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Staklinski SJ, Scheben A, Siepel A, Kilberg MS. Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564808. [PMID: 37961642 PMCID: PMC10634951 DOI: 10.1101/2023.10.30.564808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
AlphaMissense is a recently developed method that is designed to classify missense variants into pathogenic, benign, or ambiguous categories across the entire human proteome. Asparagine Synthetase Deficiency (ASNSD) is a developmental disorder associated with severe symptoms, including congenital microcephaly, seizures, and premature death. Diagnosing ASNSD relies on identifying mutations in the asparagine synthetase (ASNS) gene through DNA sequencing and determining whether these variants are pathogenic or benign. Pathogenic ASNS variants are predicted to disrupt the protein's structure and/or function, leading to asparagine depletion within cells and inhibition of cell growth. AlphaMissense offers a promising solution for the rapid classification of ASNS variants established by DNA sequencing and provides a community resource of pathogenicity scores and classifications for newly diagnosed ASNSD patients. Here, we assessed AlphaMissense's utility in ASNSD by benchmarking it against known critical residues in ASNS and evaluating its performance against a list of previously reported ASNSD-associated variants. We also present a pipeline to calculate AlphaMissense scores for any protein in the UniProt database. AlphaMissense accurately attributed a high average pathogenicity score to known critical residues within the two ASNS active sites and the connecting intramolecular tunnel. The program successfully categorized 78.9% of known ASNSD-associated missense variants as pathogenic. The remaining variants were primarily labeled as ambiguous, with a smaller proportion classified as benign. This study underscores the potential role of AlphaMissense in classifying ASNS variants in suspected cases of ASNSD, potentially providing clarity to patients and their families grappling with ongoing diagnostic uncertainty.
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Affiliation(s)
- Stephen J. Staklinski
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Box 100245, Gainesville, FL 326010-0245
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Chang MC, Staklinski SJ, Merritt ME, Kilberg MS. A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. Biol Methods Protoc 2023; 8:bpad026. [PMID: 37965492 PMCID: PMC10641120 DOI: 10.1093/biomethods/bpad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Human asparagine synthetase (ASNS) catalyzes the conversion of aspartate to asparagine in an ATP-dependent reaction that utilizes glutamine as a nitrogen source while generating glutamate, AMP, and pyrophosphate as additional products. Asparagine Synthetase Deficiency (ASNSD) is an inborn error of metabolism in which children present with homozygous or compound heterozygous mutations in the ASNS gene. These mutations result in ASNS variant protein expression. It is believed that these variant ASNS proteins have reduced enzymatic activity or stability resulting in a lack of sufficient asparagine production for cell function. Reduced asparagine production by ASNS appears to severely hinder fetal brain development. Although a variety of approaches for assaying ASNS activity have been reported, we present here a straightforward method for the in vitro enzymatic analysis by detection of AMP production. Our method overcomes limitations in technical feasibility, signal detection, and reproducibility experienced by prior methods like high-performance liquid chromatography, ninhydrin staining, and radioactive tracing. After purification of FLAG-tagged R49Q, G289A, and T337I ASNS variants from stably expressing HEK 293T cells, this method revealed a reduction in activity of 90, 36, and 96%, respectively. Thus, ASNS protein expression and purification, followed by enzymatic activity analysis, has provided a relatively simple protocol to evaluate structure-function relationships for ASNS variants reported for ASNSD patients.
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Affiliation(s)
- Mario C Chang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, United States
| | - Stephen J Staklinski
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, United States
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, United States
| | - Michael S Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, United States
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Altıntaş M, Yıldırım M, Uçar Çİ, Köse E, Bektaş Ö, Teber S. Ketogenic diet-responsive drug-resistant epilepsy in a case of asparagine synthetase deficiency with a novel compound heterozygous missense variant. Clin Neurol Neurosurg 2023; 230:107772. [PMID: 37167844 DOI: 10.1016/j.clineuro.2023.107772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Asparagine synthetase deficiency (ASNSD) is a rare autosomal recessive neurometabolic disorder caused by homozygous or compound heterozygous mutations in the ASNS gene. Most of the patients have early-onset intractable seizures. A 7-year-old boy was first admitted to our clinic with intractable febrile and afebrile seizures that started when he was 6 months old. He had axial hypotonia with spastic quadriparesis, mild facial dysmorphism, and acquired microcephaly at 1 year-old. Metabolic tests showed a borderline-low serum asparagine level. The electroencephalogram demonstrated epileptic discharges with a high incidence of multifocal spike-wave activity. Brain MRI showed mild cerebral atrophy. His seizures continued despite combinations of multiple antiseizure agents. Whole-exome sequencing (WES) revealed a novel compound heterozygous missense variant of the ASNS gene, and the variants were confirmed by Sanger sequencing. He was started on a ketogenic diet at five years and six months of age. In the first month of the ketogenic diet, we observed that the frequency of seizures significantly decreased. He showed a remarkable improvement in seizures and milder improvement in cognitive skills. To our knowledge, our case is the first report describing significant improvement with a ketogenic diet in intractable seizures due to ASNSD.
