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Nieto-Romero V, García-Torralba A, Molinos-Vicente A, Moya FJ, Rodríguez-Perales S, García-Escudero R, Salido E, Segovia JC, García-Bravo M. Restored glyoxylate metabolism after AGXT gene correction and direct reprogramming of primary hyperoxaluria type 1 fibroblasts. iScience 2024; 27:109530. [PMID: 38577102 PMCID: PMC10993186 DOI: 10.1016/j.isci.2024.109530] [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: 04/03/2023] [Revised: 01/18/2024] [Accepted: 03/16/2024] [Indexed: 04/06/2024] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare inherited metabolic disorder characterized by oxalate overproduction in the liver, resulting in renal damage. It is caused by mutations in the AGXT gene. Combined liver and kidney transplantation is currently the only permanent curative treatment. We combined locus-specific gene correction and hepatic direct cell reprogramming to generate autologous healthy induced hepatocytes (iHeps) from PH1 patient-derived fibroblasts. First, site-specific AGXT corrected cells were obtained by homology directed repair (HDR) assisted by CRISPR-Cas9, following two different strategies: accurate point mutation (c.731T>C) correction or knockin of an enhanced version of AGXT cDNA. Then, iHeps were generated, by overexpression of hepatic transcription factors. Generated AGXT-corrected iHeps showed hepatic gene expression profile and exhibited in vitro reversion of oxalate accumulation compared to non-edited PH1-derived iHeps. This strategy set up a potential alternative cellular source for liver cell replacement therapy and a personalized PH1 in vitro disease model.
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Affiliation(s)
- Virginia Nieto-Romero
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Aida García-Torralba
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Andrea Molinos-Vicente
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Francisco José Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)-ISCIII, Research Institute Hospital 12 de Octubre (imas12)-University Hospital 12 de Octubre, 28040 Madrid, Spain
| | - Eduardo Salido
- Pathology Department, Hospital Universitario de Canarias, Universidad La Laguna, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 38320 Tenerife, Spain
| | - José-Carlos Segovia
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - María García-Bravo
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
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2
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Vankova P, Pacheco-Garcia JL, Loginov DS, Gómez-Mulas A, Kádek A, Martín-Garcia JM, Salido E, Man P, Pey AL. Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. FEBS Lett 2024; 598:485-499. [PMID: 38243391 DOI: 10.1002/1873-3468.14800] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Primary hyperoxaluria type I (PH1) is caused by deficient alanine:glyoxylate aminotransferase (AGT) activity. PH1-causing mutations in AGT lead to protein mistargeting and aggregation. Here, we use hydrogen-deuterium exchange (HDX) to characterize the wild-type (WT), the LM (a polymorphism frequent in PH1 patients) and the LM G170R (the most common mutation in PH1) variants of AGT. We provide the first experimental analysis of AGT structural dynamics, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants only show local destabilization. Enzymatic transamination of the pyridoxal 5-phosphate cofactor bound to AGT hardly affects stability. Our study, thus, supports that AGT misfolding is not caused by dramatic effects on structural dynamics.
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Affiliation(s)
- Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Alan Kádek
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - José Manuel Martín-Garcia
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Spain
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3
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Gatticchi L, Grottelli S, Ambrosini G, Pampalone G, Gualtieri O, Dando I, Bellezza I, Cellini B. CRISPR/Cas9-mediated knock-out of AGXT1 in HepG2 cells as a new in vitro model of Primary Hyperoxaluria Type 1. Biochimie 2022; 202:110-122. [PMID: 35964771 DOI: 10.1016/j.biochi.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/02/2022]
Abstract
AGXT1 encodes alanine:glyoxylate aminotransferase 1 (AGT1), a liver peroxisomal pyridoxal 5'-phosphate dependent-enzyme whose deficit causes Primary Hyperoxaluria Type 1 (PH1). PH1 is a rare disease characterized by overproduction of oxalate, first leading to kidney stones formation, and possibly evolving to life-threatening systemic oxalosis. A minority of PH1 patients is responsive to pyridoxine, while the option for non-responders is liver-kidney transplantation. Therefore, huge efforts are currently focused on the identification of new therapies, including the promising approaches based on RNA silencing recently approved. Many PH1-associated mutations are missense and lead to a variety of kinetic and/or folding defects on AGT1. In this context, the availability of a reliable in vitro disease model would be essential to better understand the phenotype of known or newly-identified pathogenic variants as well as to test novel drug candidates. Here, we took advantage of the CRISPR/Cas9 technology to specifically knock-out AGXT1 in HepG2 cells, a hepatoma-derived cell model exhibiting a conserved glyoxylate metabolism. AGXT1-KO HepG2 displayed null AGT1 expression and significantly reduced transaminase activity leading to an enhanced secretion of oxalate upon glycolate challenge. Known pathogenic AGT1 variants expressed in AGXT1-KO HepG2 cells showed alteration in both protein levels and specific transaminase activity, as well as a partial mitochondrial mistargeting when associated with a common polymorphism. Notably, pyridoxine treatment was able to partially rescue activity and localization of clinically-responsive variants. Overall, our data validate AGXT1-KO HepG2 cells as a novel cellular model to investigate PH1 pathophysiology, and as a platform for drug discovery and development.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy
| | - Silvia Grottelli
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy
| | - Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, Biochemistry Section, University of Verona, 37134, Verona, Italy
| | - Gioena Pampalone
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy
| | - Ottavia Gualtieri
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy
| | - Ilaria Dando
- Department of Neurosciences, Biomedicine and Movement Sciences, Biochemistry Section, University of Verona, 37134, Verona, Italy
| | - Ilaria Bellezza
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy.
