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Tummala H, Walne A, Buccafusca R, Alnajar J, Szabo A, Robinson P, McConkie-Rosell A, Wilson M, Crowley S, Kinsler V, Ewins AM, Madapura PM, Patel M, Pontikos N, Codd V, Vulliamy T, Dokal I. Germline thymidylate synthase deficiency impacts nucleotide metabolism and causes dyskeratosis congenita. Am J Hum Genet 2022; 109:1472-1483. [PMID: 35931051 PMCID: PMC9388389 DOI: 10.1016/j.ajhg.2022.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2022] [Indexed: 11/19/2022] Open
Abstract
Dyskeratosis congenita (DC) is an inherited bone-marrow-failure disorder characterized by a triad of mucocutaneous features that include abnormal skin pigmentation, nail dystrophy, and oral leucoplakia. Despite the identification of several genetic variants that cause DC, a significant proportion of probands remain without a molecular diagnosis. In a cohort of eight independent DC-affected families, we have identified a remarkable series of heterozygous germline variants in the gene encoding thymidylate synthase (TYMS). Although the inheritance appeared to be autosomal recessive, one parent in each family had a wild-type TYMS coding sequence. Targeted genomic sequencing identified a specific haplotype and rare variants in the naturally occurring TYMS antisense regulator ENOSF1 (enolase super family 1) inherited from the other parent. Lymphoblastoid cells from affected probands have severe TYMS deficiency, altered cellular deoxyribonucleotide triphosphate pools, and hypersensitivity to the TYMS-specific inhibitor 5-fluorouracil. These defects in the nucleotide metabolism pathway resulted in genotoxic stress, defective transcription, and abnormal telomere maintenance. Gene-rescue studies in cells from affected probands revealed that post-transcriptional epistatic silencing of TYMS is occurring via elevated ENOSF1. These cell and molecular abnormalities generated by the combination of germline digenic variants at the TYMS-ENOSF1 locus represent a unique pathogenetic pathway for DC causation in these affected individuals, whereas the parents who are carriers of either of these variants in a singular fashion remain unaffected.
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Affiliation(s)
- Hemanth Tummala
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK.
| | - Amanda Walne
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Roberto Buccafusca
- School of Physical and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, UK
| | - Jenna Alnajar
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Anita Szabo
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, 11-43 Bath St, London EC1V 9EL, UK
| | - Peter Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | | | - Meredith Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Suzanne Crowley
- Department of Paediatrics, St George's Healthcare NHS Trust, London, UK
| | - Veronica Kinsler
- Department of Paediatric Dermatology, Great Ormond Street Hospital, The Francis Crick Institute, London, UK
| | - Anna-Maria Ewins
- Haematology/Oncology Department, Royal Hospital for Sick Children, Glasgow, UK
| | - Pradeepa M Madapura
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Manthan Patel
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Nikolas Pontikos
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, 11-43 Bath St, London EC1V 9EL, UK
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Tom Vulliamy
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Inderjeet Dokal
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK; Barts Health NHS Trust, London, UK
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