Nephrin Mutations Can Cause Childhood-Onset Steroid-Resistant Nephrotic Syndrome
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Genotyping of Breech Flystrike Resource – Update
Project No: ON-00515 Contract No: PO4500010753 AWI Project Manager: Bridget Peachey Contractor Name: CSIRO Agriculture and Food Prepared by: Dr Sonja Dominik Publication Date: July 2019 Genotyping of breech flystrike resource – update Published by Australian Wool Innovation Limited, Level 6, 68 Harrington Street, THE ROCKS, NSW, 2000 This publication should only be used as a general aid and is not a substitute for specific advice. To the extent permitted by law, we exclude all liability for loss or damage arising from the use of the information in this publication. AWI invests in research, development, innovation and marketing activities along the global supply chain for Australian wool. AWI is grateful for its funding, which is primarily provided by Australian woolgrowers through a wool levy and by the Australian Government which provides a matching contribution for eligible R&D activities © 2019 Australian Wool Innovation Ltd. All rights reserved. Contents Executive Summary .................................................................................................................... 3 1 Introduction/Hypothesis .................................................................................................... 5 2 Literature Review ............................................................................................................... 6 3 Project Objectives .............................................................................................................. 8 4 Success in Achieving Objectives ........................................................................................ -
Evaluation of Variability in Human Kidney Organoids
ARTICLES https://doi.org/10.1038/s41592-018-0253-2 Evaluation of variability in human kidney organoids Belinda Phipson 1, Pei X. Er1, Alexander N. Combes1,2, Thomas A. Forbes1,3,4, Sara E. Howden1,2, Luke Zappia1,5, Hsan-Jan Yen1, Kynan T. Lawlor1, Lorna J. Hale1,4, Jane Sun6, Ernst Wolvetang6, Minoru Takasato1,7, Alicia Oshlack1,5 and Melissa H. Little 1,2,4* The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although individ- ual organoids within a differentiation batch showed strong transcriptional correlation, we noted significant variation between experimental batches, particularly in genes associated with temporal maturation. Single-cell profiling revealed shifts in neph- ron patterning and proportions of component cells. Distinct induced pluripotent stem cell clones showed congruent transcrip- tional programs, with interexperimental and interclonal variation also strongly associated with nephron patterning. Epithelial cells isolated from organoids aligned with total organoids at the same day of differentiation, again implicating relative matura- tion as a confounder. This understanding of experimental variation facilitated an optimized analysis of organoid-based disease modeling, thereby increasing the utility of kidney organoids for personalized medicine and functional genomics. he ability to derive induced pluripotent stem cells (iPSCs) In this study, we provide a comprehensive transcriptional from the somatic cells of patients1, together with directed dif- and morphological evaluation of our kidney organoid protocol. Tferentiation protocols, provides a capacity to model the cell Applying RNA sequencing (RNA-seq) to 57 whole organoids and types affected by disease. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Identification of Novel Kirrel3 Gene Splice Variants in Adult Human
