1
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Steinberg-Shemer O, Yacobovich J, Noy-Lotan S, Dgany O, Krasnov T, Barg A, Landau YE, Kneller K, Somech R, Gilad O, Brik Simon D, Orenstein N, Izraeli S, Del Caño-Ochoa F, Tamary H, Ramón-Maiques S. Biallelic hypomorphic variants in CAD cause uridine-responsive macrocytic anaemia with elevated haemoglobin-A2. Br J Haematol 2024; 204:1067-1071. [PMID: 37984840 DOI: 10.1111/bjh.19215] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/14/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Biallelic pathogenic variants in CAD, that encode the multienzymatic protein required for de-novo pyrimidine biosynthesis, cause early infantile epileptic encephalopathy-50. This rare disease, characterized by developmental delay, intractable seizures and anaemia, is amenable to treatment with uridine. We present a patient with macrocytic anaemia, elevated haemoglobin-A2 levels, anisocytosis, poikilocytosis and target cells in the blood smear, and mild developmental delay. A next-generation sequencing panel revealed biallelic variants in CAD. Functional studies did not support complete abrogation of protein function; however, the patient responded to uridine supplement. We conclude that biallelic hypomorphic CAD variants may cause a primarily haematological phenotype.
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Affiliation(s)
- Orna Steinberg-Shemer
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joanne Yacobovich
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Assaf Barg
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Yuval E Landau
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Metabolic Disease Service, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Katya Kneller
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Raz Somech
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Oded Gilad
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dafna Brik Simon
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Naama Orenstein
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Shai Izraeli
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Francisco Del Caño-Ochoa
- Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Hannah Tamary
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Santiago Ramón-Maiques
- Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
- Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain
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2
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Francisco-Velilla R, Embarc-Buh A, Del Caño-Ochoa F, Abellan S, Vilar M, Alvarez S, Fernandez-Jaen A, Kour S, Rajan DS, Pandey UB, Ramón-Maiques S, Martinez-Salas E. Functional and structural deficiencies of Gemin5 variants associated with neurological disorders. Life Sci Alliance 2022; 5:5/7/e202201403. [PMID: 35393353 PMCID: PMC8989681 DOI: 10.26508/lsa.202201403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/10/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
Dysfunction of RNA-binding proteins is often linked to a wide range of human disease, particularly with neurological conditions. Gemin5 is a member of the survival of the motor neurons (SMN) complex, a ribosome-binding protein and a translation reprogramming factor. Recently, pathogenic mutations in Gemin5 have been reported, but the functional consequences of these variants remain elusive. Here, we report functional and structural deficiencies associated with compound heterozygosity variants within the Gemin5 gene found in patients with neurodevelopmental disorders. These clinical variants are located in key domains of Gemin5, the tetratricopeptide repeat (TPR)-like dimerization module and the noncanonical RNA-binding site 1 (RBS1). We show that the TPR-like variants disrupt protein dimerization, whereas the RBS1 variant confers protein instability. All mutants are defective in the interaction with protein networks involved in translation and RNA-driven pathways. Importantly, the TPR-like variants fail to associate with native ribosomes, hampering its involvement in translation control and establishing a functional difference with the wild-type protein. Our study provides insights into the molecular basis of disease associated with malfunction of the Gemin5 protein.
