic γ-secretase inhibition may cause significant side effects due to inhibition of cleavage of multiple substrates. This review provides a list of 149 γ-secretase substrates identified to date and highlights by which expeirmental approach substrate cleavage was validated. Additionally, the review lists the cleavage sites where they are known and discusses the functional implications of γ-secretase cleavage with a focus on substrates identified in the recent past, such as CHL1, TREM2 and TNFR1. A comparative analysis demonstrates that γ-secretase substrates mostly have a long extracellular domain and require ectodomain shedding before γ-secretase cleavage, but that γ-secretase is also able to cleave naturally short substrates, such as the B cell maturation antigen. Taken together, the list of substrates provides a resource that may help in the future development of drugs inhibiting or modulating γ-secretase activity in a substrate-specific manner.
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Affiliation(s)
- Gökhan Güner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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17
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Cilia and polycystic kidney disease. Semin Cell Dev Biol 2020; 110:139-148. [PMID: 32475690 DOI: 10.1016/j.semcdb.2020.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 11/20/2022]
Abstract
Polycystic kidney disease (PKD), comprising autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD), is characterized by incessant cyst formation in the kidney and liver. ADPKD and ARPKD represent the leading genetic causes of renal disease in adults and children, respectively. ADPKD is caused by mutations in PKD1 encoding polycystin1 (PC1) and PKD2 encoding polycystin 2 (PC2). PC1/2 are multi-pass transmembrane proteins that form a complex localized in the primary cilium. Predominant ARPKD cases are caused by mutations in polycystic kidney and hepatic disease 1 (PKHD1) gene that encodes the Fibrocystin/Polyductin (FPC) protein, whereas a small subset of cases are caused by mutations in DAZ interacting zinc finger protein 1 like (DZIP1L) gene. FPC is a type I transmembrane protein, localizing to the cilium and basal body, in addition to other compartments, and DZIP1L encodes a transition zone/basal body protein. Apparently, PC1/2 and FPC are signaling molecules, while the mechanism that cilia employ to govern renal tubule morphology and prevent cyst formation is unclear. Nonetheless, recent genetic and biochemical studies offer a glimpse of putative physiological malfunctions and the pathomechanisms underlying both disease entities. In this review, I summarize the results of genetic studies that deduced the function of PC1/2 on cilia and of cilia themselves in cyst formation in ADPKD, and I discuss studies regarding regulation of polycystin biogenesis and cilia trafficking. I also summarize the synergistic genetic interactions between Pkd1 and Pkhd1, and the unique tissue patterning event controlled by FPC, but not PC1. Interestingly, while DZIP1L mutations generate compromised PC1/2 cilia expression, FPC deficiency does not affect PC1/2 biogenesis and ciliary localization, indicating that divergent mechanisms could lead to cyst formation in ARPKD. I conclude by outlining promising areas for future PKD research and highlight rationales for potential therapeutic interventions for PKD treatment.
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18
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Ta CM, Vien TN, Ng LCT, DeCaen PG. Structure and function of polycystin channels in primary cilia. Cell Signal 2020; 72:109626. [PMID: 32251715 DOI: 10.1016/j.cellsig.2020.109626] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
Variants in genes which encode for polycystin-1 and polycystin-2 cause most forms of autosomal dominant polycystic disease (ADPKD). Despite our strong understanding of the genetic determinants of ADPKD, we do not understand the structural features which govern the function of polycystins at the molecular level, nor do we understand the impact of most disease-causing variants on the conformational state of these proteins. These questions have remained elusive because polycystins localize to several organelle membranes, including the primary cilia. Primary cilia are microtubule based organelles which function as cellular antennae. Polycystin-2 and related polycystin-2 L1 are members of the transient receptor potential (TRP) ion channel family, and form distinct ion channels in the primary cilia of disparate cell types which can be directly measured. Polycystin-1 has both ion channel and adhesion G-protein coupled receptor (GPCR) features-but its role in forming a channel complex or as a channel subunit chaperone is undetermined. Nonetheless, recent polycystin structural determination by cryo-EM has provided a molecular template to understand their biophysical regulation and the impact of disease-causing variants. We will review these advances and discuss hypotheses regarding the regulation of polycystin channel opening by their structural domains within the context of the primary cilia.
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Affiliation(s)
- Chau My Ta
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, IL 60611, USA
| | - Thuy N Vien
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, IL 60611, USA
| | - Leo C T Ng
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, IL 60611, USA
| | - Paul G DeCaen
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, IL 60611, USA.
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19
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Lea WA, McGreal K, Sharma M, Parnell SC, Zelenchuk L, Charlesworth MC, Madden BJ, Johnson KL, McCormick DJ, Hogan MC, Ward CJ. Analysis of the polycystin complex (PCC) in human urinary exosome-like vesicles (ELVs). Sci Rep 2020; 10:1500. [PMID: 32001768 PMCID: PMC6992733 DOI: 10.1038/s41598-020-58087-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 01/05/2020] [Indexed: 12/21/2022] Open
Abstract
The polycystin-1 (PC1), polycystin-2 (PC2) and fibrocystin proteins, the respective products of the PKD1, PKD2 and PKHD1 genes, are abundant in urinary exosome-like vesicles (ELVs) where they form the polycystin complex (PCC). ELVs are 100 nm diameter membrane vesicles shed into the urine by the cells lining the nephron. Using MS/MS analysis of ELVs from individuals with PKD1 mutations and controls, we show that in addition to the well-described GPS/GAIN cleavage event in PC1 at 3048 aa and the proprotein convertase cleavage (PPC) event in fibrocystin at 3616 aa, there are multiple other cleavage events in these proteins. The C-terminal 11 transmembrane portion of PC1 undergoes three cleavage events in vivo. The absence of peptides from the C-terminal cytoplasmic tail of fibrocystin implies a cleavage event close to its single TM domain prior to loading onto the ELVs. There is also evidence that the C-terminal tail of PC2 is also cleaved in ELVs. Native gel analysis of the PCC shows that the entire complex is > 2 MDa in size and that N-terminal GPS/GAIN cleaved PC1 and PPC cleaved fibrocystin ectodomains can be released under non-reducing conditions and resolve at 300 kDa. This paper shows that the three major human cystogene proteins are detectable in human urinary ELVs and that all three undergo post-translational proteolytic processing. Human urinary ELVs may be a useful source of material in the search for proteins that interact with the PCC.