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Affiliation(s)
- Mert Altıntaş
- Department of Pediatrics, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Miraç Yıldırım
- Department of Pediatric Neurology, Ankara University Faculty of Medicine, Ankara, Turkey.
| | - Çiğdem İlter Uçar
- Department of Pediatric Neurology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Engin Köse
- Department of Pediatric Metabolism and Nutrition, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ömer Bektaş
- Department of Pediatric Neurology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Serap Teber
- Department of Pediatric Neurology, Ankara University Faculty of Medicine, Ankara, Turkey
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Chang MC, Staklinski SJ, Malut VR, Pierre GL, Kilberg MS, Merritt ME. Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells. Nutrients 2023; 15:1938. [PMID: 37111157 PMCID: PMC10145675 DOI: 10.3390/nu15081938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The natural amino acid asparagine (Asn) is required by cells to sustain function and proliferation. Healthy cells can synthesize Asn through asparagine synthetase (ASNS) activity, whereas specific cancer and genetically diseased cells are forced to obtain asparagine from the extracellular environment. ASNS catalyzes the ATP-dependent synthesis of Asn from aspartate by consuming glutamine as a nitrogen source. Asparagine Synthetase Deficiency (ASNSD) is a disease that results from biallelic mutations in the ASNS gene and presents with congenital microcephaly, intractable seizures, and progressive brain atrophy. ASNSD often leads to premature death. Although clinical and cellular studies have reported that Asn deprivation contributes to the disease symptoms, the global metabolic effects of Asn deprivation on ASNSD-derived cells have not been studied. We analyzed two previously characterized cell culture models, lymphoblastoids and fibroblasts, each carrying unique ASNS mutations from families with ASNSD. Metabolomics analysis demonstrated that Asn deprivation in ASNS-deficient cells led to disruptions across a wide range of metabolites. Moreover, we observed significant decrements in TCA cycle intermediates and anaplerotic substrates in ASNS-deficient cells challenged with Asn deprivation. We have identified pantothenate, phenylalanine, and aspartate as possible biomarkers of Asn deprivation in normal and ASNSD-derived cells. This work implies the possibility of a novel ASNSD diagnostic via targeted biomarker analysis of a blood draw.
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Affiliation(s)
- Mario C. Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Stephen J. Staklinski
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vinay R. Malut
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Geraldine L. Pierre
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Matthew E. Merritt
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Staklinski SJ, Chang MC, Ahrens‐Nicklas RC, Kaur S, Stefanatos AK, Dudenhausen EE, Merritt ME, Kilberg MS. Characterizing asparagine synthetase deficiency variants in lymphoblastoid cell lines. JIMD Rep 2023; 64:167-179. [PMID: 36873094 PMCID: PMC9981421 DOI: 10.1002/jmd2.12356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 01/08/2023] Open
Abstract
Asparagine synthetase (ASNS) catalyzes the synthesis of asparagine (Asn) from aspartate and glutamine. Biallelic mutations in the ASNS gene result in ASNS Deficiency (ASNSD). Children with ASNSD exhibit congenital microcephaly, epileptic-like seizures, and continued brain atrophy, often leading to premature mortality. This report describes a 4-year-old male with global developmental delay and seizures with two novel mutations in the ASNS gene, c.614A > C (maternal) and c.1192dupT (paternal) encoding p.H205P and p.Y398Lfs*4 variants, respectively. We employed the novel use of immortalized lymphoblastoid cell lines (LCL) to show that the proliferation of the heterozygotic parental LCL was not severely affected by culture in Asn-free medium, but growth of the child's cells was suppressed by about 50%. Asn production by the LCL from both the father and the child was significantly decreased relative to the mother's cells. mRNA and protein analysis of the paternal LCL cells for the Y398Lfs*4 variant revealed reductions in both. Attempts to ectopically express the truncated Y398Lfs*4 variant in either HEK293T or ASNS-null cells resulted in little or no detectable protein. Expression and purification of the H205P variant from HEK293T cells revealed enzymatic activity similar to wild-type ASNS. Stable expression of WT ASNS rescued the growth of ASNS-null JRS cells in Asn-free medium and the H205P variant was only slightly less effective. However, the Y398Lfs*4 variant appeared to be unstable in JRS cells. These results indicate that co-expression of the H205P and Y398Lfs*4 variants leads to a significant reduction in Asn synthesis and cellular growth.