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Affiliation(s)
- Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Cientificas - Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Azman Embarc-Buh
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Cientificas - Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Salvador Abellan
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Cientificas - Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Marçal Vilar
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Sara Alvarez
- New Integrated Medical Genetics (NIMGENETICS), Madrid, Spain
| | - Alberto Fernandez-Jaen
- Neuropediatric Department, Hospital Universitario Quirónsalud, Madrid, Spain.,School of Medicine, Universidad Europea de Madrid, Madrid, Spain
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Cientificas - Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
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3
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Briso-Montiano A, Del Caño-Ochoa F, Vilas A, Velázquez-Campoy A, Rubio V, Pérez B, Ramón-Maiques S. Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures. J Inherit Metab Dis 2022; 45:318-333. [PMID: 34859900 DOI: 10.1002/jimd.12461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/12/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022]
Abstract
Phosphomannomutase 2 (PMM2) deficiency, the most frequent congenital disorder of glycosylation (PMM2-CDG), is a severe condition, which has no cure. Due to the identification of destabilizing mutations, our group aims at increasing residual activity in PMM2-CDG patients, searching for pharmacochaperones. Detailed structural knowledge of hPMM2 might help identify variants amenable to pharmacochaperoning. hPMM2 structural information is limited to one incomplete structure deposited in the Protein Databank without associated publication, which lacked ligands and residues from a crucial loop. Here we report five complete crystal structures of hPMM2, three for wild-type and two for the p.Thr237Met variant frequently found among Spanish PMM2-CDG patients, free and bound to the essential activator glucose-1,6-bisphosphate (Glc-1,6-P2 ). In the hPMM2 homodimer, each subunit has a different conformation, reflecting movement of the distal core domain relative to the dimerization cap domain, supporting an opening/closing process during catalysis. Two Mg2+ ions bind to the core domain, one catalytic and one structural. In the cap domain, the site for Glc-1,6-P2 is well delineated, while a Cl- ion binding at the intersubunit interface is predicted to strengthen dimerization. Patient-found amino acid substitutions are nonhomogeneously distributed throughout hPMM2, reflecting differential functional or structural importance for various parts of the protein. We classify 93 of 101 patient-reported single amino acid variants according to five potential pathogenetic mechanism affecting folding of the core and cap domains, linker 2 flexibility, dimerization, activator binding, and catalysis. We propose that ~80% and ~50% of the respective core and cap domains substitutions are potential candidates for pharmacochaperoning treatment.
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Affiliation(s)
- Alvaro Briso-Montiano
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Alicia Vilas
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Departament of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
- Protein Targets Group, Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
- Group CB06/04/0066, Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), Madrid, Spain
- Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
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4
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Del Caño-Ochoa F, Ramón-Maiques S. Deciphering CAD: Structure and function of a mega-enzymatic pyrimidine factory in health and disease. Protein Sci 2021; 30:1995-2008. [PMID: 34288185 PMCID: PMC8442968 DOI: 10.1002/pro.4158] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD's architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
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5
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Tu HF, Ko CJ, Lee CT, Lee CF, Lan SW, Lin HH, Lin HY, Ku CC, Lee DY, Chen IC, Chuang YH, Del Caño-Ochoa F, Ramón-Maiques S, Ho CC, Lee MS, Chang GD. Afatinib Exerts Immunomodulatory Effects by Targeting the Pyrimidine Biosynthesis Enzyme CAD. Cancer Res 2021; 81:3270-3282. [PMID: 33771897 DOI: 10.1158/0008-5472.can-20-3436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/24/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022]
Abstract
Current clinical trials of combined EGFR-tyrosine kinase inhibitors (TKI) and immune checkpoint blockade (ICB) therapies show no additional effect. This raises questions regarding whether EGFR-TKIs attenuate ICB-enhanced CD8+ T lymphocyte function. Here we show that the EGFR-TKI afatinib suppresses CD8+ T lymphocyte proliferation, and we identify CAD, a key enzyme of de novo pyrimidine biosynthesis, to be a novel afatinib target. Afatinib reduced tumor-infiltrating lymphocyte numbers in Lewis lung carcinoma (LLC)-bearing mice. Early afatinib treatment inhibited CD8+ T lymphocyte proliferation in patients with non-small cell lung cancer, but their proliferation unexpectedly rebounded following long-term treatment. This suggests a transient immunomodulatory effect of afatinib on CD8+ T lymphocytes. Sequential treatment of afatinib with anti-PD1 immunotherapy substantially enhanced therapeutic efficacy in MC38 and LLC-bearing mice, while simultaneous combination therapy showed only marginal improvement over each single treatment. These results suggest that afatinib can suppress CD8+ T lymphocyte proliferation by targeting CAD, proposing a timing window for combined therapy that may prevent the dampening of ICB efficacy by EGFR-TKIs. SIGNIFICANCE: This study elucidates a mechanism of afatinib-mediated immunosuppression and provides new insights into treatment timing for combined targeted therapy and immunotherapy. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/12/3270/F1.large.jpg.
