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Guerriero CJ, Carattino MD, Sharp KG, Kantz LJ, Gresko NP, Caplan MJ, Brodsky JL. Identification of polycystin 2 missense mutants targeted for endoplasmic reticulum-associated degradation. Am J Physiol Cell Physiol 2025; 328:C483-C499. [PMID: 39714991 DOI: 10.1152/ajpcell.00776.2024] [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: 10/15/2024] [Revised: 12/05/2024] [Accepted: 12/05/2024] [Indexed: 12/25/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder leading to end-stage renal disease. ADPKD arises from mutations in the PKD1 and PKD2 genes, which encode polycystin 1 (PC1) and polycystin 2 (PC2), respectively. PC2 is a nonselective cation channel, and disease-linked mutations disrupt normal cellular processes, including signaling and fluid secretion. In this study, we investigate whether disease-causing missense mutations compromise PC2 folding, an event that can lead to endoplasmic reticulum-associated degradation (ERAD). To this end, we first developed a new yeast PC2 expression system. We show that the yeast system provides a tractable model to investigate PC2 biogenesis and that a disease-associated PC2 mutant, D511V, exhibits increased polyubiquitination and accelerated proteasome-dependent degradation compared with wild-type PC2. In contrast to wild-type PC2, the PC2 D511V variant also failed to improve the growth of yeast strains that lack endogenous potassium transporters, highlighting a loss of channel function at the cell surface and a new assay for loss-of-function PKD2 variants. In HEK293 cells, both D511V along with another disease-associated mutant, R322Q, were targeted for ERAD. Consistent with defects in protein folding, the surface localization of these PC2 variants was increased by incubation at low-temperature in HEK293 cells, underscoring the potential to pharmacologically rescue these and perhaps other misfolded PC2 alleles. Together, our study supports the hypothesis that select PC2 missense variants are degraded by ERAD, the potential for screening PKD2 alleles in a new genetic system, and the possibility that chemical chaperone-based therapeutic interventions might be used to treat ADPKD.NEW & NOTEWORTHY This study indicates that select missense mutations in PC2, a protein that when mutated leads to ADPKD, result in protein misfolding and degradation via the ERAD pathway. Our work leveraged a new yeast model and an HEK293 cell model to discover the mechanism underlying PC2 instability and demonstrates the potential for pharmacological rescue. We also suggest that targeting the protein misfolding phenotype with chemical chaperones may offer new therapeutic strategies to manage ADPKD-related protein dysfunction.
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Affiliation(s)
- Christopher J Guerriero
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Marcelo D Carattino
- Departments of Medicine and Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Katherine G Sharp
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Luke J Kantz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Nikolay P Gresko
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, United States
| | - Michael J Caplan
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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Packer M, Ferreira JP, Butler J, Filippatos G, Januzzi JL, González Maldonado S, Panova-Noeva M, Pocock SJ, Prochaska JH, Saadati M, Sattar N, Sumin M, Anker SD, Zannad F. Reaffirmation of Mechanistic Proteomic Signatures Accompanying SGLT2 Inhibition in Patients With Heart Failure: A Validation Cohort of the EMPEROR Program. J Am Coll Cardiol 2024; 84:1979-1994. [PMID: 39217550 DOI: 10.1016/j.jacc.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Sodium-glucose cotransporter 2 (SGLT2) inhibitors exert a distinctive pattern of direct biological effects on the heart and kidney under experimental conditions, but the meaningfulness of these signatures for patients with heart failure has not been fully defined. OBJECTIVES We performed the first mechanistic validation study of large-scale proteomics in a double-blind randomized trial of any treatment in patients with heart failure. METHODS In a discovery cohort from the EMPEROR (Empagliflozin Outcome Trial in Patients With Chronic Heart Failure and Reduced Ejection Fraction) program, we studied the effect of randomized treatment with placebo or empagliflozin on 1,283 circulating proteins in 1,134 patients with heart failure with a reduced or preserved ejection fraction. In a validation cohort, we expanded the number to 2,155 assessed proteins, which were measured in 1,120 EMPEROR participants who had not been studied