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4
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Infantes L, Rivera-Moreno M, Daniel-Mozo M, Benavente JL, Ocaña-Cuesta J, Coego A, Lozano-Juste J, Rodriguez PL, Albert A. Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop. FRONTIERS IN PLANT SCIENCE 2022; 13:884029. [PMID: 35734246 PMCID: PMC9207482 DOI: 10.3389/fpls.2022.884029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The binding of the plant phytohormone Abscisic acid (ABA) to the family of ABA receptors (PYR/PYL/RCAR) triggers plant responses to abiotic stress. Thus, the implementation of genetic or chemical strategies to modulate PYR/PYL activity might be biotechnologically relevant. We have employed the available structural information on the PYR/PYL receptors to design SlPYL1, a tomato receptor, harboring a single point mutation that displays enhanced ABA dependent and independent activity. Interestingly, crystallographic studies show that this mutation is not directly involved in ABA recognition or in the downstream phosphatase (PP2C) inhibitory interaction, rather, molecular dynamic based ensemble refinement restrained by crystallographic data indicates that it enhances the conformational variability required for receptor activation and it is involved in the stabilization of an active form of the receptor. Moreover, structural studies on this receptor have led to the identification of niacin as an ABA antagonist molecule in vivo. We have found that niacin blocks the ABA binding site by mimicking ABA receptor interactions, and the niacin interaction inhibits the biochemical activity of the receptor.
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Affiliation(s)
- Lourdes Infantes
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Maria Rivera-Moreno
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Miguel Daniel-Mozo
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Luis Benavente
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Javier Ocaña-Cuesta
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Armando Albert
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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5
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Dindo M, Pascarelli S, Chiasserini D, Grottelli S, Costantini C, Uechi G, Giardina G, Laurino P, Cellini B. Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase. Protein Sci 2022; 31:e4303. [PMID: 35481644 PMCID: PMC8996469 DOI: 10.1002/pro.4303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 01/24/2023]
Abstract
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT-Ma) and a minor polymorphic form (AGT-Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT-Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT-Mi. An in-depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT-Ma and AGT-Mi. Finally, co-immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein-protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well-defined fitness window, thus expanding the adaptability potential of the protein.
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Affiliation(s)
- Mirco Dindo
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Stefano Pascarelli
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | | | - Silvia Grottelli
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
| | | | - Gen‐Ichiro Uechi
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Giorgio Giardina
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Barbara Cellini
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
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Shee K, Stoller ML. Perspectives in primary hyperoxaluria - historical, current and future clinical interventions. Nat Rev Urol 2021; 19:137-146. [PMID: 34880452 PMCID: PMC8652378 DOI: 10.1038/s41585-021-00543-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/19/2022]
Abstract
Primary hyperoxalurias are a devastating family of diseases leading to multisystem oxalate deposition, nephrolithiasis, nephrocalcinosis and end-stage renal disease. Traditional treatment paradigms are limited to conservative management, dialysis and combined transplantation of the kidney and liver, of which the liver is the primary source of oxalate production. However, transplantation is associated with many potential complications, including operative risks, graft rejection, post-transplant organ failure, as well as lifelong immunosuppressive medications and their adverse effects. New therapeutics being developed for primary hyperoxalurias take advantage of biochemical knowledge about oxalate synthesis and metabolism, and seek to specifically target these pathways with the goal of decreasing the accumulation and deposition of oxalate in the body. Primary hyperoxalurias are a devastating family of diseases that eventually lead to end-stage renal disease. In this Review, Shee and Stoller discuss current treatment paradigms for primary hyperoxalurias, new therapeutics and their mechanisms of action, and future directions for novel research in the field. Primary hyperoxalurias (PHs) are a devastating family of rare, autosomal-recessive genetic disorders that lead to multisystem oxalate deposition, nephrolithiasis, nephrocalcinosis and end-stage renal disease. Traditional treatment paradigms are limited to conservative management, dialysis and inevitably transplantation of the kidney and liver, which is associated with high morbidity and the need for lifelong immunosuppression. New therapeutics being developed for PHs take advantage of biochemical knowledge about oxalate synthesis and metabolism to specifically target these pathways, with the goal of decreasing the accumulation and deposition of plasma oxalate in the body. New therapeutics can be divided into classes, and include substrate reduction therapy, intestinal oxalate degradation, chaperone therapy, enzyme restoration therapy and targeting of the inflammasome. Lumasiran, a mRNA therapeutic targeting glycolate oxidase, was the first primary hyperoxaluria-specific therapeutic approved by the European Medicines Agency and the FDA in 2020. Future work includes further clinical trials for promising therapeutics in the pipeline, identification of biomarkers of response to PH-directed therapy, optimization of drug development and delivery of new therapeutics.
