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Kmochová T, Kidd KO, Orr A, Hnízda A, Hartmannová H, Hodaňová K, Vyleťal P, Naušová K, Brinsa V, Trešlová H, Sovová J, Barešová V, Svojšová K, Vrbacká A, Stránecký V, Robins VC, Taylor A, Martin L, Rivas-Chavez A, Payne R, Bleyer HA, Williams A, Rennke HG, Weins A, Short PJ, Agrawal V, Storsley LJ, Waikar SS, McPhail ED, Dasari S, Leung N, Hewlett T, Yorke J, Gaston D, Geldenhuys L, Samuels M, Levine AP, West M, Hůlková H, Pompach P, Novák P, Weinberg RB, Bedard K, Živná M, Sikora J, Bleyer AJ, Kmoch S. Autosomal dominant ApoA4 mutations present as tubulointerstitial kidney disease with medullary amyloidosis. Kidney Int 2024; 105:799-811. [PMID: 38096951 DOI: 10.1016/j.kint.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 01/21/2024]
Abstract
Sporadic cases of apolipoprotein A-IV medullary amyloidosis have been reported. Here we describe five families found to have autosomal dominant medullary amyloidosis due to two different pathogenic APOA4 variants. A large family with autosomal dominant chronic kidney disease (CKD) and bland urinary sediment underwent whole genome sequencing with identification of a chr11:116692578 G>C (hg19) variant encoding the missense mutation p.L66V of the ApoA4 protein. We identified two other distantly related families from our registry with the same variant and two other distantly related families with a chr11:116693454 C>T (hg19) variant encoding the missense mutation p.D33N. Both mutations are unique to affected families, evolutionarily conserved and predicted to expand the amyloidogenic hotspot in the ApoA4 structure. Clinically affected individuals suffered from CKD with a bland urinary sediment and a mean age for kidney failure of 64.5 years. Genotyping identified 48 genetically affected individuals; 44 individuals had an estimated glomerular filtration rate (eGFR) under 60 ml/min/1.73 m2, including all 25 individuals with kidney failure. Significantly, 11 of 14 genetically unaffected individuals had an eGFR over 60 ml/min/1.73 m2. Fifteen genetically affected individuals presented with higher plasma ApoA4 concentrations. Kidney pathologic specimens from four individuals revealed amyloid deposits limited to the medulla, with the mutated ApoA4 identified by mass-spectrometry as the predominant amyloid constituent in all three available biopsies. Thus, ApoA4 mutations can cause autosomal dominant medullary amyloidosis, with marked amyloid deposition limited to the kidney medulla and presenting with autosomal dominant CKD with a bland urinary sediment. Diagnosis relies on a careful family history, APOA4 sequencing and pathologic studies.
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Affiliation(s)
- Tereza Kmochová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kendrah O Kidd
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Andrew Orr
- Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Aleš Hnízda
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karolína Naušová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vítězslav Brinsa
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Klára Svojšová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alena Vrbacká
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Victoria C Robins
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Abbigail Taylor
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Lauren Martin
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Ana Rivas-Chavez
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Riley Payne
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Heidi A Bleyer
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Adrienne Williams
- Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Helmut G Rennke
- Pathology Department, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Astrid Weins
- Pathology Department, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Varun Agrawal
- Division of Nephrology and Hypertension, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Leroy J Storsley
- Department of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sushrut S Waikar
- Section of Nephrology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ellen D McPhail
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Nelson Leung
- Division of Nephrology and Hypertension, Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tom Hewlett
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jake Yorke
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laurette Geldenhuys
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mark Samuels
- Department of Medicine Université de Montréal, Montreal, Quebec, Canada; Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada; Centre de Recherche du CHU Ste-Justine, Montreal, Quebec, Canada
| | - Adam P Levine
- Research Department of Pathology, University College London, London, UK
| | - Michael West
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Helena Hůlková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Institute of Pathology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Pompach
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Richard B Weinberg
- Section on Gastroenterology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA; Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Karen Bedard
- Department of Pathology and Laboratory Medicine, Izaak Walton Killam Hospital, Halifax Nova Scotia, Canada
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Jakub Sikora
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Institute of Pathology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Anthony J Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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2
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Jorge S, Kidd K, Vylet’al P, Nogueira E, Martin L, Howard K, Barešová V, Hodaňová K, Hnízda A, Moldovan O, Silveira C, Coutinho AM, Lopes JA, Bleyer AJ, Kmoch S, Živná M. Bi-allelic REN Mutations and Undetectable Plasma Renin Activity in a Patient With Progressive CKD. Kidney Int Rep 2023; 8:1112-1116. [PMID: 37180515 PMCID: PMC10166736 DOI: 10.1016/j.ekir.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Affiliation(s)
- Sofia Jorge
- Department of Nephrology and Renal Transplant, Hospital de Santa Maria, CHULN, EPE, Lisbon, Portugal
| | - Kendrah Kidd
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Petr Vylet’al
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Estela Nogueira
- Department of Nephrology and Renal Transplant, Hospital de Santa Maria, CHULN, EPE, Lisbon, Portugal
| | - Lauren Martin
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Katrice Howard
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Aleš Hnízda
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Oana Moldovan
- Genetic Department of Hospital de Santa Maria, CHULN, EPE, Lisbon, Portugal
| | - Catarina Silveira
- GenoMed - Diagnósticos de Medicina Molecular, S.A., Lisbon, Portugal
| | | | - José António Lopes
- Department of Nephrology and Renal Transplant, Hospital de Santa Maria, CHULN, EPE, Lisbon, Portugal
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
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3
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Hnízda A, Tesina P, Nguyen TB, Kukačka Z, Kater L, Chaplin AK, Beckmann R, Ascher DB, Novák P, Blundell TL. SAP domain forms a flexible part of DNA aperture in Ku70/80. FEBS J 2021; 288:4382-4393. [PMID: 33511782 PMCID: PMC8653891 DOI: 10.1111/febs.15732] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/26/2022]
Abstract
Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA breaks and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions of the Ku70 C-terminal domain, known as the SAP domain. Using single-particle cryo-electron microscopy, mass spectrometric analysis of intermolecular cross-linking and molecular modelling simulations, we captured variable positions of the SAP domain depending on DNA binding. The first position was localized at the DNA aperture in the Ku70/80 apo form but was not observed in the DNA-bound state. The second position, which was observed in both apo and DNA-bound states, was found below the DNA aperture, close to the helical arm of Ku70. The localization of the SAP domain in the DNA aperture suggests a function as a flexible entry gate for broken DNA. DATABASES: EM maps have been deposited in EMDB (EMD-11933). Coordinates have been deposited in Protein Data Bank (PDB 7AXZ). Other data are available from corresponding authors upon a request.