Durcan et al. BMC Physiology 2014, 14:11 http://www.biomedcentral.com/1472-6793/14/11 RESEARCH ARTICLE Open Access Identification of novel Kirrel3 gene splice variants in adult human skeletal muscle Peter Joseph Durcan1, Johannes D Conradie1, Mari Van deVyver2 and Kathryn Helen Myburgh1* Abstract Background: Multiple cell types including trophoblasts, osteoclasts and myoblasts require somatic cell fusion events as part of their physiological functions. In Drosophila Melanogaster the paralogus type 1 transmembrane receptors and members of the immunoglobulin superfamily Kin of Irre (Kirre) and roughest (Rst) regulate myoblast fusion during embryonic development. Present within the human genome are three homologs to Kirre termed Kin of Irre like (Kirrel) 1, 2 and 3. Currently it is unknown if Kirrel3 is expressed in adult human skeletal muscle. Results: We investigated (using PCR and Western blot) Kirrel3 in adult human skeletal muscle samples taken at rest and after mild exercise induced muscle damage. Kirrel3 mRNA expression was verified by sequencing and protein presence via blotting with 2 different anti-Kirrel3 protein antibodies. Evidence for three alternatively spliced Kirrel3 mRNA transcripts in adult human skeletal muscle was obtained. Kirrel3 mRNA in adult human skeletal muscle was detected at low or moderate levels, or not at all. This sporadic expression suggests that Kirrel3 is expressed in a pulsatile manner. Several anti Kirrel3 immunoreactive proteins were detected in all adult human skeletal muscle samples analysed and results suggest the presence of different isoforms or posttranslational modification, or both. Conclusion: The results presented here demonstrate for the first time that there are at least 3 splice variants of Kirrel3 expressed in adult human skeletal muscle, two of which have never previously been identified in human muscle. -
Nephrin Is Specifically Located at the Slit Diaphragm of Glomerular Podocytes
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 7962–7967, July 1999 Cell Biology Nephrin is specifically located at the slit diaphragm of glomerular podocytes VESA RUOTSALAINEN*†,PA¨IVI LJUNGBERG*‡§,JORMA WARTIOVAARA¶,ULLA LENKKERI†,MARJO KESTILA¨†, ʈ HANNU JALANKO‡,CHRISTER HOLMBERG‡, AND KARL TRYGGVASON† †Biocenter and Department of Biochemistry, University of Oulu, 90570 Oulu, Finland; ‡Hospital for Children and Adolescents, University Hospital of Helsinki, 00014 Helsinki, Finland; §Department of Bacteriology and Immunology, Haartman Institute and ¶Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; and ʈDivision of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden Communicated by Peter A. Reichard, Karolinska Institute, Stockholm, Sweden, April 9, 1999 (Received for review February 12, 1999) ABSTRACT We describe here the size and location of tight junction protein ZO-1 (17) has been localized in the nephrin, the first protein to be identified at the glomerular glomerulus, predominantly to points where the slit diaphragm podocyte slit diaphragm. In Western blots, nephrin antibodies is inserted into the lateral cell membrane of the foot process generated against the two terminal extracellular Ig domains of (18). The ZO-1 protein possibly connects the slit diaphragm, recombinant human nephrin recognized a 180-kDa protein in directly or indirectly, to the cytoskeleton. lysates of human glomeruli and a 150-kDa protein in trans- In numerous primary and secondary diseases of the kidney, fected COS-7 cell lysates. In immunofluorescence, antibodies the filtration barrier is affected, resulting in proteinuria, i.e., to this transmembrane protein revealed reactivity in the leakage of albumin and larger plasma proteins into the urine, glomerular basement membrane region, whereas the podocyte with edema and nephrotic syndrome as a consequence. -
NPHS2 Antibody (Podocin) (R30382)