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Affiliation(s)
- Kevin Shee
- Department of Urology, UCSF, San Francisco, CA, USA.
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7
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Small Molecule-Based Enzyme Inhibitors in the Treatment of Primary Hyperoxalurias. J Pers Med 2021; 11:jpm11020074. [PMID: 33513899 PMCID: PMC7912158 DOI: 10.3390/jpm11020074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Primary hyperoxalurias (PHs) are a group of inherited alterations of the hepatic glyoxylate metabolism. PHs classification based on gene mutations parallel a variety of enzymatic defects, and all involve the harmful accumulation of calcium oxalate crystals that produce systemic damage. These geographically widespread rare diseases have a deep impact in the life quality of the patients. Until recently, treatments were limited to palliative measures and kidney/liver transplants in the most severe forms. Efforts made to develop pharmacological treatments succeeded with the biotechnological agent lumasiran, a siRNA product against glycolate oxidase, which has become the first effective therapy to treat PH1. However, small molecule drugs have classically been preferred since they benefit from experience and have better pharmacological properties. The development of small molecule inhibitors designed against key enzymes of glyoxylate metabolism is on the focus of research. Enzyme inhibitors are successful and widely used in several diseases and their pharmacokinetic advantages are well known. In PHs, effective enzymatic targets have been determined and characterized for drug design and interesting inhibitory activities have been achieved both in vitro and in vivo. This review describes the most recent advances towards the development of small molecule enzyme inhibitors in the treatment of PHs, introducing the multi-target approach as a more effective and safe therapeutic option.
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8
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Zheng R, Li Y, Wang L, Fang X, Zhang J, He L, Yang L, Li D, Geng H. CRISPR/Cas9-mediated metabolic pathway reprogramming in a novel humanized rat model ameliorates primary hyperoxaluria type 1. Kidney Int 2020; 98:947-957. [PMID: 32464217 DOI: 10.1016/j.kint.2020.04.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022]
Abstract
Primary hyperoxaluria type I is caused by mutations in the alanine glyoxylate aminotransferase gene (AGXT), leading to accumulation of glyoxylate and subsequent production of oxalate and urolithiasis. Here, we generated a novel rat model of primary hyperoxaluria type I that carries a D205N mutation in the partially humanized Agxt gene through the CRISPR/Cas9 system. The AgxtD205N mutant rats showed undetectable alanine glyoxylate aminotransferase protein expression, developed hyperoxaluria at 1 month of age and exhibited severe renal calcium oxalate deposition after ethylene glycol challenge. This suggests our novel model is more relevant to the human disease than existing animal models. To test whether this model could be used for the development of innovative therapeutics, SaCas9 targeting hydroxyacid oxidase 1, responsible for metabolizing glycolate into glyoxylate, was delivered via adeno-associated viral vectors into newborn rats with primary hyperoxaluria type 1. This approach generated nearly 30% indels in the Hao1 gene in the liver, leading to 42% lower urine oxalate levels in the treated group than in the control group and preventing the rats with primary hyperoxaluria type 1 from undergoing severe nephrocalcinosis for at least 12 months. Thus, our results demonstrate that this partially humanized AgxtD205N rat strain is a high-performing model of primary hyperoxaluria type 1 for understanding pathology, and the development of novel therapeutics, such as reprogramming of the metabolic pathway through genome editing.
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Affiliation(s)
- Rui Zheng
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China
| | - Yueyan Li
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China
| | - Liren Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiaoliang Fang
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China
| | - Junqi Zhang
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China
| | - Lei He
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China
| | - Lei Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Hongquan Geng
- Department of Pediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Children's Stone Treatment Center of the National Health and Family Planning Commission of the People's Republic of China, Shanghai, China.