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Affiliation(s)
- Wendy A Lea
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Kerri McGreal
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Madhulika Sharma
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Stephen C Parnell
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Lesya Zelenchuk
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - M Cristine Charlesworth
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Benjamin J Madden
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Kenneth L Johnson
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Daniel J McCormick
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Marie C Hogan
- Division of Nephrology, Department of Internal Medicine, Mayo Clinic, Rochester, USA
| | - Christopher J Ward
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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20
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Olson RJ, Hopp K, Wells H, Smith JM, Furtado J, Constans MM, Escobar DL, Geurts AM, Torres VE, Harris PC. Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. J Am Soc Nephrol 2019; 30:2113-2127. [PMID: 31427367 PMCID: PMC6830782 DOI: 10.1681/asn.2019020150] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocystin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD's mild phenotype in murine models versus in humans has hampered investigating its pathogenesis. METHODS To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. RESULTS The genetic interaction was synergistic in both species, with digenic animals exhibiting phenotypes of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction between Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached. Pkhd1 loss did not alter expression, maturation, or localization of the ADPKD polycystin proteins, with no interaction detected between the ARPKD FPC protein and polycystins. RNA-seq analysis in the digenic and monogenic mouse models highlighted the ciliary compartment as a common dysregulated target, with enhanced ciliary expression and length changes in the digenic models. CONCLUSIONS These data indicate that FPC and the polycystins work independently, with separate disease-causing thresholds; however, a combined protein threshold triggers the synergistic, cystogenic response because of enhanced dysregulation of primary cilia. These insights into pathogenesis highlight possible common therapeutic targets.
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Affiliation(s)
- Rory J Olson
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota
| | - Katharina Hopp
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, Colorado
| | - Harrison Wells
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Jessica M Smith
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Jessica Furtado
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota
- Biological and Biomedical Sciences Program, Yale University School of Medicine, New Haven, Connecticut; and
| | - Megan M Constans
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Diana L Escobar
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Aron M Geurts
- Gene Editing Rat Resource Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota;
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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21
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Fabris L, Fiorotto R, Spirli C, Cadamuro M, Mariotti V, Perugorria MJ, Banales JM, Strazzabosco M. Pathobiology of inherited biliary diseases: a roadmap to understand acquired liver diseases. Nat Rev Gastroenterol Hepatol 2019; 16:497-511. [PMID: 31165788 PMCID: PMC6661007 DOI: 10.1038/s41575-019-0156-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bile duct epithelial cells, also known as cholangiocytes, regulate the composition of bile and its flow. Acquired, congenital and genetic dysfunctions in these cells give rise to a set of diverse and complex diseases, often of unknown aetiology, called cholangiopathies. New knowledge has been steadily acquired about genetic and congenital cholangiopathies, and this has led to a better understanding of the mechanisms of acquired cholangiopathies. This Review focuses on findings from studies on Alagille syndrome, polycystic liver diseases, fibropolycystic liver diseases (Caroli disease and congenital hepatic fibrosis) and cystic fibrosis-related liver disease. In particular, knowledge on the role of Notch signalling in biliary repair and tubulogenesis has been advanced by work on Alagille syndrome, and investigations in polycystic liver diseases have highlighted the role of primary cilia in biliary pathophysiology and the concept of biliary angiogenic signalling and its role in cyst growth and biliary repair. In fibropolycystic liver disease, research has shown that loss of fibrocystin generates a signalling cascade that increases β-catenin signalling, activates the NOD-, LRR- and pyrin domain-containing 3 inflammasome, and promotes production of IL-1β and other chemokines that attract macrophages and orchestrate the process of pericystic and portal fibrosis, which are the main mechanisms of progression in cholangiopathies. In cystic fibrosis-related liver disease, lack of cystic fibrosis transmembrane conductance regulator increases the sensitivity of epithelial Toll-like receptor 4 that sustains the secretion of nuclear factor-κB-dependent cytokines and peribiliary inflammation in response to gut-derived products, providing a model for primary sclerosing cholangitis. These signalling mechanisms may be targeted therapeutically and they offer a possibility for the development of novel treatments for acquired cholangiopathies.
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Affiliation(s)
- Luca Fabris
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Romina Fiorotto
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
| | - Carlo Spirli
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
| | | | - Valeria Mariotti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Mario Strazzabosco
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA.
- Department of Molecular Medicine, University of Padova, Padova, Italy.
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22
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Abstract
Cystic kidneys are common causes of end-stage renal disease, both in children and in adults. Autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD) are cilia-related disorders and the two main forms of monogenic cystic kidney diseases. ADPKD is a common disease that mostly presents in adults, whereas ARPKD is a rarer and often more severe form of polycystic kidney disease (PKD) that usually presents perinatally or in early childhood. Cell biological and clinical research approaches have expanded our knowledge of the pathogenesis of ADPKD and ARPKD and revealed some mechanistic overlap between them. A reduced 'dosage' of PKD proteins is thought to disturb cell homeostasis and converging signalling pathways, such as Ca2+, cAMP, mechanistic target of rapamycin, WNT, vascular endothelial growth factor and Hippo signalling, and could explain the more severe clinical course in some patients with PKD. Genetic diagnosis might benefit families and improve the clinical management of patients, which might be enhanced even further with emerging therapeutic options. However, many important questions about the pathogenesis of PKD remain. In this Primer, we provide an overview of the current knowledge of PKD and its treatment.
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Affiliation(s)
- Carsten Bergmann
- Department of Medicine, University Hospital Freiburg, Freiburg, Germany.
| | - Lisa M. Guay-Woodford
- Center for Translational Science, Children’s National Health System, Washington, DC, USA
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Shigeo Horie
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Dorien J. M. Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Vicente E. Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
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23
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Lea WA, Ward CJ. A new epitope-tagged Pkhd1 allele sheds light on fibrocystin signaling. Kidney Int 2018; 92:1041-1043. [PMID: 29055424 DOI: 10.1016/j.kint.2017.05.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 10/18/2022]
Abstract
In this issue of Kidney International, Outeda et al. present a new epitope-tagged allele of murine Pkhd1 that allows the monitoring of functional fibrocystin in vivo from the extreme C-terminus of the molecule. This work also shows that the removal of two-thirds of the intracellular tail of fibrocystin does not result in cystogenesis in either the liver or kidney, with major implications for our understanding of Pkhd1 function and polycystic kidney disease in general.
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Affiliation(s)
- Wendy A Lea
- Department of Nephrology, The Jared Grantham Kidney Institute at the University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Christopher J Ward
- Department of Nephrology, The Jared Grantham Kidney Institute at the University of Kansas Medical Center, Kansas City, Kansas, USA.
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24
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Janssens P, Weydert C, De Rechter S, Wissing KM, Liebau MC, Mekahli D. Expanding the role of vasopressin antagonism in polycystic kidney diseases: From adults to children? Pediatr Nephrol 2018; 33:395-408. [PMID: 28455745 DOI: 10.1007/s00467-017-3672-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/21/2017] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
Abstract
Polycystic kidney disease (PKD) encompasses a group of genetic disorders that are common causes of renal failure. The two classic forms of PKD are autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD). Despite their clinical differences, ARPKD and ADPKD share many similarities. Altered intracellular Ca2+ and increased cyclic adenosine monophosphate (cAMP) concentrations have repetitively been described as central anomalies that may alter signaling pathways leading to cyst formation. The vasopressin V2 receptor (V2R) antagonist tolvaptan lowers cAMP in cystic tissues and slows renal cystic progression and kidney function decline when given over 3 years in adult ADPKD patients. Tolvaptan is currently approved for the treatment of rapidly progressive disease in adult ADPKD patients. On the occasion of the recent initiation of a clinical trial with tolvaptan in pediatric ADPKD patients, we aim to describe the most important aspects in the literature regarding the AVP-cAMP axis and the clinical use of tolvaptan in PKD.