NPHS2 Antibody (Podocin) (R30382) Catalog No. Formulation Size R30382 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human, Mouse, Rat Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Antigen affinity Buffer Lyophilized from 1X PBS with 2.5% BSA and 0.025% sodium azide/thimerosal UniProt Q9NP85 Applications Western blot : 0.5-1ug/ml Limitations This NPHS2 antibody is available for research use only. Western blot testing of NPHS2 antibody and rat kidney tissue lysate. Predicted molecular weight ~42kDa. Description NPHS2, also called Podocin (PDCN), is a protein which lines the podocytes and assists in maintaining the barrier at the glomerular basement membrane. NPHS2 is a causative gene for Familial idiopathic nephrotic syndromes, which represents a heterogeneous group of kidney disorders, and include autosomal recessive steroid-resistant nephrotic syndrome, which is characterized by early childhood onset of proteinuria, rapid progression to end-stage renal disease and focal segmental glomerulosclerosis. By positional cloning, it was mapped to 1q25-31. It is almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli, and encodes a new integral membrane protein, podocin, belonging to the stomatin protein family. Boute et al.(2000) found ten different NPHS2 mutations, comprising nonsense, frameshift and missense mutations, to segregate with the disease, demonstrating a crucial role for podocin in the function of the glomerular filtration barrier. Application Notes The stated application concentrations are suggested starting amounts. Titration of the NPHS2 antibody may be required due to differences in protocols and secondary/substrate sensitivity. -
NPHS2 Gene Mutation, Atopy, and Gender As Risk Factors for Steroid-Resistant Nephrotic Syndrome in Indonesians
Paediatrica Indonesiana VOLUME 51 September NUMBER 5 Original Article NPHS2 gene mutation, atopy, and gender as risk factors for steroid-resistant nephrotic syndrome in Indonesians Dedi Rachmadi, Dany Hilmanto, Ponpon Idjradinata, Abdurahman Sukadi Abstract QUHFHQW\HDUVPROHFXODUJHQHWLFVWXGLHVKDYH Background 6WHURLGUHVLVWDQWQHSKURWLFV\QGURPH 6516 RIWHQ EHHQZHOOGHYHORSHGLQFOXGLQJVWXGLHVIRU GHYHORSVLQWRHQGVWDJHUHQDOGLVHDVH3UHYLRXVVWXGLHVKDYH JHQHVLQYROYHGLQWKHSDWKRJHQHVLVRIQHSKURWLF reported that NPHS2JHQHPXWDWLRQJHQGHUDQGDWRSLFKLVWRU\ V\QGURPH2ISDUWLFXODULQWHUHVWLVWKHJHQH DUHULVNIDFWRUVDVVRFLDWHGZLWK6516,QWHUHWKQLFVRFLRFXOWXUDO I DQGHQYLURQPHQWDOGLIIHUHQFHVKDYHDOVREHHQVXJJHVWHGWRDIIHFW encoding a protein that maintains the diaphragm slit WKHVHPXWDWLRQV RISRGRF\WHV*HQHPXWDWLRQDQDO\VLVLVLPSRUWDQW Objective7RDQDO\]HSRVVLEOHULVNIDFWRUVIRU6516LQFOXGLQJ with regards to phenotype and predicting the severity NPHS2JHQHPXWDWLRQV &o7DQGGHO* JHQGHUDQG RIFOLQLFDOPDQLIHVWDWLRQV The NPHS2 gene encodes DWRSLFKLVWRU\LQ,QGRQHVLDQVXEMHFWVZLWK6516 the podocin protein and is located on chromosome Methods$FDVHFRQWUROVWXG\ZLWKVXEMHFWVFRQVLVWLQJRI 6516SDWLHQWVDQGFRQWUROVXEMHFWVZDVXQGHUWDNHQLQ T0XWDWLRQRIWKLVJHQHKDVEHHQDVVRFLDWHG ,QGRQHVLDQWHDFKLQJFHQWUHKRVSLWDOVIURP6HSWHPEHUWR ZLWKSRRUVWHURLGUHVSRQVHLQWUHDWPHQWRIQHSKURWLF 'HFHPEHU$QDO\VLVRIWKHNPHS2JHQHPXWDWLRQLQ V\QGURPH 16 3UHYLRXVVWXGLHVKDYHVKRZQWKDW &o7ZDVSHUIRUPHGE\DPSOLILFDWLRQUHIUDFWRU\PXWDWLRQV\VWHP SRNS patients with an NPHS2JHQHPXWDWLRQKDG SRO\PHUDVHFKDLQUHDFWLRQ $5063&5 ZKLOHWKDWIRUWKH NPHS2JHQHPXWDWLRQLQGHO*ZDVSHUIRUPHGE\UHVWULFWLRQ -
CG/CA Genotypes Represent Novel Markers in the NPHS2 Gene Region Associated with Nephrotic Syndrome
Journal of Genetics (2020)99:33 Ó Indian Academy of Sciences https://doi.org/10.1007/s12041-020-1188-9 (0123456789().,-volV)(0123456789().,-volV) RESEARCH ARTICLE CG/CA genotypes represent novel markers in the NPHS2 gene region associated with nephrotic syndrome LEILA ESMAELI CHAMGORDANI, NASIM EBRAHIMI, FARZANE AMIRMAHANI and SADEQ VALLIAN* Genetics Division, Faculty of Biological Sciences and Technologies, Department of Cellular and Molecular Biology and Microbiology, University of Isfahan, Isfahan, Iran *For correspondence. E-mail: [email protected]. Received 15 November 2019; revised 10 January 2020; accepted 14 January 2020 Abstract. Nephrotic syndrome (NS) is considered as a primary disease of the kidney that represents a heterogeneous group of glomerular disorders occurring mainly in children. It is generally divided into steroid-sensitive and steroid-resistant forms, depending upon the patient’s response to steroid