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Affiliation(s)
- Hsin-Fang Tu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Jung Ko
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ching-Tai Lee
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Fan Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shao-Wei Lan
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hsien Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Ying Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Chi Ku
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine/Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - I-Chun Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Hui Chuang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Ming-Shyue Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Geen-Dong Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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6
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Del Caño-Ochoa F, Ng BG, Abedalthagafi M, Almannai M, Cohn RD, Costain G, Elpeleg O, Houlden H, Karimiani EG, Liu P, Manzini MC, Maroofian R, Muriello M, Al-Otaibi A, Patel H, Shimon E, Sutton VR, Toosi MB, Wolfe LA, Rosenfeld JA, Freeze HH, Ramón-Maiques S. Cell-based analysis of CAD variants identifies individuals likely to benefit from uridine therapy. Genet Med 2020; 22:1598-1605. [PMID: 32461667 PMCID: PMC7521996 DOI: 10.1038/s41436-020-0833-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 03/11/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 12/27/2022] Open
Abstract
Purpose Pathogenic autosomal recessive variants in CAD, encoding the multienzymatic protein initiating pyrimidine de novo biosynthesis, cause a severe inborn metabolic disorder treatable with a dietary supplement of uridine. This condition is difficult to diagnose given the large size of CAD with over 1000 missense variants and the nonspecific clinical presentation. We aimed to develop a reliable and discerning assay to assess the pathogenicity of CAD variants and to select affected individuals that might benefit from uridine therapy. Methods Using CRISPR/Cas9, we generated a human CAD-knockout cell line that requires uridine supplements for survival. Transient transfection of the knockout cells with recombinant CAD restores growth in absence of uridine. This system determines missense variants that inactivate CAD and do not rescue the growth phenotype. Results We identified 25 individuals with biallelic variants in CAD and a phenotype consistent with a CAD deficit. We used the CAD-knockout complementation assay to test a total of 34 variants, identifying 16 as deleterious for CAD activity. Combination of these pathogenic variants confirmed 11 subjects with a CAD deficit, for whom we describe the clinical phenotype. Conclusions We designed a cell-based assay to test the pathogenicity of CAD variants, identifying 11 CAD-deficient individuals who could benefit from uridine therapy.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain.,Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ronald D Cohn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Orly Elpeleg
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Henry Houlden
- Department of Neuromuscular disorders, UCL Institute of Neurology University College, London, UK
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, UK
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - M Chiara Manzini
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Reza Maroofian
- Department of Neuromuscular disorders, UCL Institute of Neurology University College, London, UK
| | - Michael Muriello
- Department of Pediatrics/Division of Genetics, Medical College of Wisconsin, Milwaukee, WI, USA.,Genomic Science and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ali Al-Otaibi
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hema Patel
- Department of Neurology (Section of pediatric neurology) Children's Hospital of Wisconsin, Medical of College of Wisconsin, Milwaukee, WI, USA
| | - Edvardson Shimon
- Pediatric Neurology Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - V Reid Sutton
- Department of Molecular, Human Genetics Baylor College of Medicine & Texas Children's Hospital, Houston, TX, USA
| | - Mehran Beiraghi Toosi
- Department of Pediatric Diseases, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Lynne A Wolfe
- Undiagnosed Diseases Program, Common Fund, National Institutes of Health, Bethesda, MD, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Santiago Ramón-Maiques
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain. .,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain. .,Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
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7
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Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein that carries the enzymatic activities for the first three steps in the de novo biosynthesis of pyrimidine nucleotides: glutamine-dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase and Dihydroorotase. This metabolic pathway is essential for cell growth and proliferation and is conserved in all living organisms. However, the fusion of the first three enzymatic activities of the pathway into a single multienzymatic protein only occurs in animals. In prokaryotes, by contrast, these activities are encoded as distinct monofunctional enzymes that function independently or by forming more or less transient complexes. Whereas the structural information about these enzymes in bacteria is abundant, the large size and instability of CAD has only allowed a fragmented characterization of its structure. Here we retrace some of the most significant efforts to decipher the architecture of CAD and to understand its catalytic and regulatory mechanisms.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - María Moreno-Morcillo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - Santiago Ramón-Maiques
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain.