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Affiliation(s)
- Peter Janssens
- Laboratory of Pediatrics, University Hospitals Leuven, Leuven, Belgium. .,Department of Nephrology, University Hospitals Brussel, Brussel, Belgium.
| | - Caroline Weydert
- Laboratory of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Stephanie De Rechter
- Laboratory of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Department of Pediatric Nephrology, University Hospitals Leuven, Leuven, Belgium
| | | | - Max Christoph Liebau
- Pediatric Nephrology, Department of Pediatrics and Center for Molecular Medicine, University Hospital of Cologne, Cologne, Germany.,Department II of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Djalila Mekahli
- Laboratory of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Department of Pediatric Nephrology, University Hospitals Leuven, Leuven, Belgium
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25
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Abstract
INTRODUCTION Polycystic kidney disease (PKD) is clinically and genetically heterogeneous and constitutes the most common heritable kidney disease. Most patients are affected by the autosomal dominant form (ADPKD) which generally is an adult-onset multisystem disorder. By contrast, the rarer recessive form ARPKD usually already manifests perinatally or in childhood. In some patients, however, ADPKD and ARPKD can phenotypically overlap with early manifestation in ADPKD and only late onset in ARPKD. Progressive fibrocystic renal changes are often accompanied by severe hepatobiliary changes or other extrarenal abnormalities. Areas covered: A reduced dosage of disease proteins disturbs cell homeostasis and explains a more severe clinical course in some PKD patients. Cystic kidney disease is also a common feature of other ciliopathies and genetic syndromes. Genetic diagnosis may guide clinical management and helps to avoid invasive measures and to detect renal and extrarenal comorbidities early in the clinical course. Expert Commentary: The broad phenotypic and genetic heterogeneity of cystic and polycystic kidney diseases make NGS a particularly powerful approach. Interpretation of data becomes the challenge and bench and bedside benefit from digitized multidisciplinary interrelationships.
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Affiliation(s)
- Carsten Bergmann
- a Center for Human Genetics , Bioscientia , Ingelheim , Germany.,b Department of Medicine , University Hospital Freiburg , Freiburg , Germany
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26
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Outeda P, Menezes L, Hartung EA, Bridges S, Zhou F, Zhu X, Xu H, Huang Q, Yao Q, Qian F, Germino GG, Watnick T. A novel model of autosomal recessive polycystic kidney questions the role of the fibrocystin C-terminus in disease mechanism. Kidney Int 2017; 92:1130-1144. [PMID: 28729032 PMCID: PMC6005173 DOI: 10.1016/j.kint.2017.04.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/09/2017] [Accepted: 04/27/2017] [Indexed: 12/11/2022]
Abstract
Autosomal recessive polycystic kidney disease (OMIM 263200) is a serious condition of the kidney and liver caused by mutations in a single gene, PKHD1. This gene encodes fibrocystin/polyductin (FPC, PD1), a large protein shown by in vitro studies to undergo Notch-like processing. Its cytoplasmic tail, reported to include a ciliary targeting sequence, a nuclear localization signal, and a polycystin-2 binding domain, is thought to traffic to the nucleus after cleavage. We now report a novel mouse line with a triple HA-epitope "knocked-in" to the C-terminus along with lox P sites flanking exon 67, which encodes most of the C-terminus (Pkhd1Flox67HA). The triple HA-epitope has no functional effect as assayed by phenotype and allows in vivo tracking of Fibrocystin. We used the HA tag to identify previously predicted Fibrocystin cleavage products in tissue. In addition, we found that Polycystin-2 fails to co-precipitate with Fibrocystin in kidney samples. Immunofluorescence studies with anti-HA antibodies demonstrate that Fibrocystin is primarily present in a sub-apical location the in kidney, biliary duct, and pancreatic ducts, partially overlapping with the Golgi. In contrast to previous studies, the endogenous protein in the primary cilia was not detectable in mouse tissues. After Cre-mediated deletion, homozygous Pkhd1Δ67 mice are completely normal. Thus, Pkhd1Flox67HA is a valid model to track Pkhd1-derived products containing the C-terminus. Significantly, exon 67 containing the nuclear localization signal and the polycystin-2 binding domain is not essential for Fibrocystin function in our model.
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Affiliation(s)
- Patricia Outeda
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Luis Menezes
- Kidney Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Erum A Hartung
- Division of Nephrology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stacey Bridges
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Fang Zhou
- Kidney Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Xianjun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Study, Sichuan Academy of Sciences and Sichuan Provincial People's Hospital Chengdue, Sichuan, China
| | - Hangxue Xu
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Qiong Huang
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Qin Yao
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Gregory G Germino
- Kidney Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| | - Terry Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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NEDD4-family E3 ligase dysfunction due to PKHD1/Pkhd1 defects suggests a mechanistic model for ARPKD pathobiology. Sci Rep 2017; 7:7733. [PMID: 28798345 PMCID: PMC5552802 DOI: 10.1038/s41598-017-08284-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 07/04/2017] [Indexed: 01/17/2023] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is an important childhood nephropathy, occurring 1 in 20,000 live births. The major clinical phenotypes are expressed in the kidney with dilatation of the collecting ducts, systemic hypertension, and progressive renal insufficiency, and in the liver with biliary dysgenesis, portal tract fibrosis, and portal hypertension. The systemic hypertension has been attributed to enhanced distal sodium reabsorption in the kidney, the structural defects have been ascribed to altered cellular morphology, and fibrosis to increased TGF-β signaling in the kidney and biliary tract, respectively. The pathogenic mechanisms underlying these abnormalities have not been determined. In the current report, we find that disrupting PKHD1 results in altered sub-cellular localization and function of the C2-WWW-HECT domain E3 family of ligases regulating these processes. We also demonstrate altered activity of RhoA and increased TGF-β signaling and ENaC activity. Linking these phenomena, we found that vesicles containing the PKHD1/Pkhd1 gene product, FPC, also contain the NEDD4 ubiquitin ligase interacting protein, NDFIP2, which interacts with multiple members of the C2-WWW-HECT domain E3 family of ligases. Our results provide a mechanistic explanation for both the cellular effects and in vivo phenotypic abnormalities in mice and humans that result from Pkhd1/PKHD1 mutation.