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9
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Estève J, Blouin JM, Lalanne M, Azzi-Martin L, Dubus P, Bidet A, Harambat J, Llanas B, Moranvillier I, Bedel A, Moreau-Gaudry F, Richard E. Targeted gene therapy in human-induced pluripotent stem cells from a patient with primary hyperoxaluria type 1 using CRISPR/Cas9 technology. Biochem Biophys Res Commun 2019; 517:677-683. [PMID: 31402115 DOI: 10.1016/j.bbrc.2019.07.109] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 12/12/2022]
Abstract
Primary hyperoxaluria type 1 (PH1) is an inherited metabolic disorder caused by a deficiency of the peroxisomal enzyme alanine-glyoxylate aminotransferase (AGT), which leads to overproduction of oxalate by the liver and results in urolithiasis, nephrocalcinosis and renal failure. The only curative treatment for PH1 is combined liver and kidney transplantation, which is limited by the lack of suitable organs, significant complications, and the life-long requirement for immunosuppressive agents to maintain organ tolerance. Hepatocyte-like cells (HLCs) generated from CRISPR/Cas9 genome-edited human-induced pluripotent stem cells would offer an attractive unlimited source of autologous gene-corrected liver cells as an alternative to orthotopic liver transplantation (OLT). Here we report the CRISPR/Cas9 nuclease-mediated gene targeting of a single-copy AGXT therapeutic minigene into the safe harbour AAVS1 locus in PH1-induced pluripotent stem cells (PH1-iPSCs) without off-target inserts. We obtained a robust expression of a codon-optimized AGT in HLCs derived from AAVS1 locus-edited PH1-iPSCs. Our study provides the proof of concept that CRISPR/Cas9-mediated integration of an AGXT minigene into the AAVS1 safe harbour locus in patient-specific iPSCs is an efficient strategy to generate functionally corrected hepatocytes, which in the future may serve as a source for an autologous cell-based gene therapy for the treatment of PH1.
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Affiliation(s)
- Julie Estève
- Univ. Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076, Bordeaux, France
| | - Jean-Marc Blouin
- Univ. Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076, Bordeaux, France
| | - Magalie Lalanne
- Univ. Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076, Bordeaux, France
| | - Lamia Azzi-Martin
- Univ. Bordeaux, INSERM, Bordeaux Research in Translational Oncology, U1053, CHU Bordeaux, 33076, Bordeaux, France
| | - Pierre Dubus
- Univ. Bordeaux, INSERM, Bordeaux Research in Translational Oncology, U1053, CHU Bordeaux, 33076, Bordeaux, France
| | - Audrey Bidet
- Laboratoire d'Hématologie, CHU de Bordeaux, Bordeaux, France
| | - Jérôme Harambat
- Service de Néphrologie Pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000, Bordeaux, France
| | - Brigitte Llanas
- Service de Néphrologie Pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000, Bordeaux, France
| | | | - Aurélie Bedel
- Univ. Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076, Bordeaux, France
| | | | - Emmanuel Richard
- Univ. Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076, Bordeaux, France.
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10
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Estève J, Blouin JM, Lalanne M, Azzi-Martin L, Dubus P, Bidet A, Harambat J, Llanas B, Moranvillier I, Bedel A, Moreau-Gaudry F, Richard E. Generation of induced pluripotent stem cells-derived hepatocyte-like cells for ex vivo gene therapy of primary hyperoxaluria type 1. Stem Cell Res 2019; 38:101467. [PMID: 31151050 DOI: 10.1016/j.scr.2019.101467] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/30/2019] [Accepted: 05/19/2019] [Indexed: 12/17/2022] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disorder of the liver metabolism due to functional deficiency of the peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). AGT deficiency results in overproduction of oxalate which complexes with calcium to form insoluble calcium-oxalate salts in urinary tracts, ultimately leading to end-stage renal disease. Currently, the only curative treatment for PH1 is combined liver-kidney transplantation, which is limited by donor organ shortage and lifelong requirement for immunosuppression. Transplantation of genetically modified autologous hepatocytes is an attractive therapeutic option for PH1. However, the use of fresh primary hepatocytes suffers from limitations such as organ availability, insufficient cell proliferation, loss of function, and the risk of immune rejection. We developed patient-specific induced pluripotent stem cells (PH1-iPSCs) free of reprogramming factors as a source of renewable and genetically defined autologous PH1-hepatocytes. We then investigated additive gene therapy using a lentiviral vector encoding wild-type AGT under the control of the liver-specific transthyretin promoter. Genetically modified PH1-iPSCs successfully provided hepatocyte-like cells (HLCs) that exhibited significant AGT expression at both RNA and protein levels after liver-specific differentiation process. These results pave the way for cell-based therapy of PH1 by transplantation of genetically modified autologous HLCs derived from patient-specific iPSCs.
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Affiliation(s)
- Julie Estève
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | - Jean-Marc Blouin
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | - Magalie Lalanne
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | | | - Pierre Dubus
- Univ.Bordeaux, INSERM, BARITON, U1053, CHU Bordeaux, 33076, France
| | - Audrey Bidet
- Laboratoire d'hématologie, CHU Bordeaux, Bordeaux, France
| | - Jérôme Harambat
- Service de Néphrologie pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000 Bordeaux, France
| | - Brigitte Llanas
- Service de Néphrologie pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000 Bordeaux, France
| | | | - Aurélie Bedel
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | | | - Emmanuel Richard
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France.