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Affiliation(s)
- Aleš Hnízda
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petr Tesina
- Gene Center and Department of Biochemistry, University of Munich, Germany
| | - Thanh-Binh Nguyen
- Computational and Systems Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Zdeněk Kukačka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lukas Kater
- Gene Center and Department of Biochemistry, University of Munich, Germany
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, University of Munich, Germany
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Computational and Systems Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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4
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Živná M, Kidd K, Zaidan M, Vyleťal P, Barešová V, Hodaňová K, Sovová J, Hartmannová H, Votruba M, Trešlová H, Jedličková I, Sikora J, Hůlková H, Robins V, Hnízda A, Živný J, Papagregoriou G, Mesnard L, Beck BB, Wenzel A, Tory K, Häeffner K, Wolf MTF, Bleyer ME, Sayer JA, Ong ACM, Balogh L, Jakubowska A, Łaszkiewicz A, Clissold R, Shaw-Smith C, Munshi R, Haws RM, Izzi C, Capelli I, Santostefano M, Graziano C, Scolari F, Sussman A, Trachtman H, Decramer S, Matignon M, Grimbert P, Shoemaker LR, Stavrou C, Abdelwahed M, Belghith N, Sinclair M, Claes K, Kopel T, Moe S, Deltas C, Knebelmann B, Rampoldi L, Kmoch S, Bleyer AJ. An international cohort study of autosomal dominant tubulointerstitial kidney disease due to REN mutations identifies distinct clinical subtypes. Kidney Int 2020; 98:1589-1604. [PMID: 32750457 DOI: 10.1016/j.kint.2020.06.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/05/2023]
Abstract
There have been few clinical or scientific reports of autosomal dominant tubulointerstitial kidney disease due to REN mutations (ADTKD-REN), limiting characterization. To further study this, we formed an international cohort characterizing 111 individuals from 30 families with both clinical and laboratory findings. Sixty-nine individuals had a REN mutation in the signal peptide region (signal group), 27 in the prosegment (prosegment group), and 15 in the mature renin peptide (mature group). Signal group patients were most severely affected, presenting at a mean age of 19.7 years, with the prosegment group presenting at 22.4 years, and the mature group at 37 years. Anemia was present in childhood in 91% in the signal group, 69% prosegment, and none of the mature group. REN signal peptide mutations reduced hydrophobicity of the signal peptide, which is necessary for recognition and translocation across the endoplasmic reticulum, leading to aberrant delivery of preprorenin into the cytoplasm. REN mutations in the prosegment led to deposition of prorenin and renin in the endoplasmic reticulum-Golgi intermediate compartment and decreased prorenin secretion. Mutations in mature renin led to deposition of the mutant prorenin in the endoplasmic reticulum, similar to patients with ADTKD-UMOD, with a rate of progression to end stage kidney disease (63.6 years) that was significantly slower vs. the signal (53.1 years) and prosegment groups (50.8 years) (significant hazard ratio 0.367). Thus, clinical and laboratory studies revealed subtypes of ADTKD-REN that are pathophysiologically, diagnostically, and clinically distinct.
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Affiliation(s)
- Martina Živná
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kendrah Kidd
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Mohamad Zaidan
- Service de Néphrologie‒Transplantation, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Petr Vyleťal
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Barešová
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Miroslav Votruba
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Trešlová
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivana Jedličková
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jakub Sikora
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Hůlková
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Victoria Robins
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Aleš Hnízda
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Živný
- Institute of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Gregory Papagregoriou
- Center of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus
| | - Laurent Mesnard
- Sorbonne Université, Urgences Néphrologiques et Transplantation Rénale, Assistance Publique-Hôpitaux de Paris (APHP), Hôpital Tenon, Paris, France
| | - Bodo B Beck
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Center for Rare Diseases Cologneies(ZSEK), Cologne, Germany
| | - Andrea Wenzel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Center for Rare Diseases Cologneies(ZSEK), Cologne, Germany
| | - Kálmán Tory
- MTA-SE Lendület Nephrogenetic Laboratory, Semmelweis University, Budapest, Hungary; First Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Karsten Häeffner
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center, Faculty of Medicine, Universitätsklinikum Freiburg, Freiburg, Germany
| | - Matthias T F Wolf
- Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael E Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - John A Sayer
- Renal Services, The Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - Lídia Balogh
- First Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Anna Jakubowska
- Department of Pediatric Nephrology Medical University Wrocław, Poland
| | - Agnieszka Łaszkiewicz
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Rhian Clissold
- Exeter Kidney Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Charles Shaw-Smith
- Exeter Kidney Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Raj Munshi
- Division of Nephrology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | - Robert M Haws
- Pediatrics-Nephrology, Marshfield Medical Center, Marshfield, Wisconsin, USA
| | - Claudia Izzi
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and Montichiari Hospital, Brescia, Italy
| | - Irene Capelli
- Department of Experimental Diagnostic and Specialty Medicine, Nephrology, Dialysis and Renal Transplant Unit, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | | | - Claudio Graziano
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and Montichiari Hospital, Brescia, Italy
| | - Amy Sussman
- Department of Medicine, Division of Nephrology, University of Arizona Health Sciences Center, Tucson, Arizona, USA
| | - Howard Trachtman
- Division of Nephrology, Department of Pediatrics, New York University School of Medicine, New York, New York, USA
| | - Stephane Decramer