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28
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Tien WS, Chen JH, Wu KP. SheddomeDB: the ectodomain shedding database for membrane-bound shed markers. BMC Bioinformatics 2017; 18:42. [PMID: 28361715 PMCID: PMC5374707 DOI: 10.1186/s12859-017-1465-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A number of membrane-anchored proteins are known to be released from cell surface via ectodomain shedding. The cleavage and release of membrane proteins has been shown to modulate various cellular processes and disease pathologies. Numerous studies revealed that cell membrane molecules of diverse functional groups are subjected to proteolytic cleavage, and the released soluble form of proteins may modulate various signaling processes. Therefore, in addition to the secreted protein markers that undergo secretion through the secretory pathway, the shed membrane proteins may comprise an additional resource of noninvasive and accessible biomarkers. In this context, identifying the membrane-bound proteins that will be shed has become important in the discovery of clinically noninvasive biomarkers. Nevertheless, a data repository for biological and clinical researchers to review the shedding information, which is experimentally validated, for membrane-bound protein shed markers is still lacking. RESULTS In this study, the database SheddomeDB was developed to integrate publicly available data of the shed membrane proteins. A comprehensive literature survey was performed to collect the membrane proteins that were verified to be cleaved or released in the supernatant by immunological-based validation experiments. From 436 studies on shedding, 401 validated shed membrane proteins were included, among which 199 shed membrane proteins have not been annotated or validated yet by existing cleavage databases. SheddomeDB attempted to provide a comprehensive shedding report, including the regulation of shedding machinery and the related function or diseases involved in the shedding events. In addition, our published tool ShedP was embedded into SheddomeDB to support researchers for predicting the shedding event on unknown or unrecorded membrane proteins. CONCLUSIONS To the best of our knowledge, SheddomeDB is the first database for the identification of experimentally validated shed membrane proteins and currently may provide the most number of membrane proteins for reviewing the shedding information. The database included membrane-bound shed markers associated with numerous cellular processes and diseases, and some of these markers are potential novel markers because they are not annotated or validated yet in other databases. SheddomeDB may provide a useful resource for discovering membrane-bound shed markers. The interactive web of SheddomeDB is publicly available at http://bal.ym.edu.tw/SheddomeDB/ .
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Affiliation(s)
- Wei-Sheng Tien
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, 112, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
| | - Jun-Hong Chen
- Department of Computer Science, National Taipei University of Education, Taipei, 106, Taiwan
| | - Kun-Pin Wu
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, 112, Taiwan.
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29
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Pei J, Grishin NV. Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54. Protein Sci 2017; 26:617-630. [PMID: 27977898 DOI: 10.1002/pro.3096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
SEA (sea urchin sperm protein, enterokinase, agrin) domains, many of which possess autoproteolysis activity, have been found in a number of cell surface and secreted proteins. Despite high sequence divergence, SEA domains were also proposed to be present in dystroglycan based on a conserved autoproteolysis motif and receptor-type protein phosphatase IA-2 based on structural similarity. The presence of a SEA domain adjacent to the transmembrane segment appears to be a recurring theme in quite a number of type I transmembrane proteins on the cell surface, such as MUC1, dystroglycan, IA-2, and Notch receptors. By comparative sequence and structural analyses, we identified dystroglycan-like proteins with SEA domains in Capsaspora owczarzaki of the Filasterea group, one of the closest single-cell relatives of metazoans. We also detected novel and divergent SEA domains in a variety of cell surface proteins such as EpCAM, α/ε-sarcoglycan, PTPRR, collectrin/Tmem27, amnionless, CD34, KIAA0319, fibrocystin-like protein, and a number of cadherins. While these proteins are mostly from metazoans or their single cell relatives such as choanoflagellates and Filasterea, fibrocystin-like proteins with SEA domains were found in several other eukaryotic lineages including green algae, Alveolata, Euglenozoa, and Haptophyta, suggesting an ancient evolutionary origin. In addition, the intracellular protein Nucleoporin 54 (Nup54) acquired a divergent SEA domain in choanoflagellates and metazoans.
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Affiliation(s)
| | - Nick V Grishin
- Howard Hughes Medical Institute.,Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
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30
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Bergmann C. Genetics of Autosomal Recessive Polycystic Kidney Disease and Its Differential Diagnoses. Front Pediatr 2017; 5:221. [PMID: 29479522 PMCID: PMC5811498 DOI: 10.3389/fped.2017.00221] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/02/2017] [Indexed: 01/09/2023] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a hepatorenal fibrocystic disorder that is characterized by enlarged kidneys with progressive loss of renal function and biliary duct dilatation and congenital hepatic fibrosis that leads to portal hypertension in some patients. Mutations in the PKHD1 gene are the primary cause of ARPKD; however, the disease is genetically not as homogeneous as long thought and mutations in several other cystogenes can phenocopy ARPKD. The family history usually is negative, both for recessive, but also often for dominant disease genes due to de novo arisen mutations or recessive inheritance of variants in genes that usually follow dominant patterns such as the main ADPKD genes PKD1 and PKD2. Considerable progress has been made in the understanding of polycystic kidney disease (PKD). A reduced dosage of disease proteins leads to the disruption of signaling pathways underlying key mechanisms involved in cellular homeostasis, which may help to explain the accelerated and severe clinical progression of disease course in some PKD patients. A comprehensive knowledge of disease-causing genes is essential for counseling and to avoid genetic misdiagnosis, which is particularly important in the prenatal setting (e.g., preimplantation genetic diagnosis/PGD). For ARPKD, there is a strong demand for early and reliable prenatal diagnosis, which is only feasible by molecular genetic analysis. A clear genetic diagnosis is helpful for many families and improves the clinical management of patients. Unnecessary and invasive measures can be avoided and renal and extrarenal comorbidities early be detected in the clinical course. The increasing number of genes that have to be considered benefit from the advances of next-generation sequencing (NGS) which allows simultaneous analysis of a large group of genes in a single test at relatively low cost and has become the mainstay for genetic diagnosis. The broad phenotypic and genetic heterogeneity of cystic and polycystic kidney diseases make NGS a particularly powerful approach for these indications. Interpretation of genetic data becomes the challenge and requires deep clinical understanding.
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Affiliation(s)
- Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany.,Department of Medicine, University Hospital Freiburg, Freiburg, Germany
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31
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Ezratty EJ, Pasolli HA, Fuchs E. A Presenilin-2-ARF4 trafficking axis modulates Notch signaling during epidermal differentiation. J Cell Biol 2016; 214:89-101. [PMID: 27354375 PMCID: PMC4932368 DOI: 10.1083/jcb.201508082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
How primary cilia impact epidermal growth and differentiation during embryogenesis is poorly understood. Here, we show that during skin development, Notch signaling occurs within the ciliated, differentiating cells of the first few suprabasal epidermal layers. Moreover, both Notch signaling and cilia disappear in the upper layers, where key ciliary proteins distribute to cell-cell borders. Extending this correlation, we find that Presenilin-2 localizes to basal bodies/cilia through a conserved VxPx motif. When this motif is mutated, a GFP-tagged Presenilin-2 still localizes to intercellular borders, but basal body localization is lost. Notably, in contrast to wild type, this mutant fails to rescue epidermal differentiation defects seen upon Psen1 and 2 knockdown. Screening components implicated in ciliary targeting and polarized exocytosis, we provide evidence that the small GTPase ARF4 is required for Presenilin basal body localization, Notch signaling, and subsequent epidermal differentiation. Collectively, our findings raise the possibility that ARF4-dependent polarized exocytosis acts through the basal body-ciliary complex to spatially regulate Notch signaling during epidermal differentiation.