previously. RESULTS In the validation cohort, 25 proteins were the most differentially enriched by empagliflozin (ie, ≥15% between-group difference and false discovery rate <1% at 12 weeks with known effects on the heart or kidney): 1) 13 proteins promote autophagy and other cellular quality-control functions (IGFBP1, OTUB1, DNAJB1, DNAJC9, RBP2, IST1, HSPA8, H-FABP, FABP6, ATPIFI, TfR1, EPO, IGBP1); 2) 12 proteins enhance mitochondrial health and ATP production (UMtCK, TBCA, L-FABP, H-FABP, FABP5, FABP6, RBP2, IST1, HSPA8, ATPIFI, TfR1, EPO); 3) 7 proteins augment cellular iron mobilization or erythropoiesis (TfR1, EPO, IGBP1, ERMAP, UROD, ATPIF1, SNCA); 4) 3 proteins influence renal tubular sodium handling; and 5) 9 proteins have restorative effects in the heart or kidneys, with many proteins exerting effects in >1 domain. These biological signatures replicated those observed in our discovery cohort. When the threshold for a meaningful between-group difference was lowered to ≥10%, there were 58 additional differentially enriched proteins with actions on the heart and kidney, but the biological signatures remained the same. CONCLUSIONS The replication of mechanistic signatures across discovery and validation cohorts closely aligns with the experimental effects of SGLT2 inhibitors. Thus, the actions of SGLT2 inhibitors-to promote autophagy, restore mitochondrial health and production of ATP, promote iron mobilization and erythropoiesis, influence renal tubular ion reabsorption, and normalize cardiac and renal structure and function-are likely to be relevant to patients with heart failure. (EMPagliflozin outcomE tRial in Patients With chrOnic heaRt Failure With Preserved Ejection Fraction [EMPEROR-Preserved], NCT03057951; EMPagliflozin outcomE tRial in Patients With chrOnic heaRt Failure With Reduced Ejection Fraction [EMPEROR-Reduced], NCT03057977).
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Affiliation(s)
- Milton Packer
- Baylor Heart and Vascular Institute, Baylor University Medical Center, Dallas, Texas, USA; Imperial College London, London, United Kingdom.
| | - João Pedro Ferreira
- UnIC@RISE, Cardiovascular Research and Development Center, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal; Baylor Scott and White Research Institute, Dallas, Texas, USA
| | - Javed Butler
- Baylor Scott and White Research Institute, Dallas, Texas, USA; University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Gerasimos Filippatos
- National and Kapodistrian University of Athens School of Medicine, Athens University Hospital Attikon, Athens, Greece
| | - James L Januzzi
- National and Kapodistrian University of Athens School of Medicine, Athens University Hospital Attikon, Athens, Greece; Massachusetts General Hospital and Baim Institute for Clinical Research, Boston, Massachusetts, USA
| | | | - Marina Panova-Noeva
- Boehringer Ingelheim Pharma GmbH & Co KG, Ingelheim, Germany; Center for Thrombosis and Haemostasis, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stuart J Pocock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jürgen H Prochaska
- Boehringer Ingelheim International GmbH, Ingelheim, Germany; Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maral Saadati
- Elderbrook Solutions GmbH, on behalf of Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mikhail Sumin
- Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - Stefan D Anker
- Department of Cardiology (CVK) of German Heart Center Charité, Institute of Health Center for Regenerative Therapies (BCRT), German Centre for Cardiovascular Research (DZHK) partner site Berlin, Charité Universitätsmedizin, Berlin, Germany
| | - Faiez Zannad
- Centre d'Investigations Cliniques Plurithématique 1433, INSERM, Université de Lorraine, Nancy, France; F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists), INSERM U1116, Centre Hospitalier Régional Universitaire de Nancy, Nancy, France
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Nguyen NH, Sheng S, Banerjee A, Guerriero CJ, Chen J, Wang X, Mackie TD, Welling PA, Kleyman TR, Bahar I, Carlson AE, Brodsky JL. Characterization of hyperactive mutations in the renal potassium channel ROMK uncovers unique effects on channel biogenesis and ion conductance. Mol Biol Cell 2024; 35:ar119. [PMID: 39024255 PMCID: PMC11449386 DOI: 10.1091/mbc.e23-12-0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Hypertension affects one billion people worldwide and is the most common risk factor for cardiovascular disease, yet a comprehensive picture of its underlying genetic factors is incomplete. Amongst regulators of blood pressure is the renal outer medullary potassium (ROMK) channel. While select ROMK mutants are prone to premature degradation