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van de Stadt SIW, Mooyer PAW, Dijkstra IME, Dekker CJM, Vats D, Vera M, Ruzhnikov MRZ, van Haren K, Tang N, Koop K, Willemsen MA, Hui J, Vaz FM, Ebberink MS, Engelen M, Kemp S, Ferdinandusse S. Biochemical Studies in Fibroblasts to Interpret Variants of Unknown Significance in the ABCD1 Gene. Genes (Basel) 2021; 12:genes12121930. [PMID: 34946879 PMCID: PMC8701351 DOI: 10.3390/genes12121930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Due to newborn screening for X-linked adrenoleukodystrophy (ALD), and the use of exome sequencing in clinical practice, the detection of variants of unknown significance (VUS) in the ABCD1 gene is increasing. In these cases, functional tests in fibroblasts may help to classify a variant as (likely) benign or pathogenic. We sought to establish reference ranges for these tests in ALD patients and control subjects with the aim of helping to determine the pathogenicity of VUS in ABCD1. Fibroblasts from 36 male patients with confirmed ALD, 26 healthy control subjects and 17 individuals without a family history of ALD, all with an uncertain clinical diagnosis and a VUS identified in ABCD1, were included. We performed a combination of tests: (i) a test for very-long-chain fatty acids (VLCFA) levels, (ii) a D3-C22:0 loading test to study the VLCFA metabolism and (iii) immunoblotting for ALD protein. All ALD patient fibroblasts had elevated VLCFA levels and a reduced peroxisomal ß-oxidation capacity (as measured by the D3-C16:0/D3-C22:0 ratio in the D3-C22:0 loading test) compared to the control subjects. Of the VUS cases, the VLCFA metabolism was not significantly impaired (most test results were within the reference range) in 6/17, the VLCFA metabolism was significantly impaired (most test results were within/near the ALD range) in 9/17 and a definite conclusion could not be drawn in 2/17 of the cases. Biochemical studies in fibroblasts provided clearly defined reference and disease ranges for the VLCFA metabolism. In 15/17 (88%) VUS we were able to classify the variant as being likely benign or pathogenic. This is of great clinical importance as new variants will be detected.
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Affiliation(s)
- Stephanie I. W. van de Stadt
- Department of Pediatric Neurology, Emma Children’s Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.I.W.v.d.S.); (M.E.)
| | - Petra A. W. Mooyer
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
| | - Inge M. E. Dijkstra
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
| | - Conny J. M. Dekker
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
| | - Divya Vats
- Regional Metabolic Clinic, Department of Medical Genetics, Southern California Permanente Medical Group, Los Angeles, CA 90027, USA; (D.V.); (M.V.)
| | - Moin Vera
- Regional Metabolic Clinic, Department of Medical Genetics, Southern California Permanente Medical Group, Los Angeles, CA 90027, USA; (D.V.); (M.V.)
| | - Maura R. Z. Ruzhnikov
- Departments of Neurology and Neurological Sciences and Pediatrics, Stanford, CA 94305, USA; (M.R.Z.R.); (K.v.H.)
| | - Keith van Haren
- Departments of Neurology and Neurological Sciences and Pediatrics, Stanford, CA 94305, USA; (M.R.Z.R.); (K.v.H.)
| | - Nelson Tang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Klaas Koop
- Department of Metabolic Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, 3584 EA Utrecht, The Netherlands;
| | - Michel A. Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands;
| | - Joannie Hui
- Department of Pediatrics & Adolescent Medicine, Hong Kong Children’s Hospital, Hong Kong, China;
| | - Frédéric M. Vaz
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
| | - Merel S. Ebberink
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
| | - Marc Engelen
- Department of Pediatric Neurology, Emma Children’s Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.I.W.v.d.S.); (M.E.)
| | - Stephan Kemp
- Department of Pediatric Neurology, Emma Children’s Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.I.W.v.d.S.); (M.E.)
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
- Correspondence:
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (P.A.W.M.); (I.M.E.D.); (C.J.M.D.); (F.M.V.); (M.S.E.); (S.F.)
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Ebberink MS, Mooyer PAW, Koster J, Dekker CJM, Eyskens FJM, Dionisi-Vici C, Clayton PT, Barth PG, Wanders RJA, Waterham HR. Genotype-phenotype correlation in PEX5-deficient peroxisome biogenesis defective cell lines. Hum Mutat 2009; 30:93-8. [PMID: 18712838 DOI: 10.1002/humu.20833] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins destined for the peroxisomal matrix are targeted by virtue of a peroxisomal targeting sequence type 1 (PTS1) or type 2 (PTS2). In humans, targeting of either class of proteins relies on a cytosolic receptor protein encoded by the PEX5 gene. Alternative splicing of PEX5 results in two protein variants, PEX5S and PEX5L. PEX5S is exclusively involved in PTS1 protein import, whereas PEX5L mediates the import of both PTS1 and PTS2 proteins. Genetic complementation testing with over 500 different fibroblast cell lines from patients diagnosed with a peroxisome biogenesis disorder (PBD) identified 11 cell lines with a defect in PEX5. The aim of this study was to characterize these cell lines at a biochemical and genetic level. To this end, the cultured fibroblasts were analyzed for very long chain fatty acid (VLCFA) concentrations, peroxisomal beta-and alpha-oxidation, dihydroxyacetone-phosphate acyltransferase (DHAPAT) activity, peroxisomal thiolase, and catalase immunofluorescence. Mutation analysis of the PEX5 gene revealed 11 different mutations, eight of which are novel. PTS1- and PTS2-protein import capacity was assessed by transfection of the cells with green fluorescent protein (GFP) tagged with either PTS1 or PTS2. Six cell lines showed a defect in both PTS1 and PTS2 protein import, whereas four cell lines only showed a defect in PTS1 protein import. The location of the different mutations within the PEX5 amino acid sequence correlates rather well with the peroxisomal protein import defect observed in the cell lines.
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Affiliation(s)
- Merel S Ebberink
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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