- Pediatric Nephrology, Centre Hospitalier Universitaire de Toulouse (CHU de Toulouse), Toulouse, France; France Rare Renal Disease Reference Centre (SORARE), Toulouse, France; Centre Hospitalier Universitaire de Toulouse (CHU de Toulouse), Toulouse, France
| | - Marie Matignon
- AP-HP (Assistance Publique-Hôpitaux de Paris), Nephrology and Renal Transplantation Department, Institut Francilien de Recherche en Néphrologie et Transplantation (IFRNT), Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Créteil, France; Université Paris-Est-Créteil, (UPEC), DHU (Département Hospitalo-Universitaire) VIC (Virus-Immunité-Cancer), IMRB (Institut Mondor de Recherche Biomédicale), Equipe 21, INSERM U 955, Créteil, France
| | - Philippe Grimbert
- AP-HP (Assistance Publique-Hôpitaux de Paris), Nephrology and Renal Transplantation Department, Institut Francilien de Recherche en Néphrologie et Transplantation (IFRNT), Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Créteil, France; Université Paris-Est-Créteil, (UPEC), DHU (Département Hospitalo-Universitaire) VIC (Virus-Immunité-Cancer), IMRB (Institut Mondor de Recherche Biomédicale), Equipe 21, INSERM U 955, Créteil, France; AP-HP (Assistance Publique-Hôpitaux de Paris), CIC-BT 504, Créteil, France
| | - Lawrence R Shoemaker
- Division of Nephrology, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | | | - Mayssa Abdelwahed
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Neila Belghith
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia; Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Matthew Sinclair
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA; Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Kathleen Claes
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium; Laboratory of Nephrology, Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Tal Kopel
- Nephrology Division, University of Montreal Hospital Centre, Hopital Saint-Luc, Montréal, Québec, Canada
| | - Sharon Moe
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Constantinos Deltas
- Center of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus
| | - Bertrand Knebelmann
- Department of Nephrology‒Transplantation, Necker Hospital, APHP, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Paris, France; Département Biologie cellulaire, INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stanislav Kmoch
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Anthony J Bleyer
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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5
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Moriyama T, Liu S, Li J, Meyer J, Zhao X, Yang W, Shao Y, Heath R, Hnízda A, Carroll WL, Yang JJ. Mechanisms of NT5C2-Mediated Thiopurine Resistance in Acute Lymphoblastic Leukemia. Mol Cancer Ther 2019; 18:1887-1895. [PMID: 31358663 DOI: 10.1158/1535-7163.mct-18-1112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/15/2019] [Accepted: 07/23/2019] [Indexed: 02/02/2023]
Abstract
Relapse remains a formidable challenge for acute lymphoblastic leukemia (ALL). Recently, recurrent mutations in NT5C2 were identified as a common genomic lesion unique in relapsed ALL and were linked to acquired thiopurine resistance. However, molecular mechanisms by which NT5C2 regulates thiopurine cytotoxicity were incompletely understood. To this end, we sought to comprehensively characterize the biochemical and cellular effects of NT5C2 mutations. Compared with wild-type NT5C2, mutant proteins showed elevated 5'-nucleotidase activity with a stark preference of thiopurine metabolites over endogenous purine nucleotides, suggesting neomorphic effects specific to thiopurine metabolism. Expression of mutant NT5C2 mutations also significantly reduced thiopurine uptake in vitro with concomitant increase in efflux of 6-mercaptopurine (MP) metabolites, plausibly via indirect effects on drug transporter pathways. Finally, intracellular metabolomic profiling revealed significant shifts in nucleotide homeostasis induced by mutant NT5C2 at baseline; MP treatment also resulted in global changes in metabolomic profiles with completely divergent effects in cells with mutant versus wild-type NT5C2. Collectively, our data indicated that NT5C2 mutations alter thiopurine metabolism and cellular disposition, but also influence endogenous nucleotide homeostasis and thiopurine-induced metabolomic response. These complex mechanisms contributed to NT5C2-mediated drug resistance in ALL and pointed to potential opportunities for therapeutic targeting in relapsed ALL.
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Affiliation(s)
- Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Shuguang Liu
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jing Li
- Department of Oncology, Pharmacology Core, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Youming Shao
- Protein Production Center, St. Jude Children's Hospital, Memphis, Tennessee
| | - Richard Heath
- Protein Production Center, St. Jude Children's Hospital, Memphis, Tennessee
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - William L Carroll
- New York University Cancer Institute, New York University Langone Medical Center, New York, New York.,Department of Pathology, New York University Langone Medical Center, New York, New York.,Department of Pediatrics, New York University Langone Medical Center, New York, New York
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
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6
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Man P, Fábry M, Sieglová I, Kavan D, Novák P, Hnízda A. Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site. Biochim Biophys Acta Proteins Proteom 2019; 1867:376-381. [PMID: 30639426 DOI: 10.1016/j.bbapap.2019.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/16/2018] [Accepted: 01/06/2019] [Indexed: 01/18/2023]
Abstract
Germline mutations in NUDT15 cause thiopurine intolerance during treatment of leukemia or autoimmune diseases. Previously, it has been shown that the mutations affect the enzymatic activity of the NUDT15 hydrolase due to decreased protein stability in vivo. Here we provide structural insights into protein destabilization in R139C and V18I mutants using thermolysin-based proteolysis and H/D exchange followed by mass spectrometry. Both mutants exhibited destabilization of the catalytic site, which was more pronounced at higher temperature. This structural perturbation is shared by the mutations despite their different positions within the protein structure. Reaction products of NUDT15 reverted these conformational abnormalities, demonstrating the importance of ligands for stabilization of a native state of the mutants. This study shows the action of pharmacogenetic variants in NUDT15 in a context of protein structure, which might open novel directions in personalized chemotherapy.