and lead to disease, heterozygous carriers of some of these same alleles are protected from hypertension. Therefore, we hypothesized that gain-of-function (GoF) ROMK variants which increase potassium flux may predispose people to hypertension. To begin to test this hypothesis, we employed genetic screens and a candidate-based approach to identify six GoF variants in yeast. Subsequent functional assays in higher cells revealed two variant classes. The first group exhibited greater stability in the endoplasmic reticulum, enhanced channel assembly, and/or increased protein at the cell surface. The second group of variants resided in the PIP2-binding pocket, and computational modeling coupled with patch-clamp studies demonstrated lower free energy for channel opening and slowed current rundown, consistent with an acquired PIP2-activated state. Together, these findings advance our understanding of ROMK structure-function, suggest the existence of hyperactive ROMK alleles in humans, and establish a system to facilitate the development of ROMK-targeted antihypertensives.
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Affiliation(s)
- Nga H. Nguyen
- Department of Biological Sciences, School of Medicine, University of Pittsburgh, PA 15260
| | - Shaohu Sheng
- Renal-Electrolyte Division, Department of Medicine, School of Medicine, University of Pittsburgh, PA 15260
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15260
| | | | - Jingxin Chen
- Renal-Electrolyte Division, Department of Medicine, School of Medicine, University of Pittsburgh, PA 15260
| | - Xueqi Wang
- Renal-Electrolyte Division, Department of Medicine, School of Medicine, University of Pittsburgh, PA 15260
| | - Timothy D. Mackie
- Department of Biological Sciences, School of Medicine, University of Pittsburgh, PA 15260
| | - Paul A. Welling
- Division of Nephrology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Thomas R. Kleyman
- Renal-Electrolyte Division, Department of Medicine, School of Medicine, University of Pittsburgh, PA 15260
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15260
| | - Anne E. Carlson
- Department of Biological Sciences, School of Medicine, University of Pittsburgh, PA 15260
| | - Jeffrey L. Brodsky
- Department of Biological Sciences, School of Medicine, University of Pittsburgh, PA 15260
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4
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Kok M, Hartnett-Scott K, Happe CL, MacDonald ML, Aizenman E, Brodsky JL. The expression system influences stability, maturation efficiency, and oligomeric properties of the potassium-chloride co-transporter KCC2. Neurochem Int 2024; 174:105695. [PMID: 38373478 PMCID: PMC10923169 DOI: 10.1016/j.neuint.2024.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024]
Abstract
The neuron-specific K+/Cl- co-transporter 2, KCC2, which is critical for brain development, regulates γ-aminobutyric acid-dependent inhibitory neurotransmission. Consistent with its function, mutations in KCC2 are linked to neurodevelopmental disorders, including epilepsy, schizophrenia, and autism. KCC2 possesses 12 transmembrane spans and forms an intertwined dimer. Based on its complex architecture and function, reduced cell surface expression and/or activity have been reported when select disease-associated mutations are present in the gene encoding the protein, SLC12A5. These data suggest that KCC2 might be inherently unstable, as seen for other complex polytopic ion channels, thus making it susceptible to cellular quality control pathways that degrade misfolded proteins. To test these hypotheses, we examined KCC2 stability and/or maturation in five model systems: yeast, HEK293 cells, primary rat neurons, and rat and human brain synaptosomes. Although studies in yeast revealed that KCC2 is selected for endoplasmic reticulum-associated degradation (ERAD), experiments in HEK293 cells supported a more subtle role for ERAD in maintaining steady-state levels of KCC2. Nevertheless, this system allowed for an analysis of KCC2 glycosylation in the ER and Golgi, which serves as a read-out for transport through the secretory pathway. In turn, KCC2 was remarkably stable in primary rat neurons, suggesting that KCC2 folds efficiently in more native systems. Consistent with these data, the mature glycosylated form of KCC2 was abundant in primary rat neurons as well as in rat and human brain. Together, this work details the first insights into the influence that the cellular and membrane environments have on several fundamental KCC2 properties, acknowledges the advantages and disadvantages of each system, and helps set the stage for future experiments to assess KCC2 in a normal or disease setting.