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11
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Kukreja A, Lasaro M, Cobaugh C, Forbes C, Tang JP, Gao X, Martin-Higueras C, Pey AL, Salido E, Sobolov S, Subramanian RR. Systemic Alanine Glyoxylate Aminotransferase mRNA Improves Glyoxylate Metabolism in a Mouse Model of Primary Hyperoxaluria Type 1. Nucleic Acid Ther 2019; 29:104-113. [PMID: 30676254 DOI: 10.1089/nat.2018.0740] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Primary Hyperoxaluria Type 1 (PH1) is an autosomal recessive disorder of glyoxylate metabolism. Loss of alanine glyoxylate aminotransferase (AGT) function to convert intermediate metabolite glyoxylate to glycine causes the accumulation and reduction of glyoxylate to glycolate, which eventually is oxidized to oxalate. Excess oxalate in PH1 patients leads to the formation and deposition of calcium oxalate crystals in the kidney and urinary tract. Oxalate crystal deposition causes a decline in renal function, systemic oxalosis, and eventually end-stage renal disease and premature death. mRNA-based therapies are a new class of drugs that work by replacing the missing enzyme. mRNA encoding AGT has the potential to restore normal glyoxylate to glycine metabolism, thus preventing the buildup of calcium oxalate in various organs. Panels of codon-optimized AGT mRNA constructs were screened in vitro and in wild-type mice for the production of a functional AGT enzyme. Two human constructs, wild-type and engineered AGT (RHEAM), were tested in Agxt-/- mice. Repeat dosing in Agxt-/- mice resulted in a 40% reduction in urinary oxalate, suggesting therapeutic benefit. These studies suggest that mRNA encoding AGT led to increased expression and activity of the AGT enzyme in liver that translated into decrease in urinary oxalate levels. Taken together, our data indicate that AGT mRNA may have the potential to be developed into a therapeutic for PH1.
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Affiliation(s)
- Anjli Kukreja
- 1 Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut
| | - Melissa Lasaro
- 1 Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut
| | | | - Chris Forbes
- 1 Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut
| | - Jian-Ping Tang
- 2 Clinical Pharmacology, Alexion Pharmaceuticals, Inc., New Haven, Connecticut
| | - Xiang Gao
- 3 Pharmacometrics and Physiologically Based PKPD Modeling and Simulation Clinical Development, Alexion Pharmaceuticals, Inc., Boston, Massachusetts
| | - Cristina Martin-Higueras
- 4 Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Angel L Pey
- 5 Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Salido
- 4 Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Susan Sobolov
- 1 Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut
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12
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Fernández-Higuero JÁ, Betancor-Fernández I, Mesa-Torres N, Muga A, Salido E, Pey AL. Structural and functional insights on the roles of molecular chaperones in the mistargeting and aggregation phenotypes associated with primary hyperoxaluria type I. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:119-152. [PMID: 30635080 DOI: 10.1016/bs.apcsb.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To carry out their biological function in cells, proteins must be folded and targeted to the appropriate subcellular location. These processes are controlled by a vast collection of interacting proteins collectively known as the protein homeostasis network, in which molecular chaperones play a prominent role. Protein homeostasis can be impaired by inherited mutations leading to genetic diseases. In this chapter, we focus on a particular disease, primary hyperoxaluria type 1 (PH1), in which disease-associated mutations exacerbate protein aggregation in the cell and mistarget the peroxisomal alanine:glyoxylate aminotransferase (AGT) protein to mitochondria, in part due to native state destabilization and enhanced interaction with Hsp60, 70 and 90 chaperone systems. After a general introduction of molecular chaperones and PH1, we review our current knowledge on the structural and energetic features of PH1-causing mutants that lead to these particular pathogenic mechanisms. From this perspective, and in the context of the key role of molecular chaperones in PH1 pathogenesis, we present and discuss current and future perspectives for pharmacological treatments for this disease.
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Affiliation(s)
- José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain.
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13
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Dindo M, Conter C, Oppici E, Ceccarelli V, Marinucci L, Cellini B. Molecular basis of primary hyperoxaluria: clues to innovative treatments. Urolithiasis 2018; 47:67-78. [PMID: 30430197 DOI: 10.1007/s00240-018-1089-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
Primary hyperoxalurias (PHs) are rare inherited disorders of liver glyoxylate metabolism, characterized by the abnormal production of endogenous oxalate, a metabolic end-product that is eliminated by urine. The main symptoms are related to the precipitation of calcium oxalate crystals in the urinary tract with progressive renal damage and, in the most severe form named Primary Hyperoxaluria Type I (PH1), to systemic oxalosis. The therapies currently available for PH are either poorly effective, because they address the symptoms and not the causes of the disease, or highly invasive. In the last years, advances in our understanding of the molecular bases of PH have paved the way for the development of new therapeutic strategies. They include (i) substrate-reduction therapies based on small-molecule inhibitors or the RNA interference technology, (ii) gene therapy, (iii) enzyme administration approaches, (iv) colonization with oxalate-degrading intestinal microorganisms, and, in PH1, (v) design of pharmacological chaperones. This paper reviews the basic principles of these new therapeutic strategies and what is currently known about their application to PH.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Veronica Ceccarelli
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Lorella Marinucci
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy.
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14
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Mesa-Torres N, Betancor-Fernández I, Oppici E, Cellini B, Salido E, Pey AL. Evolutionary Divergent Suppressor Mutations in Conformational Diseases. Genes (Basel) 2018; 9:E352. [PMID: 30011855 PMCID: PMC6071075 DOI: 10.3390/genes9070352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/26/2022] Open
Abstract
Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.