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Affiliation(s)
- Ellen J Ezratty
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065
| | - H Amalia Pasolli
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065
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32
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Agnati LF, Marcoli M, Maura G, Fuxe K, Guidolin D. The multi-facet aspects of cell sentience and their relevance for the integrative brain actions: role of membrane protein energy landscape. Rev Neurosci 2016; 27:347-63. [DOI: 10.1515/revneuro-2015-0049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022]
Abstract
AbstractSeveral ion channels can be randomly and spontaneously in an open state, allowing the exchange of ion fluxes between extracellular and intracellular environments. We propose that the random changes in the state of ion channels could be also due to proteins exploring their energy landscapes. Indeed, proteins can modify their steric conformation under the effects of the physicochemical parameters of the environments with which they are in contact, namely, the extracellular, intramembrane and intracellular environments. In particular, it is proposed that the random walk of proteins in their energy landscape is towards attractors that can favor the open or close condition of the ion channels and/or intrinsic activity of G-protein-coupled receptors. The main aspect of the present proposal is that some relevant physicochemical parameters of the environments (e.g. molecular composition, temperature, electrical fields) with which some signaling-involved plasma membrane proteins are in contact alter their conformations. In turn, these changes can modify their information handling via a modulatory action on their random walk towards suitable attractors of their energy landscape. Thus, spontaneous and/or signal-triggered electrical activities of neurons occur that can have emergent properties capable of influencing the integrative actions of brain networks. Against this background, Cook’s hypothesis on ‘cell sentience’ is developed by proposing that physicochemical parameters of the environments with which the plasma-membrane proteins of complex cellular networks are in contact fulfill a fundamental role in their spontaneous and/or signal-triggered activity. Furthermore, it is proposed that a specialized organelle, the primary cilium, which is present in most cells (also neurons and astrocytes), could be of peculiar importance to pick up chemical signals such as ions and transmitters and to detect physical signals such as pressure waves, thermal gradients, and local field potentials.
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Affiliation(s)
| | - Manuela Marcoli
- 3University of Genova, Department of Pharmacy and Center of Excellence for Biomedical Research, Viale Cembrano 4, I-16148 Genova, Italy
| | - Guido Maura
- 3University of Genova, Department of Pharmacy and Center of Excellence for Biomedical Research, Viale Cembrano 4, I-16148 Genova, Italy
| | - Kjell Fuxe
- 2Karolinska Institutet, Department of Neuroscience, S-17177 Stockholm, Sweden
| | - Diego Guidolin
- 4University of Padova, Department of Molecular Medicine, I-35122 Padova, Italy
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33
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Mohieldin AM, Haymour HS, Lo ST, AbouAlaiwi WA, Atkinson KF, Ward CJ, Gao M, Wessely O, Nauli SM. Protein composition and movements of membrane swellings associated with primary cilia. Cell Mol Life Sci 2015; 72:2415-29. [PMID: 25650235 PMCID: PMC4503369 DOI: 10.1007/s00018-015-1838-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/31/2014] [Accepted: 01/12/2015] [Indexed: 12/15/2022]
Abstract
Dysfunction of many ciliary proteins has been linked to a list of diseases, from cystic kidney to obesity and from hypertension to mental retardation. We previously proposed that primary cilia are unique communication organelles that function as microsensory compartments that house mechanosensory molecules. Here we report that primary cilia exhibit membrane swellings or ciliary bulbs, which based on their unique ultrastructure and motility, could be mechanically regulated by fluid-shear stress. Together with the ultrastructure analysis of the swelling, which contains monosialodihexosylganglioside (GM3), our results show that ciliary bulb has a distinctive set of functional proteins, including GM3 synthase (GM3S), bicaudal-c1 (Bicc1), and polycystin-2 (PC2). In fact, results from our cilia isolation demonstrated for the first time that GM3S and Bicc1 are members of the primary cilia proteins. Although these proteins are not required for ciliary membrane swelling formation under static condition, fluid-shear stress induced swelling formation is partially modulated by GM3S. We therefore propose that the ciliary bulb exhibits a sensory function within the mechano-ciliary structure. Overall, our studies provided an important step towards understanding the ciliary bulb function and structure.
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Affiliation(s)
- Ashraf M. Mohieldin
- Department of Medicinal and Biological Chemistry, University of Toledo, Health Science Building, 3000 Arlington Ave, Toledo, OH 43614, USA
- Department of Pharmacology and Experimental Therapeutics, University of Toledo, Health Science Building, Toledo, OH 43614, USA
| | - Hanan S. Haymour
- Department of Pharmacology and Experimental Therapeutics, University of Toledo, Health Science Building, Toledo, OH 43614, USA
| | - Shao T. Lo
- Department of Pharmacology and Experimental Therapeutics, University of Toledo, Health Science Building, Toledo, OH 43614, USA
| | - Wissam A. AbouAlaiwi
- Department of Pharmacology and Experimental Therapeutics, University of Toledo, Health Science Building, Toledo, OH 43614, USA
| | - Kimberly F. Atkinson
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, CA 92618-1908, USA
| | - Christopher J. Ward
- Department of Medicine, The Kidney Institute, University of Kansas Medical Center, Kansas, KS 66160, USA
| | - Min Gao
- Liquid Crystal Institute, Kent State University, 1425 University Esplanade, Kent, OH 44242, USA
| | - Oliver Wessely
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Surya M. Nauli
- Department of Medicinal and Biological Chemistry, University of Toledo, Health Science Building, 3000 Arlington Ave, Toledo, OH 43614, USA
- Department of Pharmacology and Experimental Therapeutics, University of Toledo, Health Science Building, Toledo, OH 43614, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, CA 92618-1908, USA
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34
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Frank V, Zerres K, Bergmann C. Transcriptional complexity in autosomal recessive polycystic kidney disease. Clin J Am Soc Nephrol 2014; 9:1729-36. [PMID: 25104275 DOI: 10.2215/cjn.00920114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND AND OBJECTIVES Autosomal recessive polycystic kidney disease (ARPKD) is caused by mutations in the PKHD1 gene. The longest open reading frame comprises 66 exons encoding polyductin or fibrocystin, a type I transmembrane protein with 4074 amino acids. Functional investigations are considerably hampered by its large size and lack of expression in tissues that are usually available for analysis such as lymphocytes or fibroblasts. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Allegedly strong and clear-cut genotype-phenotype correlations for the type of PKHD1 mutation could be established. Thus far, practically all patients with two truncating mutations showed perinatal or neonatal demise and at least one hypomorphic missense mutation is thought to be indispensable for survival. Mutation analysis of >500 ARPKD families was performed by conventional and next-generation sequencing techniques. RESULTS This study presents four unrelated patients with ARPKD with a nonlethal, moderate clinical course despite the burden of two PKHD1 mutations expected to lead to premature termination of translation. In line with parental consanguinity, all mutations occurred in the homozygous state and segregated with the disorder in these families. To try to unravel the mechanisms that underlie this obvious contradiction, these patients were further analyzed in detail by utilizing different methods. In all cases, complex transcriptional alterations were detected. Alternative splicing patterns might disrupt a critical stoichiometric and temporal balance between different protein products and may play a crucial role in defining the phenotype of these patients. CONCLUSIONS Although these findings represent rare events, they are of importance for genetic counseling and illustrate that some caution is warranted in the interpretation of mutations and their clinical significance. The authors hypothesize that expression of a minimal amount of functional protein is needed for survival of the neonatal period in ARPKD.