therapy. Among the genes involved, the NPHS2 gene has been reported as the causative gene in steroid resistant form of nephrotic syndrome. In the present study, heterozygosity rate, allelic frequency and linkage of rs2274625 and rs3829795 markers were investigated in the NPHS2 gene region. To determine the SNP alleles, tetra-primer ARMS PCR was used. After genotyping rs2274625 and rs3829795 polymorphic markers in 120 unrelated individuals and nine trios families, the data were analysed using various computer programs such as UCSC Genome Browser, dbSNP and SNPper. Based on the statistical analysis of the results, for rs2274625 marker, allele frequency for C and T alleles was 97% and 3%, respectively. For rs3829795 marker allele frequency for G and A alleles was 55% and 45%, respectively. -
Selective Impairment of Gene Expression and Assembly of Nephrin in Human Diabetic Nephropathy
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Kidney International, Vol. 65 (2004), pp. 2193–2200 Selective impairment of gene expression and assembly of nephrin in human diabetic nephropathy ARIELA BENIGNI,ELENA GAGLIARDINI,SUSANNA TOMASONI,MAURO ABBATE,PIERO RUGGENENTI, RAGHU KALLURI, and GIUSEPPE REMUZZI Mario Negri Institute for Pharmacological Research, Negri Bergamo Laboratories, Bergamo, Italy; Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; and Division of Nephrology and Dialysis, Azienda Ospedaliera, Ospedali Riuniti, Bergamo, Italy Selective impairment of gene expression and assembly of The nephropathy associated with diabetes is the lead- nephrin in human diabetic nephropathy. ing cause of end-stage renal disease (ESRD) worldwide Background. Recent disclosure of podocyte proteins has un- [1, 2]. In North America, 40% of patients adhering to raveled previously rather mysterious mechanisms that govern glomerular perm-selectivity in health and disease. Here we ad- dialysis transplantation programs in 1998 were diabetic. dressed the role of nephrin, CD2-associated protein (CD2AP), Related treatment costs were estimated at $51,000 per and podocin together with the integrity of the slit diaphragm year (i.e., about $12,000 more than the costs for nondia- in the pathogenesis of proteinuria of patients with diabetes and betics). nephropathy. Diabetic nephropathy, defined as urinary protein ex- Methods. Nephrin mRNA and protein expression were eval- > uated in parallel in adult diabetic patients by in situ hybridiza- cretion rate 0.5 g/24 hours (clinical proteinuria), man- tion and immunohistochemistry. For comparison, nondiabetic ifests within 15 to 20 years after the onset of disease in patients with minimal change nephrosis and normal control 20% to 40% of patients. -
NPHS2 (Podocin) Mutations in Nephrotic Syndrome
0031-3998/05/5705-0054R PEDIATRIC RESEARCH Vol. 57, No. 5, Pt 2, 2005 Copyright © 2005 International Pediatric Research Foundation, Inc. Printed in U.S.A. NPHS2 (Podocin) Mutations in Nephrotic Syndrome. Clinical Spectrum and Fine Mechanisms GIANLUCA CARIDI, FRANCESCO PERFUMO, AND GIAN MARCO GHIGGERI Laboratory on Pathophysiology of Uremia [G.C., G.M.C.], and Renal Unit [F.P., G.M.C.], Istituto Giannina Gaslini, 16148 Genova, Italy. ABSTRACT Nephrotic syndrome (NS) is the most frequent cause of iments with the common R229Q polymorphism demonstrated an proteinuria in children and is emerging as a leading cause of altered interaction with nephrin that affects the stability of the uremia. Molecular studies in families with recessive NS have led functional unit. Overall, data are here presented that underscore to the discovery of specialized molecules endowed in podocytes a major role of inherited defects of NPHS2 in NS in children that play a role in proteinuria. This review focalizes the key (including a relevant impact in sporadic cases) and give the position of podocin (NPHS2 gene) in this rapidly evolving field functional rationale for the association. A practical compendium and furnishes a compendium to those involved in clinics and is also given to clinicians involved in the management of NS that genetics of NS. Screening for NPHS2 mutations have been done should modify the classic therapeutic approach. (Pediatr Res 57: in sporadic NS and familial cases with recessive inheritance, 54R–61R, 2005) documenting a mutation detection rate of 45–55% in families and 8–20% in sporadic NS according to the different groups and considering all the clinical phenotypes. -