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Affiliation(s)
- Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic.
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7
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Zhang Y, Gao Y, Zhang H, Zhang J, He F, Hnízda A, Qian M, Liu X, Gocho Y, Pui CH, Cheng T, Wang Q, Yang JJ, Zhu X, Liu X. PDGFRB mutation and tyrosine kinase inhibitor resistance in Ph-like acute lymphoblastic leukemia. Blood 2018; 131:2256-2261. [PMID: 29434033 PMCID: PMC5958655 DOI: 10.1182/blood-2017-11-817510] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/02/2018] [Indexed: 12/21/2022] Open
Abstract
Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) comprises ∼10% to 15% of childhood ALL cases, many of which respond exquisitely to tyrosine kinase inhibitors (TKIs), for example, imatinib in PDGFRB-rearranged ALL. However, some cases developed drug resistance to TKIs and the mechanisms are poorly understood. In this study, we identified a novel PDGFRB fusion gene, namely AGGF1-PDGFRB, and functionally characterized its oncogenic potential in vitro. Further genomic profiling of longitudinally collected samples during treatment revealed the emergence of a mutation, PDGFRBC843G , which directly conferred resistance to all generations of ABL TKIs, including imatinib, dasatinib, nilotinib, and ponatinib. PDGFRB-mutant leukemia cells are highly sensitive to multitarget kinase inhibitor CHZ868, suggesting potential therapeutic options for some patients resistant to ABL TKIs. In summary, we describe a complex clonal evolution pattern in Ph-like ALL and identified a novel PDGFRB point mutation that drives leukemia relapse after ABL TKI treatment.
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Affiliation(s)
- Yingchi Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yufeng Gao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jingliao Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Division of Pediatric Blood Diseases Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fuhong He
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; and
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Xiaoming Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Division of Pediatric Blood Diseases Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yoshihiro Gocho
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Division of Pediatric Blood Diseases Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qianfei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Division of Pediatric Blood Diseases Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Bai M, Vozdek R, Hnízda A, Jiang C, Wang B, Kuchar L, Li T, Zhang Y, Wood C, Feng L, Dang Y, Ma DK. Conserved roles of C. elegans and human MANFs in sulfatide binding and cytoprotection. Nat Commun 2018; 9:897. [PMID: 29497057 PMCID: PMC5832864 DOI: 10.1038/s41467-018-03355-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/02/2018] [Indexed: 12/30/2022] Open
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER) protein that can be secreted and protects dopamine neurons and cardiomyocytes from ER stress and apoptosis. The mechanism of action of extracellular MANF has long been elusive. From a genetic screen for mutants with abnormal ER stress response, we identified the gene Y54G2A.23 as the evolutionarily conserved C. elegans MANF orthologue. We find that MANF binds to the lipid sulfatide, also known as 3-O-sulfogalactosylceramide present in serum and outer-cell membrane leaflets, directly in isolated forms and in reconstituted lipid micelles. Sulfatide binding promotes cellular MANF uptake and cytoprotection from hypoxia-induced cell death. Heightened ER stress responses of MANF-null C. elegans mutants and mammalian cells are alleviated by human MANF in a sulfatide-dependent manner. Our results demonstrate conserved roles of MANF in sulfatide binding and ER stress response, supporting sulfatide as a long-sought lipid mediator of MANF's cytoprotection.
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Affiliation(s)
- Meirong Bai
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Roman Vozdek
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10, Prague 6, Czech Republic
| | - Chenxiao Jiang
- Key Laboratory of Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ladislav Kuchar
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Tiejun Li
- Department of Pharmacology, Second Military Medical University, Shanghai, 200433, China
| | - Yuefan Zhang
- Department of Pharmacology, Second Military Medical University, Shanghai, 200433, China
| | - Chase Wood
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Yongjun Dang
- Key Laboratory of Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Dengke K Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA.
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9
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Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V. Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia 2018. [PMID: 29535428 DOI: 10.1038/s41375-018-0073-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activating mutations in NT5C2, a gene encoding cytosolic purine 5'-nucleotidase (cN-II), confer chemoresistance in relapsed acute lymphoblastic leukemia. Here we show that all mutants became independent of allosteric effects of ATP and thus constitutively active. Structural mapping of mutations described in patients demonstrates that 90% of leukemia-specific allelles directly affect two regulatory hotspots within the cN-II molecule-the helix A region: residues 355-365, and the intersubunit interface: helix B (232-242) and flexible interhelical loop L (400-418). Furthermore, analysis of hetero-oligomeric complexes combining wild-type (WT) and mutant subunits showed that the activation is transmitted from the mutated to the WT subunit. This intersubunit interaction forms structural basis of hyperactive NT5C2 in drug-resistant leukemia in which heterozygous NT5C2 mutation gave rise to hetero-tetramer mutant and WT proteins. This enabled us to define criteria to aid the prediction of NT5C2 drug resistance mutations in leukemia.
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Affiliation(s)
- Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic. .,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK.