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Affiliation(s)
- Valeska Frank
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
| | - Klaus Zerres
- Department of Human Genetics, RWTH Aachen University, Aachen, Germany; and
| | - Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany; Department of Human Genetics, RWTH Aachen University, Aachen, Germany; and Renal Division, Department of Medicine, University Freiburg Medical Center, Freiburg, Germany
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35
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Williams SS, Cobo-Stark P, Hajarnis S, Aboudehen K, Shao X, Richardson JA, Patel V, Igarashi P. Tissue-specific regulation of the mouse Pkhd1 (ARPKD) gene promoter. Am J Physiol Renal Physiol 2014; 307:F356-68. [PMID: 24899057 DOI: 10.1152/ajprenal.00422.2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Autosomal recessive polycystic kidney disease, an inherited disorder characterized by the formation of cysts in renal collecting ducts and biliary dysgenesis, is caused by mutations of the polycystic kidney and hepatic disease 1 (PKHD1) gene. Expression of PKHD1 is tissue specific and developmentally regulated. Here, we show that a 2.0-kb genomic fragment containing the proximal promoter of mouse Pkhd1 directs tissue-specific expression of a lacZ reporter gene in transgenic mice. LacZ is expressed in renal collecting ducts beginning during embryonic development but is not expressed in extrarenal tissues. The Pkhd1 promoter contains a binding site for the transcription factor hepatocyte nuclear factor (HNF)-1β, which is required for activity in transfected cells. Mutation of the HNF-1β-binding site abolishes the expression of the lacZ reporter gene in renal collecting ducts. Transgenes containing the 2.0-kb promoter and 2.7 kb of additional genomic sequence extending downstream to the second exon are expressed in the kidney, intrahepatic bile ducts, and male reproductive tract. This pattern overlaps with the endogenous expression of Pkhd1 and coincides with sites of expression of HNF-1β. We conclude that the proximal 2.0-kb promoter is sufficient for tissue-specific expression of Pkhd1 in renal collecting ducts in vivo and that HNF-1β is required for Pkhd1 promoter activity in collecting ducts. Additional genomic sequences located from exons 1-2 or elsewhere in the gene locus are required for expression in extrarenal tissues.
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Affiliation(s)
- Scott S Williams
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Patricia Cobo-Stark
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sachin Hajarnis
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Karam Aboudehen
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xinli Shao
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - James A Richardson
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; and Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Vishal Patel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peter Igarashi
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas;
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Wang S, Wu M, Yao G, Zhang J, Zhou J. The cytoplasmic tail of FPC antagonizes the full-length protein in the regulation of mTOR pathway. PLoS One 2014; 9:e95630. [PMID: 24851866 PMCID: PMC4031230 DOI: 10.1371/journal.pone.0095630] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/28/2014] [Indexed: 01/23/2023] Open
Abstract
FPC (fibrocystin or polyductin) is a single transmembrane receptor-like protein, responsible for the human autosomal recessive polycystic kidney disease (ARPKD). It was recently proposed that FPC undergoes a Notch-like cleavage and subsequently the cleaved carboxy(C)-terminal fragment translocates to the nucleus. To study the functions of the isolated C-tail, we expressed the intracellular domain of human FPC (hICD) in renal epithelial cells. By 3-dimensional (3D) tubulogenesis assay, we found that in contrast to tubule-like structures formed from control cells, hICD-expressing cells exclusively formed cyst-like structures. By western blotting, we showed that the Akt/mTOR pathway, indicated by increased phosphorylation of Akt at serine 473 and S6 kinase 1 at threonine 389, was constitutively activated in hICD-expressing cells, similar to that in FPC knockdown cells and ARPKD kidneys. Moreover, application of mTOR inhibitor rapamycin reduced the size of the cyst-like structures formed by hICD-expressing cells. Application of either LY294002 or wortmannin inhibited the activation of both S6K1 and Akt. Expression of full-length FPC inhibited the activation of S6 and S6 kinase whereas co-expression of hICD with full-length FPC antagonized the inhibitory effect of full-length FPC on mTOR. Taken together, we propose that FPC modulates the PI3K/Akt/mTOR pathway and the cleaved C-tail regulates the function of the full-length protein.
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Affiliation(s)
- Shixuan Wang
- Renal Division, Department of Medicine and Center of Polycystic Kidney Disease, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JZ); (SW)
| | - Maoqing Wu
- Renal Division, Department of Medicine and Center of Polycystic Kidney Disease, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gang Yao
- Renal Division, Department of Medicine and Center of Polycystic Kidney Disease, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jingjing Zhang
- Renal Division, Department of Medicine and Center of Polycystic Kidney Disease, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jing Zhou
- Renal Division, Department of Medicine and Center of Polycystic Kidney Disease, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JZ); (SW)
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Jurisch-Yaksi N, Sannerud R, Annaert W. A fast growing spectrum of biological functions of γ-secretase in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2815-27. [PMID: 24099003 DOI: 10.1016/j.bbamem.2013.04.016] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/03/2013] [Accepted: 04/11/2013] [Indexed: 12/17/2022]
Abstract
γ-secretase, which assembles as a tetrameric complex, is an aspartyl protease that proteolytically cleaves substrate proteins within their membrane-spanning domain; a process also known as regulated intramembrane proteolysis (RIP). RIP regulates signaling pathways by abrogating or releasing signaling molecules. Since the discovery, already >15 years ago, of its catalytic component, presenilin, and even much earlier with the identification of amyloid precursor protein as its first substrate, γ-secretase has been commonly associated with Alzheimer's disease. However, starting with Notch and thereafter a continuously increasing number of novel substrates, γ-secretase is becoming linked to an equally broader range of biological processes. This review presents an updated overview of the current knowledge on the diverse molecular mechanisms and signaling pathways controlled by γ-secretase, with a focus on organ development, homeostasis and dysfunction. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Nathalie Jurisch-Yaksi
- Laboratory for Membrane Trafficking, VIB-Center for the Biology of Disease & Department for Human Genetics (KU Leuven), Leuven, Belgium
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Jurisch-Yaksi N, Rose AJ, Lu H, Raemaekers T, Munck S, Baatsen P, Baert V, Vermeire W, Scales SJ, Verleyen D, Vandepoel R, Tylzanowski P, Yaksi E, de Ravel T, Yost HJ, Froyen G, Arrington CB, Annaert W. Rer1p maintains ciliary length and signaling by regulating γ-secretase activity and Foxj1a levels. ACTA ACUST UNITED AC 2013; 200:709-20. [PMID: 23479743 PMCID: PMC3601348 DOI: 10.1083/jcb.201208175] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rer1p is an ER/cis-Golgi membrane protein that maintains ciliary length and function by reducing γ-secretase complex assembly and activity (thereby balancing Notch signaling) and increasing Foxj1a expression. Cilia project from the surface of most vertebrate cells and are important for several physiological and developmental processes. Ciliary defects are linked to a variety of human diseases, named ciliopathies, underscoring the importance of understanding signaling pathways involved in cilia formation and maintenance. In this paper, we identified Rer1p as the first endoplasmic reticulum/cis-Golgi–localized membrane protein involved in ciliogenesis. Rer1p, a protein quality control receptor, was highly expressed in zebrafish ciliated organs and regulated ciliary structure and function. Both in zebrafish and mammalian cells, loss of Rer1p resulted in the shortening of cilium and impairment of its motile or sensory function, which was reflected by hearing, vision, and left–right asymmetry defects as well as decreased Hedgehog signaling. We further demonstrate that Rer1p depletion reduced ciliary length and function by increasing γ-secretase complex assembly and activity and, consequently, enhancing Notch signaling as well as reducing Foxj1a expression.