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Affiliation(s)
- Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
| | - Isabel Betancor-Fernández
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy.
| | - Eduardo Salido
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
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15
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McAuley M, Mesa-Torres N, McFall A, Morris S, Huang M, Pey AL, Timson DJ. Improving the Activity and Stability of Human Galactokinase for Therapeutic and Biotechnological Applications. Chembiochem 2018; 19:1088-1095. [DOI: 10.1002/cbic.201800025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Margaret McAuley
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry; University of Granada; Av. Fuentenueva s/n 18071 Granada Spain
| | - Aisling McFall
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Sarah Morris
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Meilan Huang
- School of Chemistry and Chemical Engineering; Queen's University; Belfast; David Keir Building Stranmillis Road Belfast BT9 5AG UK
| | - Angel L. Pey
- Department of Physical Chemistry; University of Granada; Av. Fuentenueva s/n 18071 Granada Spain
| | - David J. Timson
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
- School of Pharmacy and Biomolecular Sciences; University of Brighton; Huxley Building Lewes Road Brighton BN2 4GJ UK
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16
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Farelli JD, Asrani KH, Isaacs C, deBear JS, Stahley MR, Shah A, Lasaro MA, Cheng CJ, Subramanian RR. Leveraging Rational Protein Engineering to Improve mRNA Therapeutics. Nucleic Acid Ther 2018; 28:74-85. [PMID: 29437538 DOI: 10.1089/nat.2017.0697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Messenger RNA (mRNA) is a promising new class of therapeutics that has potential for treatment of diseases in fields such as immunology, oncology, vaccines, and inborn errors of metabolism. mRNA therapy has several advantages over DNA-based gene therapy, including the lack of the need for nuclear import and transcription, as well as limited possibility of genomic integration. One drawback of mRNA therapy, especially in cases such as metabolic disorders where repeated dosing will be necessary, is the relatively short in vivo half-life of mRNA (∼6-12 h). We hypothesize that protein engineering designed to improve translation, yielding longer-lasting protein, or modifications that would increase enzymatic activity would be helpful in alleviating this issue. In this study, we present two examples where sequence engineering improved the expression and duration, as well as enzymatic activity of target proteins in vitro. We then confirmed these findings in wild-type mice. This work shows that rational engineering of proteins can lead to improved therapies in vivo.
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Affiliation(s)
- Jeremiah D Farelli
- 1 Discovery Research, Alexion Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | - Kirtika H Asrani
- 1 Discovery Research, Alexion Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | - Cleo Isaacs
- 1 Discovery Research, Alexion Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | - Joanna S deBear
- 2 Nucleic Acid Technology, Alexion Pharmaceuticals, Inc. , New Haven, Connecticut
| | - Mary R Stahley
- 2 Nucleic Acid Technology, Alexion Pharmaceuticals, Inc. , New Haven, Connecticut
| | - Anumeha Shah
- 3 Preclinical Pharmacology, Alexion Pharmaceuticals, Inc. , New Haven, Connecticut
| | - Melissa A Lasaro
- 3 Preclinical Pharmacology, Alexion Pharmaceuticals, Inc. , New Haven, Connecticut
| | - Christopher J Cheng
- 2 Nucleic Acid Technology, Alexion Pharmaceuticals, Inc. , New Haven, Connecticut
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17
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Wanders RJA. Peroxisomal disorders: Improved laboratory diagnosis, new defects and the complicated route to treatment. Mol Cell Probes 2018; 40:60-69. [PMID: 29438773 DOI: 10.1016/j.mcp.2018.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
Abstract
Peroxisomes catalyze a number of essential metabolic functions of which fatty acid alpha- and beta-oxidation, ether phospholipid biosynthesis, glyoxylate detoxification and bile acid synthesis are the most important. The key role of peroxisomes in humans is exemplified by the existence of a group of peroxisomal disorders, caused by mutations in > 30 different genes which code for proteins with a role in either peroxisome biogenesis or one of the metabolic pathways in peroxisomes. Technological advances in laboratory methods at the metabolite-, enzyme-, and molecular level have not only allowed the identification of new peroxisomal disorders but also new phenotypes associated with already identified genetic defects thus extending the clinical spectrum. Unfortunately, progress in the field of pathogenesis and treatment has lagged behind although there are certainly new and hopeful developments with respect to X-linked adrenoleukodystrophy and hyperoxaluria type 1.