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8
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Del Caño-Ochoa F, Ramón-Maiques S. The multienzymatic protein CAD leading the de novo biosynthesis of pyrimidines localizes exclusively in the cytoplasm and does not translocate to the nucleus. Nucleosides Nucleotides Nucleic Acids 2020; 39:1320-1334. [PMID: 31997698 DOI: 10.1080/15257770.2019.1706743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CAD, the multienzymatic protein that initiates and controls the de novo biosynthesis of pyrimidines, plays a major role in nucleotide homeostasis, cell growth and proliferation. Despite its interest as a potential antitumoral target, there is a lack of understanding on CAD's structure and functioning mechanisms. Although mainly identified as a cytosolic complex, different studies support the translocation of CAD into the nucleus, where it could have a yet undefined function. Here, we track the subcellular localization of CAD by using fluorescent chimeras, cell fractionation and immunoblotting with specific antibodies. Contradicting previous studies, we demonstrate that CAD is exclusively localized at the cytosol and discard a possible translocation to the nucleus.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Santiago Ramón-Maiques
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
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9
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Del Caño-Ochoa F, Grande-García A, Reverte-López M, D'Abramo M, Ramón-Maiques S. Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. J Biol Chem 2018; 293:18903-18913. [PMID: 30315107 DOI: 10.1074/jbc.ra118.005494] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/08/2018] [Indexed: 11/06/2022] Open
Abstract
The dihydroorotase (DHOase) domain of the multifunctional protein carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) catalyzes the third step in the de novo biosynthesis of pyrimidine nucleotides in animals. The crystal structure of the DHOase domain of human CAD (huDHOase) revealed that, despite evolutionary divergence, its active site components are highly conserved with those in bacterial DHOases, encoded as monofunctional enzymes. An important element for catalysis, conserved from Escherichia coli to humans, is a flexible loop that closes as a lid over the active site. Here, we combined mutagenic, structural, biochemical, and molecular dynamics analyses to characterize the function of the flexible loop in the activity of CAD's DHOase domain. A huDHOase chimera bearing the E. coli DHOase flexible loop was inactive, suggesting the presence of distinctive elements in the flexible loop of huDHOase that cannot be replaced by the bacterial sequence. We pinpointed Phe-1563, a residue absolutely conserved at the tip of the flexible loop in CAD's DHOase domain, as a critical element for the conformational equilibrium between the two catalytic states of the protein. Substitutions of Phe-1563 with Ala, Leu, or Thr prevented the closure of the flexible loop and inactivated the protein, whereas substitution with Tyr enhanced the interactions of the loop in the closed position and reduced fluctuations and the reaction rate. Our results confirm the importance of the flexible loop in CAD's DHOase domain and explain the key role of Phe-1563 in configuring the active site and in promoting substrate strain and catalysis.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain
| | - Araceli Grande-García
- the Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain, and
| | - María Reverte-López
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain
| | - Marco D'Abramo
- the Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Santiago Ramón-Maiques
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain,
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10
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Moreno-Morcillo M, Grande-García A, Ruiz-Ramos A, Del Caño-Ochoa F, Boskovic J, Ramón-Maiques S. Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis. Structure 2017; 25:912-923.e5. [PMID: 28552578 DOI: 10.1016/j.str.2017.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 02/28/2017] [Revised: 04/05/2017] [Accepted: 04/28/2017] [Indexed: 11/17/2022]
Abstract
CAD, the multifunctional protein initiating and controlling de novo biosynthesis of pyrimidines in animals, self-assembles into ∼1.5 MDa hexamers. The structures of the dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains of human CAD have been previously determined, but we lack information on how these domains associate and interact with the rest of CAD forming a multienzymatic unit. Here, we prove that a construct covering human DHO and ATC oligomerizes as a dimer of trimers and that this arrangement is conserved in CAD-like from fungi, which holds an inactive DHO-like domain. The crystal structures of the ATC trimer and DHO-like dimer from the fungus Chaetomium thermophilum confirm the similarity with the human CAD homologs. These results demonstrate that, despite being inactive, the fungal DHO-like domain has a conserved structural function. We propose a model that sets the DHO and ATC complex as the central element in the architecture of CAD.
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Affiliation(s)
- María Moreno-Morcillo
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Alba Ruiz-Ramos
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Francisco Del Caño-Ochoa
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Jasminka Boskovic
- Electron Microscopy Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Santiago Ramón-Maiques
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera, 1, Madrid 28049, Spain.
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