Recombinant Human Kirrel3/NEPH2 Catalog Number: 4910-K3
Recombinant Human Kirrel3/NEPH2 Catalog Number: 4910-K3 DESCRIPTION Source Mouse myeloma cell line, NS0derived Leu29Ala535 & Tyr33Ala535 & Arg41Ala535, all with a Cterminal 6His tag Accession # Q8IZU9 Nterminal Sequence Leu29 Analysis Predicted Molecular 56.1 kDa, 55.7 kDa & 54.7 kDa Mass SPECIFICATIONS SDSPAGE 6585 kDa, reducing conditions Activity Measured by the ability of the immobilized protein to support the adhesion of MS1 mouse pancreatic islet endothelial cells. When 5 x 104 cells/well are added to rhKirrel3 coated plates (30 µg/mL, 100 µL/well), approximately 40%70% will adhere after 90 minutes at 37° C. Optimal dilutions should be determined by each laboratory for each application. Endotoxin Level <0.10 EU per 1 μg of the protein by the LAL method. Purity >95%, by SDSPAGE under reducing conditions and visualized by silver stain. Formulation Lyophilized from a 0.2 μm filtered solution in PBS. See Certificate of Analysis for details. PREPARATION AND STORAGE Reconstitution Reconstitute at 100 μg/mL in sterile PBS. Shipping The product is shipped at ambient temperature. Upon receipt, store it immediately at the temperature recommended below. Stability & Storage Use a manual defrost freezer and avoid repeated freezethaw cycles. l 12 months from date of receipt, 20 to 70 °C as supplied. l 1 month, 2 to 8 °C under sterile conditions after reconstitution. l 3 months, 20 to 70 °C under sterile conditions after reconstitution. BACKGROUND Kirrel3 (kin of irregular chiasm1like 3), also known as Kirre or NEPH2 (nephrinlike 2), is an ~100 kDa type I transmembrane glycoprotein belonging to the NEPH family within the immunoglobulin superfamily (1, 2). -
Human KIRREL / NEPH1 / KIRREL1 Protein (Fc Tag)
Human KIRREL / NEPH1 / KIRREL1 Protein (Fc Tag) Catalog Number: 15752-H02H General Information SDS-PAGE: Gene Name Synonym: NEPH1 Protein Construction: A DNA sequence encoding the human KIRREL (NP_060710.3) (Met1-Leu493) was expressed with the Fc region of human IgG1 at the C-terminus. Source: Human Expression Host: HEK293 Cells QC Testing Purity: > 95 % as determined by SDS-PAGE Endotoxin: Protein Description < 1.0 EU per μg of the protein as determined by the LAL method NEPH1 (KIRREL1) belongs to a family of three closely related Stability: transmembrane proteins of the Ig superfamily with a structure similar to that of nephrin. All three Neph proteins share a conserved podocin-binding ℃ Samples are stable for up to twelve months from date of receipt at -70 motif; mutation of a centrally located tyrosine residue dramatically lowers the affinity of Neph1 for podocin. Neph1 triggers AP-1 activation similarly to Gln 17 Predicted N terminal: nephrin but requires the presence of Tec family kinases for efficient Molecular Mass: transactivation. Neph1 consists of a signal peptide, five Ig-like C2-type domains with the middle domain overlapping with a PKD-like domain, an The recombinant human KIRREL/Fc comprises 715 amino acids and has a RGD sequence, a transmembrane domain and a cytoplasmic tail, which is predicted molecular mass of 78.8 kDa. The apparent molecular mass of the expressed in slit diaphragm domains of podocytes and in vertebrate and protein is approximately 96.1 kDa in SDS-PAGE under reducing conditions. invertebrate nervous systems. Neph1 is abundantly expressed in the kidney, specifically expressed in podocytes of kidney glomeruli, and plays a Formulation: significant role in the normal development and function of the glomerular permeability.