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Affiliation(s)
- Ronald J A Wanders
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Department of Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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18
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Oppici E, Dindo M, Conter C, Borri Voltattorni C, Cellini B. Folding Defects Leading to Primary Hyperoxaluria. Handb Exp Pharmacol 2018; 245:313-343. [PMID: 29071511 DOI: 10.1007/164_2017_59] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein misfolding is becoming one of the main mechanisms underlying inherited enzymatic deficits. This review is focused on primary hyperoxalurias, a group of disorders of glyoxylate detoxification associated with massive calcium oxalate deposition mainly in the kidneys. The most common and severe form, primary hyperoxaluria Type I, is due to the deficit of liver peroxisomal alanine/glyoxylate aminotransferase (AGT). Various studies performed in the last decade clearly evidence that many pathogenic missense mutations prevent the AGT correct folding, leading to various downstream effects including aggregation, increased degradation or mistargeting to mitochondria. Primary hyperoxaluria Type II and primary hyperoxaluria Type III are due to the deficit of glyoxylate reductase/hydroxypyruvate reductase (GRHPR) and 4-hydroxy-2-oxoglutarate aldolase (HOGA1), respectively. Although the molecular features of pathogenic variants of GRHPR and HOGA1 have not been investigated in detail, the data available suggest that some of them display folding defects. Thus, primary hyperoxalurias can be ranked among protein misfolding disorders, because in most cases the enzymatic deficit is due to the inability of each enzyme to reach its native and functional conformation. It follows that molecules able to improve the folding yield of the enzymes involved in each disease form could represent new therapeutic strategies.
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Affiliation(s)
- Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Mirco Dindo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Carla Borri Voltattorni
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli 1, 06132, Perugia, Italy.
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19
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Medina-Carmona E, Fuchs JE, Gavira JA, Mesa-Torres N, Neira JL, Salido E, Palomino-Morales R, Burgos M, Timson DJ, Pey AL. Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution. Hum Mol Genet 2017; 26:3531-3544. [DOI: 10.1093/hmg/ddx238] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/14/2017] [Indexed: 12/16/2022] Open
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20
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Martin-Higueras C, Torres A, Salido E. Molecular therapy of primary hyperoxaluria. J Inherit Metab Dis 2017; 40:481-489. [PMID: 28425073 DOI: 10.1007/s10545-017-0045-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/20/2017] [Accepted: 04/03/2017] [Indexed: 12/19/2022]
Abstract
During the last few decades, the molecular understanding of the mechanisms involved in primary hyperoxalurias (PHs) has set the stage for novel therapeutic approaches. The availability of PH mouse models has facilitated preclinical studies testing innovative treatments. PHs are autosomal recessive diseases where the enzymatic deficit plays a central pathogenic role. Thus, molecular therapies aimed at restoring such deficit or limiting the consequences of the metabolic derangement could be envisioned, keeping in mind the specific challenges posed by the cell-autonomous nature of the deficiency. Various molecular approaches like enzyme replacement, substrate reduction, pharmacologic chaperones, and gene and cell therapies have been explored in cells and mouse models of disease. Some of these proof-of-concept studies have paved the way to current clinical trials on PH type 1, raising hopes that much needed treatments will become available for this severe inborn error of metabolism.
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Affiliation(s)
- Cristina Martin-Higueras
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain
| | - Armando Torres
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain
| | - Eduardo Salido
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain.
- Department of Pathology, ULL School Medicine, 38320, Tenerife, Spain.
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21
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Affiliation(s)
- Barbara Cellini
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona (VR), Italy
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22
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Engineering ancestral protein hyperstability. Biochem J 2016; 473:3611-3620. [PMID: 27528732 DOI: 10.1042/bcj20160532] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 01/23/2023]
Abstract
Many experimental analyses and proposed scenarios support that ancient life was thermophilic. In congruence with this hypothesis, proteins encoded by reconstructed sequences corresponding to ancient phylogenetic nodes often display very high stability. Here, we show that such 'reconstructed ancestral hyperstability' can be further engineered on the basis of a straightforward approach that uses exclusively information afforded by the ancestral reconstruction process itself. Since evolution does not imply continuous progression, screening of the mutations between two evolutionarily related resurrected ancestral proteins may identify mutations that further stabilize the most stable one. To explore this approach, we have used a resurrected thioredoxin corresponding to the last common ancestor of the cyanobacterial, Deinococcus and Thermus groups (LPBCA thioredoxin), which has a denaturation temperature of ∼123°C. This high value is within the top 0.1% of the denaturation temperatures in the ProTherm database and, therefore, achieving further stabilization appears a priori as a challenging task. Nevertheless, experimental comparison with a resurrected thioredoxin corresponding to the last common ancestor of bacteria (denaturation temperature of ∼115°C) immediately identifies three mutations that increase the denaturation temperature of LPBCA thioredoxin to ∼128°C. Comparison between evolutionarily related resurrected ancestral proteins thus emerges as a simple approach to expand the capability of ancestral reconstruction to search sequence space for extreme protein properties of biotechnological interest. The fact that ancestral sequences for many phylogenetic nodes can be derived from a single alignment of modern sequences should contribute to the general applicability of this approach.