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Vítězslav Brinsa
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - David B Ascher
- Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 4 142 20, Czech Republic
| | - Markéta Žaliová
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
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10
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Hnízda A, Škerlová J, Fábry M, Pachl P, Šinalová M, Vrzal L, Man P, Novák P, Řezáčová P, Veverka V. Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia. BMC Biol 2016; 14:91. [PMID: 27756303 PMCID: PMC5070119 DOI: 10.1186/s12915-016-0313-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background Relapsed acute lymphoblastic leukemia (ALL) is one of the main causes of mortality in childhood malignancies. Previous genetic studies demonstrated that chemoresistant ALL is driven by activating mutations in NT5C2, the gene encoding cytosolic 5´-nucleotidase (cN-II). However, molecular mechanisms underlying this hyperactivation are still unknown. Here, we present kinetic and structural properties of cN-II variants that represent 75 % of mutated alleles in patients who experience relapsed ALL (R367Q, R238W and L375F). Results Enzyme kinetics measurements revealed that the mutants are consitutively active without need for allosteric activators. This shows that hyperactivity is not caused by a direct catalytic effect but rather by misregulation of cN-II. X-ray crystallography combined with mass spectrometry-based techniques demonstrated that this misregulation is driven by structural modulation of the oligomeric interface within the cN-II homotetrameric assembly. These specific conformational changes are shared between the studied variants, despite the relatively random spatial distribution of the mutations. Conclusions These findings define a common molecular mechanism for cN-II hyperactivity, which provides a solid basis for targeted therapy of leukemia. Our study highlights the cN-II oligomerization interface as an attractive pharmacological target. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0313-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Martina Šinalová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.
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11
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Bolar N, Golzio C, Živná M, Hayot G, Van Hemelrijk C, Schepers D, Vandeweyer G, Hoischen A, Huyghe J, Raes A, Matthys E, Sys E, Azou M, Gubler MC, Praet M, Van Camp G, McFadden K, Pediaditakis I, Přistoupilová A, Hodaňová K, Vyleťal P, Hartmannová H, Stránecký V, Hůlková H, Barešová V, Jedličková I, Sovová J, Hnízda A, Kidd K, Bleyer A, Spong R, Vande Walle J, Mortier G, Brunner H, Van Laer L, Kmoch S, Katsanis N, Loeys B. Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia. Am J Hum Genet 2016; 99:174-87. [PMID: 27392076 PMCID: PMC5005467 DOI: 10.1016/j.ajhg.2016.05.028] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/30/2016] [Indexed: 02/08/2023] Open
Abstract
Autosomal-dominant tubulo-interstitial kidney disease (ADTKD) encompasses a group of disorders characterized by renal tubular and interstitial abnormalities, leading to slow progressive loss of kidney function requiring dialysis and kidney transplantation. Mutations in UMOD, MUC1, and REN are responsible for many, but not all, cases of ADTKD. We report on two families with ADTKD and congenital anemia accompanied by either intrauterine growth retardation or neutropenia. Ultrasound and kidney biopsy revealed small dysplastic kidneys with cysts and tubular atrophy with secondary glomerular sclerosis, respectively. Exclusion of known ADTKD genes coupled with linkage analysis, whole-exome sequencing, and targeted re-sequencing identified heterozygous missense variants in SEC61A1-c.553A>G (p.Thr185Ala) and c.200T>G (p.Val67Gly)-both affecting functionally important and conserved residues in SEC61. Both transiently expressed SEC6A1A variants are delocalized to the Golgi, a finding confirmed in a renal biopsy from an affected individual. Suppression or CRISPR-mediated deletions of sec61al2 in zebrafish embryos induced convolution defects of the pronephric tubules but not the pronephric ducts, consistent with the tubular atrophy observed in the affected individuals. Human mRNA encoding either of the two pathogenic alleles failed to rescue this phenotype as opposed to a complete rescue by human wild-type mRNA. Taken together, these findings provide a mechanism by which mutations in SEC61A1 lead to an autosomal-dominant syndromic form of progressive chronic kidney disease. We highlight protein translocation defects across the endoplasmic reticulum membrane, the principal role of the SEC61 complex, as a contributory pathogenic mechanism for ADTKD.
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12
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Melenovská P, Kopecká J, Krijt J, Hnízda A, Raková K, Janošík M, Wilcken B, Kožich V. Chaperone therapy for homocystinuria: the rescue of CBS mutations by heme arginate. J Inherit Metab Dis 2015; 38:287-94. [PMID: 25331909 DOI: 10.1007/s10545-014-9781-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 02/01/2023]
Abstract
Classical homocystinuria is caused by mutations in the cystathionine β-synthase (CBS) gene. Previous experiments in bacterial and yeast cells showed that many mutant CBS enzymes misfold and that chemical chaperones enable proper folding of a number of mutations. In the present study, we tested the extent of misfolding of 27 CBS mutations previously tested in E. coli under the more folding-permissive conditions of mammalian CHO-K1 cells and the ability of chaperones to rescue the conformation of these mutations. Expression of mutations in mammalian cells increased the median activity 16-fold and the amount of tetramers 3.2-fold compared with expression in bacteria. Subsequently, we tested the responses of seven selected mutations to three compounds with chaperone-like activity. Aminooxyacetic acid and 4-phenylbutyric acid exhibited only a weak effect. In contrast, heme arginate substantially increased the formation of mutant CBS protein tetramers (up to sixfold) and rescued catalytic activity (up to ninefold) of five out of seven mutations (p.A114V, p.K102N, p.R125Q, p.R266K, and p.R369C). The greatest effect of heme arginate was observed for the mutation p.R125Q, which is non-responsive to in vivo treatment with vitamin B(6). Moreover, the heme responsiveness of the p.R125Q mutation was confirmed in fibroblasts derived from a patient homozygous for this genetic variant. Based on these data, we propose that a distinct group of heme-responsive CBS mutations may exist and that the heme pocket of CBS may become an important target for designing novel therapies for homocystinuria.