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Affiliation(s)
- Morgan Kok
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karen Hartnett-Scott
- Department of Neurobiology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cassandra L Happe
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elias Aizenman
- Department of Neurobiology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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Nguyen NH, Sarangi S, McChesney EM, Sheng S, Durrant JD, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields putative disease-associated ROMK variants with distinct defects. PLoS Genet 2023; 19:e1011051. [PMID: 37956218 PMCID: PMC10695394 DOI: 10.1371/journal.pgen.1011051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/04/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal, and there is currently no cure. Bartter syndrome type II specifically arises from mutations in KCNJ1, which encodes the renal outer medullary potassium channel, ROMK. Over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified, yet their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined genomic data in both the NIH TOPMed and ClinVar databases with the aid of Rhapsody, a verified computational algorithm that predicts mutation pathogenicity and disease severity. Subsequent phenotypic studies using a yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced cell surface expression. Another mutation (T300R) was ERAD-resistant, but defects in channel activity were apparent based on two-electrode voltage clamp measurements in X. laevis oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies to advance precision medicine.
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Affiliation(s)
- Nga H. Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Srikant Sarangi
- Paradigm4, Inc., Waltham, Massachusetts, United States of America
| | - Erin M. McChesney
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shaohu Sheng
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aidan W. Porter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas R. Kleyman
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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6
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Nguyen NH, Sarangi S, McChesney EM, Sheng S, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields new disease-associated ROMK variants with distinct defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539609. [PMID: 37214976 PMCID: PMC10197530 DOI: 10.1101/2023.05.05.539609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal. Although there is no cure for this disease, specific genes that lead to different Bartter syndrome subtypes have been identified. Bartter syndrome type II specifically arises from mutations in the KCNJ1 gene, which encodes the renal outer medullary potassium channel, ROMK. To date, over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified. Yet, their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined ROMK genomic data in both the NIH TOPMed and ClinVar databases with the aid of a computational algorithm that predicts protein misfolding and disease severity. Subsequent phenotypic studies using a high throughput yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced protein expression at the cell surface. Another ERAD-targeted ROMK mutant (L320P) was found in only one of the screens. In contrast, another mutation (T300R) was ERAD-resistant, but defects in ROMK activity were apparent after expression and two-electrode voltage clamp measurements in Xenopus oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies. Author Summary Bartter syndrome is a rare genetic disorder characterized by defective renal electrolyte handing, leading to debilitating symptoms and, in some patients, death in infancy. Currently, there is no cure for this disease. Bartter syndrome is divided into five types based on the causative gene. Bartter syndrome type II results from genetic variants in the gene encoding the ROMK protein, which is expressed in the kidney and assists in regulating sodium, potassium, and water homeostasis. Prior work established that some disease-associated ROMK mutants misfold and are destroyed soon after their synthesis in the endoplasmic reticulum (ER). Because a growing number of drugs have been identified that correct defective protein folding, we wished to identify an expanded cohort of similarly misshapen and unstable disease-associated ROMK variants. To this end, we developed a pipeline that employs computational analyses of human genome databases with genetic and biochemical assays. Next, we both confirmed the identity of known variants and uncovered previously uncharacterized ROMK variants associated with Bartter syndrome type II. Further analyses indicated that select mutants are targeted for ER-associated degradation, while another mutant compromises ROMK function. This work sets-the-stage for continued mining for ROMK loss of function alleles as well as other potassium channels, and positions select Bartter syndrome mutations for correction using emerging pharmaceuticals.