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Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited genetic disorder that results in progressive renal cyst formation with ultimate loss of renal function and other systemic disorders. These systemic disorders include abnormalities in cardiovascular, portal, pancreatic and gastrointestinal systems. ADPKD is considered to be among the ciliopathy diseases due to the association with abnormal primary cilia function. In order to understand the full course of primary cilia and its association with ADPKD, the structure, functions and role of primary cilia have been meticulously investigated. As a result, the focus on primary cilia has emerged to support the vital roles of primary cilia in ADPKD. The primary cilia have been shown to have not only a mechanosensory function but also a chemosensory function. Both structural and functional defects in primary cilia result in cystic kidney disease and vascular hypertension. Thus, the mechanosenory and chemosensory functions will be analyzed in regards to ADPKD.
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Affiliation(s)
- Sarmed H Kathem
- College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, Ohio ; College of Pharmacy, University of Baghdad, Baghdad, Iraq
| | - Ashraf M Mohieldin
- College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, Ohio
| | - Surya M Nauli
- College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, Ohio
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40
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Abstract
The Alzheimer's disease (AD)-associated amyloid-β protein precursor (AβPP) is cleaved by α-, β-, and presenilin (PS)/γ-secretases through sequential regulated proteolysis. These proteolytic events control the generation of the pathogenic amyloid-β (Aβ) peptide, which excessively accumulates in the brains of individuals afflicted by AD. A growing number of additional proteins cleaved by PS/γ-secretase continue to be discovered. Similarly to AβPP, most of these proteins are type-I transmembrane proteins involved in vital signaling functions regulating cell fate, adhesion, migration, neurite outgrowth, or synaptogenesis. All the identified proteins share common structural features, which are typical for their proteolysis. The consequences of the PS/γ-secretase-mediated cleavage on the function of many of these proteins are largely unknown. Here, we review the current literature on the proteolytic processing mediated by the versatile PS/γ-secretase complex. We begin by discussing the steps of AβPP processing and PS/γ-secretase complex composition and localization, which give clues to how and where the processing of other PS/γ-secretase substrates may take place. Then we summarize the typical features of PS/γ-secretase-mediated protein processing. Finally, we recapitulate the current knowledge on the possible physiological function of PS/γ-secretase-mediated cleavage of specific substrate proteins.
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Affiliation(s)
- Annakaisa Haapasalo
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.
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Duan J, Huang H, Lv X, Wang H, Tang Z, Sun H, Li Q, Ai J, Tan R, Liu Y, Chen M, Duan W, Wei Y, Zhou Q. PKHD1 post-transcriptionally modulated by miR-365-1 inhibits cell-cell adhesion. Cell Biochem Funct 2012; 30:382-9. [PMID: 22411058 DOI: 10.1002/cbf.2795] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 02/05/2023]
Affiliation(s)
- Jingjing Duan
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | | | - Xiaoyan Lv
- Department of Dermatology; West China Hospital, Sichuan University; Sichuan; China
| | - Honglian Wang
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Ziwei Tang
- West China School of Clinical Medicine; Sichuan University; Sichuan; China
| | - Huan Sun
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Qingwei Li
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Jianzhong Ai
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Ruizhi Tan
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Yuhang Liu
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Mianzhi Chen
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Weiwei Duan
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Yuquan Wei
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
| | - Qin Zhou
- Core Facility of Genetically Engineered Mice, State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University; Chengdu; China
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Caroli's Disease: Current Knowledge of Its Biliary Pathogenesis Obtained from an Orthologous Rat Model. Int J Hepatol 2012; 2012:107945. [PMID: 22007315 PMCID: PMC3168917 DOI: 10.1155/2012/107945] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 04/07/2011] [Indexed: 12/14/2022] Open
Abstract
Caroli's disease belongs to a group of hepatic fibropolycystic diseases and is a hepatic manifestation of autosomal recessive polycystic kidney disease (ARPKD). It is a congenital disorder characterized by segmental saccular dilatations of the large intrahepatic bile duct and is frequently associated with congenital hepatic fibrosis (CHF). The most viable theory explaining its pathogenesis suggests that it is related to ductal plate malformation. The development of the polycystic kidney (PCK) rat, an orthologous rodent model of Caroli's disease with CHF as well as ARPKD, has allowed the molecular pathogenesis of the disease and the therapeutic options for its treatment to be examined. The relevance of the findings of studies using PCK rats and/or the cholangiocyte cell line derived from them to the pathogenesis of human Caroli's disease is currently being analyzed. Fibrocystin/polyductin, the gene product responsible for ARPKD, is normally localized to primary cilia, and defects in the fibrocystin from primary cilia are observed in PCK cholangiocytes. Ciliopathies involving PCK cholangiocytes (cholangiociliopathies) appear to be associated with decreased intracellular calcium levels and increased cAMP concentrations, causing cholangiocyte hyperproliferation, abnormal cell matrix interactions, and altered fluid secretion, which ultimately result in bile duct dilatation. This article reviews the current knowledge about the pathogenesis of Caroli's disease with CHF, particularly focusing on studies of the mechanism responsible for the biliary dysgenesis observed in PCK rats.
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Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a developmental disorder that mainly affects the kidneys and the biliary tract. Affected patients often have massively enlarged cystic kidneys as well as congenital hepatic fibrosis (CHF) characterized by dilated bile ducts and associated peribiliary fibrosis. This review will examine what is known about ARPKD-associated liver disease and will highlight areas of ongoing research into its pathogenesis and potential treatment.
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Affiliation(s)
- Jessica Wen
- Division of Gastroenterology, Hepatology & Nutrition, The Children's Hospital of Philadelphia, Pennsylvania, USA.
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44
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Pardossi-Piquard R, Checler F. The physiology of the β-amyloid precursor protein intracellular domain AICD. J Neurochem 2011; 120 Suppl 1:109-124. [PMID: 22122663 DOI: 10.1111/j.1471-4159.2011.07475.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The amyloid-β precursor protein (βAPP) undergoes several cleavages by enzymatic activities called secretases. Numerous studies aimed at studying the biogenesis and catabolic fate of Aβ peptides, the proteinaceous component of the senile plaques that accumulate in Alzheimer's disease-affected brains. Relatively recently, another secretase-mediated β-APP-derived catabolite called APP IntraCellular Domain (AICD) entered the game. Whether AICD corresponded to a biologically inert by-pass product of βAPP processing or whether it could harbor its own function remained questionable. In this study, we review the mechanisms by which AICD is generated and how its production is regulated. Furthermore, we discuss the degradation mechanism underlying its rapid catabolic fate. Finally, we review putative AICD-related functions and more particularly, the numerous studies indicating that AICD could translocate to the nucleus and control at a transcriptional level, the expression of a series of proteins involved in various functions including the control of cell death and Aβ degradation.
