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      Autosomal Dominant Tubulointerstitial Kidney Disease with Adult Onset due to a Novel Renin Mutation Mapping in the Mature Protein

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          Abstract

          Autosomal dominant tubulointerstitial kidney disease (ADTKD) is a genetically heterogeneous renal disorder leading to progressive loss of renal function. ADTKD- REN is due to rare mutations in renin, all localized in the protein leader peptide and affecting its co-translational insertion in the endoplasmic reticulum (ER). Through exome sequencing in an adult-onset ADTKD family we identified a new renin variant, p.L381P, mapping in the mature protein. To assess its pathogenicity, we combined genetic data, computational and predictive analysis and functional studies. The L381P substitution affects an evolutionary conserved residue, co-segregates with renal disease, is not found in population databases and is predicted to be deleterious by in silico tools and by structural modelling. Expression of the L381P variant leads to its ER retention and induction of the Unfolded Protein Response in cell models and to defective pronephros development in zebrafish. Our work shows that REN mutations outside of renin leader peptide can cause ADTKD and delineates an adult form of ADTKD- REN, a condition which has usually its onset in childhood. This has implications for the molecular diagnosis and the estimated prevalence of the disease and points at ER homeostasis as a common pathway affected in ADTKD- REN, and possibly more generally in ADTKD.

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          Most cited references29

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          SDM: a server for predicting effects of mutations on protein stability

          Abstract Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2
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            Classical Renin-Angiotensin system in kidney physiology.

            The renin-angiotensin system has powerful effects in control of the blood pressure and sodium homeostasis. These actions are coordinated through integrated actions in the kidney, cardiovascular system and the central nervous system. Along with its impact on blood pressure, the renin-angiotensin system also influences a range of processes from inflammation and immune responses to longevity. Here, we review the actions of the "classical" renin-angiotensin system, whereby the substrate protein angiotensinogen is processed in a two-step reaction by renin and angiotensin converting enzyme, resulting in the sequential generation of angiotensin I and angiotensin II, the major biologically active renin-angiotensin system peptide, which exerts its actions via type 1 and type 2 angiotensin receptors. In recent years, several new enzymes, peptides, and receptors related to the renin-angiotensin system have been identified, manifesting a complexity that was previously unappreciated. While the functions of these alternative pathways will be reviewed elsewhere in this journal, our focus here is on the physiological role of components of the "classical" renin-angiotensin system, with an emphasis on new developments and modern concepts.
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              Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response.

              ATF6 is a member of the basic-leucine zipper family of transcription factors. It contains a transmembrane domain and is located in membranes of the endoplasmic reticulum. ATF6 has been implicated in the endoplasmic reticulum (ER) stress response pathway since it can activate expression of GRP78 and other genes induced by the ER stress response. ER stress appears to activate ATF6 by cleavage from the ER membrane and translocation to the nucleus. However, direct DNA binding by ATF6 had not been demonstrated. In this report, we have identified a consensus DNA binding sequence for ATF6. This site is related to but distinct from ATF1/CREB binding sites. The site was placed in a reporter gene and was specifically activated by ATF6 overexpression and was strongly induced by the ER stress response. A dominant negative form of ATF6 blocked ER stress induction of both ATF6 site and GRP78 reporter genes. We further found that GAL4-ATF6 could be activated by ER stress. These results demonstrate that ATF6 is a direct target of the ER stress response. A proximal sensor of the ER stress response, human IRE1 (hIRE1), was sufficient to activate the ATF6 reporter gene, while a dominant negative form of hIRE1 blocked ER stress activation, suggesting that hIRE1 is upstream of ATF6 in the ER stress signaling pathway.
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                Author and article information

                Contributors
                rampoldi.luca@hsr.it
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                12 August 2019
                12 August 2019
                2019
                : 9
                : 11601
                Affiliations
                [1 ]ISNI 0000000417581884, GRID grid.18887.3e, Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, , IRCCS San Raffaele Scientific Institute, ; Milan, Italy
                [2 ]ISNI 0000000417571846, GRID grid.7637.5, Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, , University of Brescia and Montichiari Hospital, ; Brescia, Italy
                [3 ]GRID grid.412725.7, Prenatal Diagnosis Unit, Department of Obstetrics and Gynecology, , ASST Spedali Civili, ; Brescia, Italy
                [4 ]ISNI 0000 0004 1757 3470, GRID grid.5608.b, Department of Biology, , University of Padova, ; Padova, Italy
                [5 ]ISNI 0000 0004 1763 1124, GRID grid.5611.3, Department of Biotechnology, , University of Verona, ; Verona, Italy
                [6 ]ISNI 0000000417581884, GRID grid.18887.3e, Center for Translational Genomics and Bioinformatics, , IRCCS San Raffaele Scientific Institute, ; Milan, Italy
                [7 ]ISNI 0000 0004 1760 0109, GRID grid.419504.d, Laboratory of Molecular Nephrology, , Istituto Giannina Gaslini IRCCS, ; Genoa, Italy
                [8 ]GRID grid.412725.7, Laboratory of Medical Genetics, Department of Pathology, , ASST Spedali Civili, ; Brescia, Italy
                [9 ]ISNI 0000 0004 1937 0626, GRID grid.4714.6, Department of Biosciences and Nutrition & Center for Innovative Medicine, , Karolinska Institutet, ; Huddinge, Sweden
                Author information
                http://orcid.org/0000-0001-5883-3951
                http://orcid.org/0000-0003-0384-3700
                http://orcid.org/0000-0003-4527-290X
                http://orcid.org/0000-0001-6700-3001
                http://orcid.org/0000-0002-2679-6946
                http://orcid.org/0000-0002-0544-7042
                Article
                48014
                10.1038/s41598-019-48014-6
                6691008
                31406136
                258d0982-7115-4e3e-966e-3f1dd0ebefd7
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 April 2019
                : 22 July 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003196, Ministero della Salute (Ministry of Health, Italy);
                Award ID: GR-2011-02346749
                Award ID: “5 per mille” program
                Award ID: 5 per mille program
                Award ID: RF-2010-2319394
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100002426, Fondazione Telethon (Telethon Foundation);
                Award ID: GGP14263
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                disease genetics,interstitial nephritis,mutation
                Uncategorized
                disease genetics, interstitial nephritis, mutation

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