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Nguyen NH, Brodsky JL. The cellular pathways that maintain the quality control and transport of diverse potassium channels. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194908. [PMID: 36638864 PMCID: PMC9908860 DOI: 10.1016/j.bbagrm.2023.194908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Potassium channels are multi-subunit transmembrane proteins that permit the selective passage of potassium and play fundamental roles in physiological processes, such as action potentials in the nervous system and organismal salt and water homeostasis, which is mediated by the kidney. Like all ion channels, newly translated potassium channels enter the endoplasmic reticulum (ER) and undergo the error-prone process of acquiring post-translational modifications, folding into their native conformations, assembling with other subunits, and trafficking through the secretory pathway to reach their final destinations, most commonly the plasma membrane. Disruptions in these processes can result in detrimental consequences, including various human diseases. Thus, multiple quality control checkpoints evolved to guide potassium channels through the secretory pathway and clear potentially toxic, aggregation-prone misfolded species. We will summarize current knowledge on the mechanisms underlying potassium channel quality control in the secretory pathway, highlight diseases associated with channel misfolding, and suggest potential therapeutic routes.
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Affiliation(s)
- Nga H Nguyen
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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8
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Schwabl S, Teis D. Protein quality control at the Golgi. Curr Opin Cell Biol 2022; 75:102074. [PMID: 35364487 DOI: 10.1016/j.ceb.2022.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
Abstract
The majority of the proteome in eukaryotic cells is targeted to organelles. To maintain protein homeostasis (proteostasis), distinct protein quality control (PQC) machineries operate on organelles, where they detect misfolded proteins, orphaned and mis-localized proteins and selectively target these proteins into different ubiquitin-dependent or -independent degradation pathways. Thereby, PQC prevents proteotoxic effects that would disrupt organelle integrity and cause cellular damage that leads to diseases. Here, we will discuss emerging mechanisms for PQC machineries at the Golgi apparatus, the central station for the sorting and the modification of proteins that traffic to the endo-lysosomal system, or along the secretory pathway to the PM and to the extracellular space. We will focus on Golgi PQC pathways that (1) retrieve misfolded and orphaned proteins from the Golgi back to the endoplasmic reticulum, (2) extract these proteins from Golgi membranes for proteasomal degradation, (3) or selectively target these proteins to lysosomes for degradation.
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Affiliation(s)
- Sinead Schwabl
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Austria.
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Hager NA, McAtee CK, Lesko MA, O’Donnell AF. Inwardly Rectifying Potassium Channel Kir2.1 and its "Kir-ious" Regulation by Protein Trafficking and Roles in Development and Disease. Front Cell Dev Biol 2022; 9:796136. [PMID: 35223865 PMCID: PMC8864065 DOI: 10.3389/fcell.2021.796136] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Potassium (K+) homeostasis is tightly regulated for optimal cell and organismal health. Failure to control potassium balance results in disease, including cardiac arrythmias and developmental disorders. A family of inwardly rectifying potassium (Kir) channels helps cells maintain K+ levels. Encoded by KCNJ genes, Kir channels are comprised of a tetramer of Kir subunits, each of which contains two-transmembrane domains. The assembled Kir channel generates an ion selectivity filter for K+ at the monomer interface, which allows for K+ transit. Kir channels are found in many cell types and influence K+ homeostasis across the organism, impacting muscle, nerve and immune function. Kir2.1 is one of the best studied family members with well-defined roles in regulating heart rhythm, muscle contraction and bone development. Due to their expansive roles, it is not surprising that Kir mutations lead to disease, including cardiomyopathies, and neurological and metabolic disorders. Kir malfunction is linked to developmental defects, including underdeveloped skeletal systems and cerebellar abnormalities. Mutations in Kir2.1 cause the periodic paralysis, cardiac arrythmia, and developmental deficits associated with Andersen-Tawil Syndrome. Here we review the roles of Kir family member Kir2.1 in maintaining K+ balance with a specific focus on our understanding of Kir2.1 channel trafficking and emerging roles in development and disease. We provide a synopsis of the vital work focused on understanding the trafficking of Kir2.1 and its role in development.