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Affiliation(s)
- Raphaëlle Pardossi-Piquard
- Université de Nice Sophia-Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire UMR6097 CNRS, Equipe labellisée Fondation pour la Recherche Médicale, Sophia-Antipolis, Valbonne, France
| | - Frédéric Checler
- Université de Nice Sophia-Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire UMR6097 CNRS, Equipe labellisée Fondation pour la Recherche Médicale, Sophia-Antipolis, Valbonne, France
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45
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Patel V. Tagged fibrocystin sheds its secrets. J Am Soc Nephrol 2011; 22:2148-50. [PMID: 22080423 DOI: 10.1681/asn.2011101005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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46
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Bakeberg JL, Tammachote R, Woollard JR, Hogan MC, Tuan HF, Li M, van Deursen JM, Wu Y, Huang BQ, Torres VE, Harris PC, Ward CJ. Epitope-tagged Pkhd1 tracks the processing, secretion, and localization of fibrocystin. J Am Soc Nephrol 2011; 22:2266-77. [PMID: 22021705 DOI: 10.1681/asn.2010111173] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Mutations in the PKHD1 gene, which encodes fibrocystin, cause autosomal recessive polycystic kidney disease (ARPKD). Unfortunately, the lack of specific antibodies to the mouse protein impairs the study of splicing, post-translational processing, shedding, and temporal and spatial expression of endogenous fibrocystin at the cellular and subcellular level. Here, we report using a knock-in strategy to generate a null Pkhd1 strain and a strain that expresses fibrocystin along with two SV5-Pk epitope tags engineered in-frame into the third exon, immediately C-terminal to the signal-peptide cleavage site in a poorly conserved region. By 6 mo of age, the Pkhd1-null mouse develops massive cystic hepatomegaly and proximal tubule dilation, whereas the mouse with epitope-tagged fibrocystin has histologically normal liver and kidneys at 14 mo. Although Pkhd1 was believed to generate many splice forms, our western analysis resolved fibrocystin as a 500 kD product without other forms in the 15-550 kD range. Western analysis also revealed that exosome-like vesicles (ELVs) secrete the bulk of fibrocystin in its mature cleaved form, and scanning electron microscopy identified that fibrocystin on ELVs attached to cilia. Furthermore, the addition of ELVs with epitope-tagged fibrocystin to wild-type cells showed that label transferred to primary cilia within 5 min. In summary, tagging of the endogenous Pkhd1 gene facilitates the study of the glycosylation, proteolytic cleavage, and shedding of fibrocystin.
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Affiliation(s)
- Jason L Bakeberg
- Division of Nephrology and Hypertension, Mayo Clinic, 703 Stabile Building, 200 First Street SW, Rochester, MN 55905, USA
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Ibraghimov-Beskrovnaya O, Natoli TA. mTOR signaling in polycystic kidney disease. Trends Mol Med 2011; 17:625-33. [PMID: 21775207 DOI: 10.1016/j.molmed.2011.06.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/16/2011] [Accepted: 06/07/2011] [Indexed: 12/15/2022]
Abstract
Polycystic kidney diseases (PKDs) comprise a large group of genetic disorders characterized by formation of cysts in the kidneys and other organs, ultimately leading to end-stage renal disease. Although PKDs can be caused by mutations in different genes, they converge on a set of common molecular mechanisms involved in cystogenesis and ciliary dysfunction, and can be qualified as ciliopathies. Recent advances in understanding the mechanisms regulating disease progression have led to the development of new therapies that are being tested in both preclinical and clinical trials. In this article, we briefly review a network of molecular pathways of cystogenesis that are regulated by ciliary functions. We discuss the mTOR pathway in depth, highlighting recent progress in understanding its role in PKD and the current results of clinical trials.
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48
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Lal M, Caplan M. Regulated intramembrane proteolysis: signaling pathways and biological functions. Physiology (Bethesda) 2011; 26:34-44. [PMID: 21357901 DOI: 10.1152/physiol.00028.2010] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Intramembrane cleavage of transmembrane proteins is a fundamental cellular process. Several enzymes capable of releasing domains of integral membrane proteins have been described. Transmembrane protein proteolytic cleavage is regulated and involved not only in degrading membrane spanning segments but also in generating messengers that elicit biological responses. This review examines the role of the released functional protein domain in signaling mechanisms regulating an array of cellular and physiological processes.
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Affiliation(s)
- Mark Lal
- Department of Medical Biochemistry and Biophysics, Division of Matrix Biology, Karolinska Institutet, Stockholm, Sweden.
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49
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A genetic interaction network of five genes for human polycystic kidney and liver diseases defines polycystin-1 as the central determinant of cyst formation. Nat Genet 2011; 43:639-47. [PMID: 21685914 DOI: 10.1038/ng.860] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 05/18/2011] [Indexed: 02/07/2023]
Abstract
Autosomal dominant polycystic liver disease results from mutations in PRKCSH or SEC63. The respective gene products, glucosidase IIβ and SEC63p, function in protein translocation and quality control pathways in the endoplasmic reticulum. Here we show that glucosidase IIβ and Sec63p are required in mice for adequate expression of a functional complex of the polycystic kidney disease gene products, polycystin-1 and polycystin-2. We find that polycystin-1 is the rate-limiting component of this complex and that there is a dose-response relationship between cystic dilation and levels of functional polycystin-1 following mutation of Prkcsh or Sec63. Reduced expression of polycystin-1 also serves to sensitize the kidney to cyst formation resulting from mutations in Pkhd1, the recessive polycystic kidney disease gene. Finally, we show that proteasome inhibition increases steady-state levels of polycystin-1 in cells lacking glucosidase IIβ and that treatment with a proteasome inhibitor reduces cystic disease in orthologous gene models of human autosomal dominant polycystic liver disease.
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50
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Abstract
Polycystic liver diseases (PLD) are inherited disorders of the biliary epithelium, caused by genetic defects in proteins associated with intracellular organelles, mainly the endoplasmic reticulum and the cilium. PLD are characterized by the formation and progressive enlargement of multiple cysts scattered throughout the liver parenchyma, and include different entities, classified based on their pathology, inheritance pattern, involvement of the kidney and clinical features. PLD should be considered as congenital diseases of cholangiocyte signaling. Here, we will review the changes in signaling pathways involved in liver cyst formation and progression, and their impact on cholangiocyte physiology. Each pathway represents a potential target for therapies aimed at reducing disease progression.
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Affiliation(s)
- Mario Strazzabosco
- Liver Center and Section of Digestive Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut 06520, USA.
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