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Affiliation(s)
- Stephen J. Staklinski
- Department of Biochemistry and Molecular BiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
- School of Biological SciencesCold Spring Harbor Laboratory, Cold Spring HarborNew YorkNew YorkUSA
| | - Mario C. Chang
- Department of Biochemistry and Molecular BiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Rebecca C. Ahrens‐Nicklas
- Division of Human Genetics, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Shagun Kaur
- Division of Human Genetics, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Arianna K. Stefanatos
- Department of Child and Adolescent Psychiatry and Behavioral SciencesChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Elizabeth E. Dudenhausen
- Department of Biochemistry and Molecular BiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Matthew E. Merritt
- Department of Biochemistry and Molecular BiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular BiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
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Analysis of Enzyme Activity and Cellular Function for the N80S and S480F Asparagine Synthetase Variants Expressed in a Child with Asparagine Synthetase Deficiency. Int J Mol Sci 2022; 24:ijms24010559. [PMID: 36613999 PMCID: PMC9820069 DOI: 10.3390/ijms24010559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Asparagine Synthetase Deficiency (ASNSD) is a disease caused by mutations in asparagine synthetase (ASNS). Newborns exhibit microcephaly, intractable epileptic-like seizures, progressive brain atrophy, and axial hypotonia. ASNSD results in global developmental delays and premature death. The present report describes a 9-year-old child who is a compound heterozygote with ASNS mutations c.1439C > T and c.239A > G leading to variants p.S480F and p.N80S, respectively. When grown in a complete culture medium, primary fibroblasts from the child contained ASNS mRNA and protein levels similar to an unrelated wild-type fibroblast cell line. When the child’s fibroblasts were cultured for up to 72 h in a medium lacking asparagine, proliferation was reduced by about 50%. Purification of ASNS proteins harboring either the S480F or the N80S substitution had reduced enzymatic activity by 80% and 50%, respectively. Ectopic expression of either variant in ASNS-null Jensen rat sarcoma (JRS) cells did not support proliferation in the absence of medium-supplied asparagine, whereas expression of wild-type enzyme completely restored growth. These studies add to the list of pathogenic ASNS variants and use enzyme activity and protein expression in ASNS-null cells to expand our knowledge of the biological impact of mutations in the ASNS gene.
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Staklinski SJ, Chang MC, Yu F, Collins Ruff K, Franz DN, Qian Z, Bloom LB, Merritt ME, McKenna R, Kilberg MS. Cellular and molecular characterization of two novel asparagine synthetase gene mutations linked to asparagine synthetase deficiency. J Biol Chem 2022; 298:102385. [PMID: 35985424 PMCID: PMC9478401 DOI: 10.1016/j.jbc.2022.102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022] Open
Abstract
Asparagine synthetase (ASNS) catalyzes synthesis of asparagine (Asn) and Glu from Asp and Gln in an ATP-dependent reaction. Asparagine synthetase deficiency (ASNSD) results from biallelic mutations in the ASNS gene. Affected children exhibit congenital microcephaly, continued brain atrophy, seizures, and often premature mortality. However, the underlying mechanisms are unclear. This report describes a compound heterozygotic ASNSD child with two novel mutations in the ASNS gene, c.1118G>T (paternal) and c.1556G>A (maternal), that lead to G373V or R519H ASNS variants. Structural mapping suggested that neither variant participates directly in catalysis. Growth of cultured fibroblasts from either parent was unaffected in Asn-free medium, whereas growth of the child's cells was suppressed by about 50%. Analysis of Asn levels unexpectedly revealed that extracellular rather than intracellular Asn correlated with the reduced proliferation during incubation of the child's cells in Asn-free medium. Our attempts to ectopically express the G373V variant in either HEK293T or JRS cells resulted in minimal protein production, suggesting instability. Protein expression and purification from HEK293T cells revealed reduced activity for the R519H variant relative to WT ASNS. Expression of WT ASNS in ASNS-null JRS cells resulted in nearly complete rescue of growth in Asn-free medium, whereas we observed no proliferation for the cells expressing either the G373V or R519H variant. These results support the conclusion that the coexpression of the G373V and R519H ASNS variants leads to significantly reduced Asn synthesis, which negatively impacts cellular growth. These observations are consistent with the ASNSD phenotype.
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Affiliation(s)
- Stephen J Staklinski
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Mario C Chang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Fang Yu
- Department of Medicine, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Kathleen Collins Ruff
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - David N Franz
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Zhijian Qian
- Department of Medicine, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Michael S Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA.
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