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Affiliation(s)
| | | | | | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
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SLC26A9 is selected for endoplasmic reticulum associated degradation (ERAD) via Hsp70-dependent targeting of the soluble STAS domain. Biochem J 2021; 478:4203-4220. [PMID: 34821356 PMCID: PMC8826537 DOI: 10.1042/bcj20210644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
SLC26A9, a member of the solute carrier protein family, transports chloride ions across various epithelia. SLC26A9 also associates with other ion channels and transporters linked to human health, and in some cases these heterotypic interactions are essential to support the biogenesis of both proteins. Therefore, understanding how this complex membrane protein is initially folded might provide new therapeutic strategies to overcome deficits in the function of SLC26A9 partners, one of which is associated with Cystic Fibrosis. To this end, we developed a novel yeast expression system for SLC26A9. This facile system has been used extensively with other ion channels and transporters to screen for factors that oversee protein folding checkpoints. As commonly observed for other channels and transporters, we first noted that a substantial fraction of SLC26A9 is targeted for endoplasmic reticulum associated degradation (ERAD), which destroys folding-compromised proteins in the early secretory pathway. We next discovered that ERAD selection requires the Hsp70 chaperone, which can play a vital role in ERAD substrate selection. We then created SLC26A9 mutants and found that the transmembrane-rich domain of SLC26A9 was quite stable, whereas the soluble cytosolic STAS domain was responsible for Hsp70-dependent ERAD. To support data obtained in the yeast model, we were able to recapitulate Hsp70-facilitated ERAD of the STAS domain in human tissue culture cells. These results indicate that a critical barrier to nascent membrane protein folding can reside within a specific soluble domain, one that is monitored by components associated with the ERAD machinery.
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Hou J, Daniels PN, Burke MD. Small Molecule Channels Harness Membrane Potential to Concentrate Potassium in trk1Δtrk2Δ Yeast. ACS Chem Biol 2020; 15:1575-1580. [PMID: 32427463 DOI: 10.1021/acschembio.0c00180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many protein ion channels harness membrane potential to move ions in opposition to their chemical gradient. Deficiencies of such proteins cause several human diseases, including cystic fibrosis, Bartter Syndrome, and proximal renal tubular acidosis. Using yeast as a eukaryotic model system, we asked whether, in the context of a protein ion channel deficiency in vivo, small molecule channels could similarly harness membrane potential to concentrate ions. Trk potassium transporters use membrane potential to move potassium from a relatively low concentration outside cells (∼15 mM) to one of >10× higher inside (150-500 mM); trk1Δtrk2Δ are unable to concentrate potassium or grow in standard media. Here we show that potassium-permeable, but not potassium-selective, small-molecule ion channels formed by amphotericin B can harness membrane potential to concentrate potassium and thereby restore trk1Δtrk2Δ growth. This finding expands the list of potential human channelopathies that might be addressed by a molecular prosthetics approach.