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23
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Trudeau DL, Kaltenbach M, Tawfik DS. On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins. Mol Biol Evol 2016; 33:2633-41. [PMID: 27413048 DOI: 10.1093/molbev/msw138] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the environmental temperature at the time of emergence of mammals is presumed to be similar to the present one. Additionally, the mammalian PON ancestor has superior folding properties (kinetic stability)-unlike the extant mammalian PONs, it expresses in E. coli in a soluble and functional form, and at a high yield. We discuss two potential origins of this unexpectedly high stability. First, ancestral stability may be overestimated by a "consensus effect," whereby replacing amino acids that are rare in contemporary sequences with the amino acid most common in the family increases protein stability. Comparison to other reconstructed ancestors indicates that the consensus effect may bias some but not all reconstructions. Second, we note that high stability may relate to factors other than high environmental temperature such as oxidative stress or high radiation levels. Foremost, intrinsic factors such as high rates of genetic mutations and/or of transcriptional and translational errors, and less efficient protein quality control systems, may underlie the high kinetic and thermodynamic stability of past proteins.
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Affiliation(s)
- Devin L Trudeau
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Kaltenbach
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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24
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Abstract
Galactokinase catalyses the first committed step of the Leloir pathway, i.e. the ATP-dependent phosphorylation of α-D-galactose at C1-OH. Reduced galactokinase activity results in the inherited metabolic disease type II galactosaemia. However, inhibition of galactokinase is considered a viable approach to treating more severe forms of galactosaemia (types I and III). Considerable progress has been made in the identification of high affinity, selective inhibitors. Although the structure of galactokinase from a variety of species is known, its catalytic mechanism remains uncertain. Although the bulk of evidence suggests that the reaction proceeds via an active site base mechanism, some experimental and theoretical studies contradict this. The enzyme has potential as a biocatalyst in the production of sugar 1-phosphates. This potential is limited by its high specificity. A variety of approaches have been taken to identify galactokinase variants which are more promiscuous. These have broadened galactokinase's specificity to include a wide range of D- and L-sugars. Initial studies suggest that some of these alterations result in increased flexibility at the active site. It is suggested that modulation of protein flexibility is at least as important as structural modifications in determining the success or failure of enzyme engineering.
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Mesa-Torres N, Salido E, Pey AL. The lower limits for protein stability and foldability in primary hyperoxaluria type I. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2355-65. [PMID: 25461797 DOI: 10.1016/j.bbapap.2014.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/29/2014] [Accepted: 10/10/2014] [Indexed: 01/12/2023]
Abstract
Mutational effects on protein stability and foldability are important to understand conformational diseases and protein evolution. In this work, we perform a comprehensive investigation on the energetic basis underlying mutational effects on the stability of human alanine:glyoxylate aminotransferase (AGT). We study twenty two variants whose kinetic stabilities span over eleven orders of magnitude and are classified into two groups: i) ten naturally-occurring variants, including the most common mutations causing primary hyperoxaluria type I (PH1); and ii) twelve consensus variants obtained by sequence-alignment statistics. We show that AGT dimer stability determines denaturation rates, and mutations modulate stability by changes in the effective thermodynamic stability, the aggregation propensity of partially/globally unfolded states and subtle energetic changes in the rate-limiting denaturation step. In combination with our previous expression analyses in eukaryotic cells, we propose the existence of two lower limits for AGT stability, one linked to optimal folding efficiency (close to the major allele stability) and the other setting a minimal efficiency compatible with glyoxylate detoxification in vivo (close to the minor allele stability). These lower limits could explain the high prevalence of misfolding as a disease mechanism in PH1 and support the use of pharmacological ligands aimed to increase AGT stability as therapies for this disease.
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Affiliation(s)
- Noel Mesa-Torres
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife E-38320, Spain
| | - Angel L Pey
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain.
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Structural basis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress. Proc Natl Acad Sci U S A 2014; 111:E4532-41. [PMID: 25288725 DOI: 10.1073/pnas.1407610111] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Plant cells have developed specific protective molecular machinery against environmental stresses. The family of CBL-interacting protein kinases (CIPK) and their interacting activators, the calcium sensors calcineurin B-like (CBLs), work together to decode calcium signals elicited by stress situations. The molecular basis of biological activation of CIPKs relies on the calcium-dependent interaction of a self-inhibitory NAF motif with a particular CBL, the phosphorylation of the activation loop by upstream kinases, and the subsequent phosphorylation of the CBL by the CIPK. We present the crystal structures of the NAF-truncated and pseudophosphorylated kinase domains of CIPK23 and CIPK24/SOS2. In addition, we provide biochemical data showing that although CIPK23 is intrinsically inactive and requires an external stimulation, CIPK24/SOS2 displays basal activity. This data correlates well with the observed conformation of the respective activation loops: Although the loop of CIPK23 is folded into a well-ordered structure that blocks the active site access to substrates, the loop of CIPK24/SOS2 protrudes out of the active site and allows catalysis. These structures together with biochemical and biophysical data show that CIPK kinase activity necessarily requires the coordinated releases of the activation loop from the active site and of the NAF motif from the nucleotide-binding site. Taken all together, we postulate the basis for a conserved calcium-dependent NAF-mediated regulation of CIPKs and a variable regulation by upstream kinases.
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