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Affiliation(s)
- Petra Melenovská
- Institute of Inherited Metabolic Disorders, Charles University in Prague-First Faculty of Medicine and General University Hospital in Prague, Ke Karlovu 2, 128 08, Praha 2, Czech Republic
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13
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Snášel J, Nauš P, Dostál J, Hnízda A, Fanfrlík J, Brynda J, Bourderioux A, Dušek M, Dvořáková H, Stolaříková J, Zábranská H, Pohl R, Konečný P, Džubák P, Votruba I, Hajdúch M, Rezáčová P, Veverka V, Hocek M, Pichová I. Structural basis for inhibition of mycobacterial and human adenosine kinase by 7-substituted 7-(Het)aryl-7-deazaadenine ribonucleosides. J Med Chem 2014; 57:8268-79. [PMID: 25259627 DOI: 10.1021/jm500497v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenosine kinase (ADK) from Mycobacterium tuberculosis (Mtb) was selected as a target for design of antimycobacterial nucleosides. Screening of 7-(het)aryl-7-deazaadenine ribonucleosides with Mtb and human (h) ADKs and testing with wild-type and drug-resistant Mtb strains identified specific inhibitors of Mtb ADK with micromolar antimycobacterial activity and low cytotoxicity. X-ray structures of complexes of Mtb and hADKs with 7-ethynyl-7-deazaadenosine showed differences in inhibitor interactions in the adenosine binding sites. 1D (1)H STD NMR experiments revealed that these inhibitors are readily accommodated into the ATP and adenosine binding sites of Mtb ADK, whereas they bind preferentially into the adenosine site of hADK. Occupation of the Mtb ADK ATP site with inhibitors and formation of catalytically less competent semiopen conformation of MtbADK after inhibitor binding in the adenosine site explain the lack of phosphorylation of 7-substituted-7-deazaadenosines. Semiempirical quantum mechanical analysis confirmed different affinity of nucleosides for the Mtb ADK adenosine and ATP sites.
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Affiliation(s)
- Jan Snášel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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14
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Hnízda A, Skleničková R, Pachl P, Fábry M, Tošner Z, Brynda J, Veverka V. Backbone resonance assignments of human cytosolic dNT-1 nucleotidase. Biomol NMR Assign 2014; 8:425-428. [PMID: 24234349 DOI: 10.1007/s12104-013-9531-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/09/2013] [Indexed: 06/02/2023]
Abstract
Cytosolic dNT-1 nucleotidase plays a key role in the homeostasis of pyrimidine deoxyribonucleotides in mammalian cells. The enzyme is responsible for the dephosphorylation of physiological substrates as well as nucleoside analogues that are used in antiviral and anticancer therapies, therefore selective inhibition of the dNT-1 nucleotidase activity may lead to an increase in efficacy of this type of therapeutic compounds. Here, we report the backbone ¹H, ¹³C and ¹⁵N assignments for the 47 kDa dNT-1 dimer, which will be used for structural characterisation of dNT-1 complexes with small molecule inhibitors obtained through modification of pyrimidine nucleotide scaffolds or optimisation of successful binders obtained from the screening of fragment libraries.
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Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I. Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases. Org Biomol Chem 2014; 12:7971-82. [DOI: 10.1039/c4ob01332h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.
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Affiliation(s)
- Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
- 14220 Prague 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Radka Skleničková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
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16
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Vozdek R, Hnízda A, Krijt J, Será L, Kožich V. Biochemical properties of nematode O-acetylserine(thiol)lyase paralogs imply their distinct roles in hydrogen sulfide homeostasis. Biochim Biophys Acta 2013; 1834:2691-701. [PMID: 24100226 DOI: 10.1016/j.bbapap.2013.09.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 01/08/2023]
Abstract
O-Acetylserine(thiol)lyases (OAS-TLs) play a pivotal role in a sulfur assimilation pathway incorporating sulfide into amino acids in microorganisms and plants, however, these enzymes have not been found in the animal kingdom. Interestingly, the genome of the roundworm Caenorhabditis elegans contains three expressed genes predicted to encode OAS-TL orthologs (cysl-1-cysl-3), and a related pseudogene (cysl-4); these genes play different roles in resistance to hypoxia, hydrogen sulfide and cyanide. To get an insight into the underlying molecular mechanisms we purified the three recombinant worm OAS-TL proteins, and we determined their enzymatic activities, substrate binding affinities, quaternary structures and the conformations of their active site shapes. We show that the nematode OAS-TL orthologs can bind O-acetylserine and catalyze the canonical reaction although this ligand may more likely serve as a competitive inhibitor to natural substrates instead of being a substrate for sulfur assimilation. In addition, we propose that S-sulfocysteine may be a novel endogenous substrate for these proteins. However, we observed that the three OAS-TL proteins are conformationally different and exhibit distinct substrate specificity. Based on the available evidences we propose the following model: CYSL-1 interacts with EGL-9 and activates HIF-1 that upregulates expression of genes detoxifying sulfide and cyanide, the CYSL-2 acts as a cyanoalanine synthase in the cyanide detoxification pathway and simultaneously produces hydrogen sulfide, while the role of CYSL-3 remains unclear although it exhibits sulfhydrylase activity in vitro. All these data indicate that C. elegans OAS-TL paralogs have distinct cellular functions and may play different roles in maintaining hydrogen sulfide homeostasis.