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Affiliation(s)
- Jennifer Hou
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Page N Daniels
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Martin D Burke
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, 807 South Wright Street, Champaign, Illinois 61820, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, Illinois 61801, United States
- Arnold and Mabel Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
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12
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Ponzoni L, Nguyen NH, Bahar I, Brodsky JL. Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel. PLoS Comput Biol 2020; 16:e1007749. [PMID: 32251469 PMCID: PMC7162551 DOI: 10.1371/journal.pcbi.1007749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 04/16/2020] [Accepted: 02/25/2020] [Indexed: 02/02/2023] Open
Abstract
The renal outer medullary potassium (ROMK) channel is essential for potassium transport in the kidney, and its dysfunction is associated with a salt-wasting disorder known as Bartter syndrome. Despite its physiological significance, we lack a mechanistic understanding of the molecular defects in ROMK underlying most Bartter syndrome-associated mutations. To this end, we employed a ROMK-dependent yeast growth assay and tested single amino acid variants selected by a series of computational tools representative of different approaches to predict each variants’ pathogenicity. In one approach, we used in silico saturation mutagenesis, i.e. the scanning of all possible single amino acid substitutions at all sequence positions to estimate their impact on function, and then employed a new machine learning classifier known as Rhapsody. We also used two additional tools, EVmutation and Polyphen-2, which permitted us to make consensus predictions on the pathogenicity of single amino acid variants in ROMK. Experimental tests performed for selected mutants in different classes validated the vast majority of our predictions and provided insights into variants implicated in ROMK dysfunction. On a broader scope, our analysis suggests that consolidation of data from complementary computational approaches provides an improved and facile method to predict the severity of an amino acid substitution and may help accelerate the identification of disease-causing mutations in any protein. As the number of sequenced human genomes rises, a major challenge is to identify which single amino acid variations in a protein affect function and predispose individuals to disease. While predictive algorithms are available for this purpose, a comparative analysis of recently developed algorithms has not been adequately performed, nor is it clear whether combining algorithms would improve predictive power. To this end, we compared the efficacy of three publicly available algorithms and applied the results to Bartter syndrome, a human disease for which numerous poorly-characterized single amino acid variants have been identified and for which there is no cure. In silico saturation mutagenesis, i.e., the computational prediction of pathogenesis for every possible amino acid substitution, allowed us to experimentally test predictions by measuring the activity of an ion channel linked to Bartter syndrome. Based on data from blinded experiments, we discovered that Rhapsody and EVmutation successfully predicted deleterious mutations. Moreover, Rhapsody—which takes into account evolutionary as well as structural and dynamic considerations—predicted that >90% of known Bartter syndrome mutations are deleterious. Overall, our data will aid investigators who wish to test single amino acid variants in any protein and aid biomedical researchers who wish to develop hypotheses on the potential severity of genetic variants uncovered from genome databases.
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Affiliation(s)
- Luca Ponzoni
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nga H. Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (IB); (JLB)
| | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (IB); (JLB)
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13
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Zangerl-Plessl EM, Qile M, Bloothooft M, Stary-Weinzinger A, van der Heyden MAG. Disease Associated Mutations in K IR Proteins Linked to Aberrant Inward Rectifier Channel Trafficking. Biomolecules 2019; 9:biom9110650. [PMID: 31731488 PMCID: PMC6920955 DOI: 10.3390/biom9110650] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022] Open
Abstract
The ubiquitously expressed family of inward rectifier potassium (KIR) channels, encoded by KCNJ genes, is primarily involved in cell excitability and potassium homeostasis. Channel mutations associate with a variety of severe human diseases and syndromes, affecting many organ systems including the central and peripheral neural system, heart, kidney, pancreas, and skeletal muscle. A number of mutations associate with altered ion channel expression at the plasma membrane, which might result from defective channel trafficking. Trafficking involves cellular processes that transport ion channels to and from their place of function. By alignment of all KIR channels, and depicting the trafficking associated mutations, three mutational hotspots were identified. One localized in the transmembrane-domain 1 and immediately adjacent sequences, one was found in the G-loop and Golgi-export domain, and the third one was detected at the immunoglobulin-like domain. Surprisingly, only few mutations were observed in experimentally determined Endoplasmic Reticulum (ER)exit-, export-, or ER-retention motifs. Structural mapping of the trafficking defect causing mutations provided a 3D framework, which indicates that trafficking deficient mutations form clusters. These “mutation clusters” affect trafficking by different mechanisms, including protein stability.
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Affiliation(s)
- Eva-Maria Zangerl-Plessl
- Department of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (E.-M.Z.-P.); (A.S.-W.)
| | - Muge Qile
- Department of Medical Physiology, Division of Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands; (M.Q.); (M.B.)
| | - Meye Bloothooft
- Department of Medical Physiology, Division of Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands; (M.Q.); (M.B.)
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (E.-M.Z.-P.); (A.S.-W.)
| | - Marcel A. G. van der Heyden
- Department of Medical Physiology, Division of Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands; (M.Q.); (M.B.)