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Affiliation(s)
- Roman Vozdek
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 2, 128 08, Czech Republic
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Hnízda A, Majtan T, Liu L, Pey AL, Carpenter JF, Kodíček M, Kožich V, Kraus JP. Conformational properties of nine purified cystathionine β-synthase mutants. Biochemistry 2012; 51:4755-63. [PMID: 22612060 PMCID: PMC3384745 DOI: 10.1021/bi300435e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein misfolding due to missense mutations is a common pathogenic mechanism in cystathionine β-synthase (CBS) deficiency. In our previous studies, we successfully expressed, purified, and characterized nine CBS mutant enzymes containing the following patient mutations: P49L, P78R, A114V, R125Q, E176K, R266K, P422L, I435T, and S466L. These purified mutants exhibited full heme saturation, normal tetrameric assembly, and high catalytic activity. In this work, we used several spectroscopic and proteolytic techniques to provide a more thorough insight into the conformation of these mutant enzymes. Far-UV circular dichroism, fluorescence, and second-derivative UV spectroscopy revealed that the spatial arrangement of these CBS mutants is similar to that of the wild type, although the microenvironment of the chromophores may be slightly altered. Using proteolysis with thermolysin under native conditions, we found that the majority of the studied mutants is more susceptible to cleavage, suggesting their increased local flexibility or propensity for local unfolding. Interestingly, the presence of the CBS allosteric activator, S-adenosylmethionine (AdoMet), increased the rate of cleavage of the wild type and the AdoMet-responsive mutants, while the proteolytic rate of the AdoMet-unresponsive mutants was not significantly changed. Pulse proteolysis analysis suggested that the protein structure of the R125Q and E176K mutants is significantly less stable than that of the wild type and the other mutants. Taken together, the proteolytic data shows that the conformation of the pathogenic mutants is altered despite retained catalytic activity and normal tetrameric assembly. This study demonstrates that the proteolytic techniques are useful tools for the assessment of the biochemical penalty of missense mutations in CBS.
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Affiliation(s)
- Aleš Hnízda
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague 2, Czech Republic
| | - Tomas Majtan
- Department of Pediatrics and the Colorado Intellectual and Developmental Disabilities Research Center (IDDRC), University of Colorado at Denver, 12800 E 19th Ave, Aurora, Colorado 80045, USA
- Department of Genomics & Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, 84551, Slovakia
| | - Lu Liu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado at Denver, Aurora, Colorado 80045, USA
| | - Angel L. Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - John F. Carpenter
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado at Denver, Aurora, Colorado 80045, USA
| | - Milan Kodíček
- Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Technická 5, 166 28, Prague 6, Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague 2, Czech Republic
| | - Jan P. Kraus
- Department of Pediatrics and the Colorado Intellectual and Developmental Disabilities Research Center (IDDRC), University of Colorado at Denver, 12800 E 19th Ave, Aurora, Colorado 80045, USA
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Hnízda A, Jurga V, Raková K, Kožich V. Cystathionine beta-synthase mutants exhibit changes in protein unfolding: conformational analysis of misfolded variants in crude cell extracts. J Inherit Metab Dis 2012; 35:469-77. [PMID: 22069143 PMCID: PMC3319881 DOI: 10.1007/s10545-011-9407-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 09/16/2011] [Accepted: 09/21/2011] [Indexed: 11/23/2022]
Abstract
Protein misfolding has been proposed to be a common pathogenic mechanism in many inborn errors of metabolism including cystathionine β-synthase (CBS) deficiency. In this work, we describe the structural properties of nine CBS mutants that represent a common molecular pathology in the CBS gene. Using thermolysin in two proteolytic techniques, we examined conformation of these mutants directly in crude cell extracts after expression in E. coli. Proteolysis with thermolysin under native conditions appeared to be a useful technique even for very unstable mutant proteins, whereas pulse proteolysis in a urea gradient had limited values for the study of the majority of CBS mutants due to their instability. Mutants in the active core had either slightly increased unfolding (p.A114V, p.E302K and p.G307S) or extensive unfolding with decreased stability (p.H65R, p.T191M, p.I278T and p.R369C). The extent of the unfolding inversely correlated with the previously determined degree of tetrameric assembly and with the catalytic activity. In contrast, mutants bearing aminoacid substitutions in the C-terminal regulatory domain (p.R439Q and p.D444N) had increased global stability with decreased flexibility. This study shows that proteolytic techniques can reveal conformational abnormalities even for CBS mutants that have activity and/or a degree of assembly similar to the wild-type enzyme. We present here a methodological strategy that may be used in cell lysates to evaluate properties of proteins that tend to misfold and aggregate and that may be important for conformational studies of disease-causing mutations in the field of inborn errors of metabolism.
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Affiliation(s)
- Aleš Hnízda
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague 2, Czech Republic
| | - Vojtěch Jurga
- Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Kateřina Raková
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague 2, Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague 2, Czech Republic
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Krijt J, Kopecká J, Hnízda A, Moat S, Kluijtmans LAJ, Mayne P, Kožich V. Determination of cystathionine beta-synthase activity in human plasma by LC-MS/MS: potential use in diagnosis of CBS deficiency. J Inherit Metab Dis 2011; 34:49-55. [PMID: 20821054 PMCID: PMC3026677 DOI: 10.1007/s10545-010-9178-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 06/04/2010] [Accepted: 07/19/2010] [Indexed: 11/28/2022]
Abstract
Cystathionine β-synthase (CBS) deficiency is usually confirmed by assaying the enzyme activity in cultured skin fibroblasts. We investigated whether CBS is present in human plasma and whether determination of its activity in plasma could be used for diagnostic purposes. We developed an assay to measure CBS activity in 20 μL of plasma using a stable isotope substrate - 2,3,3-(2)H serine. The activity was determined by measurement of the product of enzyme reaction, 3,3-(2)H-cystathionine, using LC-MS/MS. The median enzyme activity in control plasma samples was 404 nmol/h/L (range 66-1,066; n = 57). In pyridoxine nonresponsive CBS deficient patients, the median plasma activity was 0 nmol/ho/L (range 0-9; n = 26), while in pyridoxine responsive patients the median activity was 16 nmol/hour/L (range 0-358; n = 28); this overlapped with the enzyme activity from control subject. The presence of CBS in human plasma was confirmed by an in silico search of the proteome database, and was further evidenced by the activation of CBS by S-adenosyl-L-methionine and pyridoxal 5'-phosphate, and by configuration of the detected reaction product, 3,3-(2)H-cystathionine, which was in agreement with the previously observed CBS reaction mechanism. We hypothesize that the CBS enzyme in plasma originates from liver cells, as the plasma CBS activities in patients with elevated liver aminotransferase activities were more than 30-fold increased. In this study, we have demonstrated that CBS is present in human plasma and that its catalytic activity is detectable by LC-MS/MS. CBS assay in human plasma brings new possibilities in the diagnosis of pyridoxine nonresponsive CBS deficiency.
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Affiliation(s)
- Jakub Krijt
- Institute of Inherited Metabolic Disorders--1st Faculty of Medicine, Charles University in Prague, Praha, Czech Republic
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Vliet LK, Wilkinson TG, Duval N, Vacano G, Graham C, Zikánová M, Skopova V, Baresova V, Hnízda A, Kmoch S, Patterson D. Molecular characterization of the AdeI mutant of Chinese hamster ovary cells: a cellular model of adenylosuccinate lyase deficiency. Mol Genet Metab 2011; 102:61-8. [PMID: 20884265 PMCID: PMC3065963 DOI: 10.1016/j.ymgme.2010.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 11/19/2022]
Abstract
Adenylosuccinate lyase (ADSL, E. C. 4.3.2.2) carries out two non-sequential steps in de novo AMP synthesis, the conversion of succinylaminoimidazole carboxamide ribotide (SAICAR) to aminoimidazolecarboxamide ribotide (AICAR) and the conversion of succinyl AMP (AMPS) to AMP. In humans, mutations in ADSL lead to an inborn error of metabolism originally characterized by developmental delay, often with autistic features. There is no effective treatment for ADSL deficiency. Hypotheses regarding the pathogenesis include toxicity of high levels of SAICAR, AMPS, or their metabolites, deficiency of the de novo purine biosynthetic pathway, or lack of a completely functional purine cycle in muscle and brain. One important approach to understand ADSL deficiency is to develop cell culture models that allow investigation of the properties of ADSL mutants and the consequences of ADSL deficiency at the cellular level. We previously reported the isolation and initial characterization of mutants of Chinese hamster ovary (CHO-K1) cells (AdeI) that lack detectable ADSL activity, accumulate SAICAR and AMPS, and require adenine for growth. Here we report the cDNA sequences of ADSL from CHO-K1 and AdeI cells and describe a mutation resulting in an alanine to valine amino acid substitution at position 291 (A291V) in AdeI ADSL. This substitution lies in the "signature sequence" of ADSL, inactivates the enzyme, and validates AdeI as a cellular model of ADSL deficiency.
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Affiliation(s)
- Lydia K. Vliet
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
| | - Terry G. Wilkinson
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
| | - Nathan Duval
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
| | - Guido Vacano
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
| | - Christine Graham
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
| | - Marie Zikánová
- Center for Applied Genomics, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
- Institute of Inherited Metabolic Disorders, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
| | - Vaclava Skopova
- Center for Applied Genomics, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
- Institute of Inherited Metabolic Disorders, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
| | - Veronika Baresova
- Center for Applied Genomics, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
- Institute of Inherited Metabolic Disorders, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
| | - Aleš Hnízda
- Institute of Inherited Metabolic Disorders, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
| | - Stanislav Kmoch
- Center for Applied Genomics, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
- Institute of Inherited Metabolic Disorders, Charles University in Prague, First Faculty of Medicine, Ke Karlovu 2, 128 00 Prague 2, Czech Republic
| | - David Patterson
- Eleanor Roosevelt Institute and Department of Biological Sciences, University of Denver, 2101 E. Wesley Avenue, Denver, CO, 80208
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Hnízda A, Spiwok V, Jurga V, Kožich V, Kodíček M, Kraus JP. Cross-talk between the catalytic core and the regulatory domain in cystathionine β-synthase: study by differential covalent labeling and computational modeling. Biochemistry 2010; 49:10526-34. [PMID: 21062078 PMCID: PMC3146298 DOI: 10.1021/bi101384m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/09/2010] [Indexed: 12/22/2022]
Abstract
Cystathionine β-synthase (CBS) is a modular enzyme which catalyzes condensation of serine with homocysteine. Cross-talk between the catalytic core and the C-terminal regulatory domain modulates the enzyme activity. The regulatory domain imposes an autoinhibition action that is alleviated by S-adenosyl-l-methionine (AdoMet) binding, by deletion of the C-terminal regulatory module, or by thermal activation. The atomic mechanisms of the CBS allostery have not yet been sufficiently explained. Using pulse proteolysis in urea gradient and proteolytic kinetics with thermolysin under native conditions, we demonstrated that autoinhibition is associated with changes in conformational stability and with sterical hindrance of the catalytic core. To determine the contact area between the catalytic core and the autoinhibitory module of the CBS protein, we compared side-chain reactivity of the truncated CBS lacking the regulatory domain (45CBS) and of the full-length enzyme (wtCBS) using covalent labeling by six different modification agents and subsequent mass spectrometry. Fifty modification sites were identified in 45CBS, and four of them were not labeled in wtCBS. One differentially reactive site (cluster W408/W409/W410) is a part of the linker between the domains. The other three residues (K172 and/or K177, R336, and K384) are located in the same region of the 45CBS crystal structure; computational modeling showed that these amino acid side chains potentially form a regulatory interface in CBS protein. Subtle differences at CBS surface indicate that enzyme activity is not regulated by conformational conversions but more likely by different allosteric mechanisms.
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Affiliation(s)
- Aleš Hnízda
- Institute of Inherited Metabolic Disorders, First Medical Faculty, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 2, 128 00 Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Vojtěch Jurga
- Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders, First Medical Faculty, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 2, 128 00 Czech Republic
| | - Milan Kodíček
- Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Jan P. Kraus
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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