- Correspondence: ; Tel.: +31-887558901
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14
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Mackie TD, Brodsky JL. Investigating Potassium Channels in Budding Yeast: A Genetic Sandbox. Genetics 2018; 209:637-650. [PMID: 29967058 PMCID: PMC6028241 DOI: 10.1534/genetics.118.301026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 12/26/2022] Open
Abstract
Like all species, the model eukaryote Saccharomyces cerevisiae, or Bakers' yeast, concentrates potassium in the cytosol as an electrogenic osmolyte and enzyme cofactor. Yeast are capable of robust growth on a wide variety of potassium concentrations, ranging from 10 µM to 2.5 M, due to the presence of a high-affinity potassium uptake system and a battery of cation exchange transporters. Genetic perturbation of either of these systems retards yeast growth on low or high potassium, respectively. However, these potassium-sensitized yeast are a powerful genetic tool, which has been leveraged for diverse studies. Notably, the potassium-sensitive cells can be transformed with plasmids encoding potassium channels from bacteria, plants, or mammals, and subsequent changes in growth rate have been found to correlate with the activity of the introduced potassium channel. Discoveries arising from the use of this assay over the past three decades have increased our understanding of the structure-function relationships of various potassium channels, the mechanisms underlying the regulation of potassium channel function and trafficking, and the chemical basis of potassium channel modulation. In this article, we provide an overview of the major genetic tools used to study potassium channels in S. cerevisiae, a survey of seminal studies utilizing these tools, and a prospective for the future use of this elegant genetic approach.
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Affiliation(s)
- Timothy D Mackie
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
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Saez F, Hong NJ, Garvin JL. NADPH oxidase 4-derived superoxide mediates flow-stimulated NKCC2 activity in thick ascending limbs. Am J Physiol Renal Physiol 2018; 314:F934-F941. [PMID: 29672130 DOI: 10.1152/ajprenal.00631.2017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Luminal flow augments Na+ reabsorption in the thick ascending limb more than can be explained by increased ion delivery. This segment reabsorbs 30% of the filtered load of Na+, playing a key role in its homeostasis. Whether flow elevations enhance Na+-K+-2Cl- cotransporter (NKCC2) activity and the second messenger involved are unknown. We hypothesized that raising luminal flow augments NKCC2 activity by enhancing superoxide ([Formula: see text]) production by NADPH oxidase 4 (NOX4). NKCC2 activity was measured in thick ascending limbs perfused at either 5 or 20 nl/min with and without inhibitors of [Formula: see text] production. Raising luminal flow from 5 to 20 nl/min enhanced NKCC2 activity from 4.8 ± 0.9 to 6.3 ± 1.2 arbitrary fluorescent units (AFU)/s. Maintaining flow at 5 nl/min did not alter NKCC2 activity. The superoxide dismutase mimetic manganese (III) tetrakis (4-benzoic acid) porphyrin chloride blunted NKCC2 activity from 3.5 ± 0.4 to 2.5 ± 0.2 AFU/s when flow was 20 nl/min but not 5 nl/min. When flow was 20 nl/min, NKCC2 activity showed no change with time. The selective NOX1/4 inhibitor GKT-137831 blunted NKCC2 activity when thick ascending limbs were perfused at 20 nl/min from 7.2 ± 1.1 to 4.5 ± 0.8 AFU/s but not at 5 nl/min. The inhibitor also prevented luminal flow from elevating [Formula: see text] production. Allopurinol, a xanthine oxidase inhibitor, had no effect on NKCC2 activity when flow was 20 nl/min. Tetanus toxin prevents flow-induced stimulation of NKCC2 activity. We conclude that elevations in luminal flow enhance NaCl reabsorption in thick ascending limbs by stimulating NKCC2 via NOX4 activation and increased [Formula: see text]. NKCC2 activation is primarily the result of insertion of new transporters in the membrane.
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Affiliation(s)
- Fara Saez
- Department of Physiology and Biophysics, Case Western Reserve University , Cleveland, Ohio
| | - Nancy J Hong
- Department of Physiology and Biophysics, Case Western Reserve University , Cleveland, Ohio
| | - Jeffrey L Garvin
- Department of Physiology and Biophysics, Case Western Reserve University , Cleveland, Ohio
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