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Bi-allelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a neurodevelopmental disorder

Stephanie Efthymiou, Cailyn P Leo, Chenghong Deng, Sheng-Jia Lin, Reza Maroofian, Renee Lin, Irem Karagoz, Kejia Zhang, Rauan Kaiyrzhanov, Annarita Scardamaglia, Daniel Owrang, Valentina Turchetti, Friederike Jahnke, Kevin Huang, Cassidy Petree, Anna Powell Orcid Logo, Mark Rees, Javeria Raza Alvi, Tipu Sultan, Chumei Li, Marie-Line Jacquemont, Frederic Tran-Mau-Them, Maria Valenzuela-Palafoll, Rich Sidlow, Grace Yoon, Michelle M Morrow, Deanna Alexis Carere, Mary O'Connor, Julie Fleischer, Erica H Gerkes, Chanika Phornphutkul, Bertrand Isidor, Clotilde Rivier-Ringenbach, Christophe Philippe, Semra Hiz Kurul, Didem Soydemir, Bulent Kara, Deniz Sunnetci-Akkoyunlu, Viktoria Bothe, Konrad Platzer, Dagmar Wieczorek, Margarete Koch-Hogrebe, Nils Rahner, Ann-Charlotte Thuresson, Hans Matsson, Carina Frykholm, Sevcan Tuğ Bozdoğan, Atil Bisgin, Nicolas Chatron, Gaetan Lesca, Sara Cabet, Zeynep Tümer, Tina D Hjortshøj, Gitte Rønde, Thorsten Marquardt, Janine Reunert, Erum Afzal, Mina Zamani, Reza Azizimalamiri, Hamid Galehdari, Pardis Nourbakhsh, Niloofar Chamanrou, Seo-Kyung Chung Orcid Logo, Mohnish Suri, Paul J Benke, Maha S Zaki, Joseph G Gleeson, Daniel G Calame, Davut Pehlivan, Halil I Yilmaz, Alper Gezdirici, Aboulfazl Rad, Iman Sabri Abumansour, Gabriela Oprea, Muhammed Burak Bereketoğlu, Guillaume Banneau, Sophie Julia, Jawaher Zeighami, Saeed Ashoori, Gholamreza Shariati, Alireza Sedaghat, Alihossein Sabri, Mohammad Hamid, Sahere Parvas, Tajul Arifin Tajudin, Uzma Abdullah, Shahid Mahmood Baig, Wendy K Chung, Olga O Glazunova, Sigaudy Sabine, Huma Arshad Cheema, Giovanni Zifarelli, Peter Bauer, Jai Sidpra, Kshitij Mankad, Barbara Vona, Andrew E Fry, Gaurav K Varshney, Henry Houlden, Dragony Fu

American Journal of Human Genetics, Volume: 112, Issue: 5, Pages: 1117 - 1138

Swansea University Authors: Anna Powell Orcid Logo, Mark Rees, Seo-Kyung Chung Orcid Logo

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DOI (Published version): 10.1016/j.ajhg.2025.03.015

Abstract

The post-transcriptional modification of tRNAs plays a crucial role in tRNA structure and function. Pathogenic variants in tRNA-modification enzymes have been implicated in a wide range of human neurodevelopmental and neurological disorders. However, the molecular basis for many of these disorders r...

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Published in: American Journal of Human Genetics
ISSN: 0002-9297 1537-6605
Published: Elsevier Inc 2025
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa69406
Abstract: The post-transcriptional modification of tRNAs plays a crucial role in tRNA structure and function. Pathogenic variants in tRNA-modification enzymes have been implicated in a wide range of human neurodevelopmental and neurological disorders. However, the molecular basis for many of these disorders remains unknown. Here, we describe a comprehensive cohort of 43 individuals from 31 unrelated families with bi-allelic variants in tRNA methyltransferase 1 (TRMT1). These individuals present with a neurodevelopmental disorder universally characterized by developmental delay and intellectual disability, accompanied by variable behavioral abnormalities, epilepsy, and facial dysmorphism. The identified variants include ultra-rare TRMT1 variants, comprising missense and predicted loss-of-function variants, which segregate with the observed clinical pathology. Our findings reveal that several variants lead to mis-splicing and a consequent loss of TRMT1 protein accumulation. Moreover, cells derived from individuals harboring TRMT1 variants exhibit a deficiency in tRNA modifications catalyzed by TRMT1. Molecular analysis reveals distinct regions of TRMT1 required for tRNA-modification activity and binding. Notably, depletion of Trmt1 protein in zebrafish is sufficient to induce developmental and behavioral phenotypes along with gene-expression changes associated with disrupted cell cycle, immune response, and neurodegenerative disorders. Altogether, these findings demonstrate that loss of TRMT1-catalyzed tRNA modifications leads to intellectual disability and provides insight into the molecular underpinnings of tRNA-modification deficiency caused by pathogenic TRMT1 variants.
Keywords: intellectual disability; neurodevelopmental disorder; zebrafish; disease model; tRNA modification; TRMT1
College: Faculty of Medicine, Health and Life Sciences
Funders: The research in this paper was supported by NIH GM141038 to D.F. Studies performed in the lab of G.K.V. was funded by NIH/ORIP R24OD034438. The clinic-genetic research was funded in part by the Wellcome Trust (WT093205MA and WT104033AIA). This study was funded by the Medical Research Council (MR/S01165X/1, MR/S005021/1, and G0601943), The National Institute for Health Research University College London Hospitals Biomedical Research Centre, Rosetrees Trust, Ataxia UK, Multiple System Atrophy Trust, Brain Research United Kingdom, Sparks Great Ormond Street Hospital Charity, Muscular Dystrophy United Kingdom (MDUK), Muscular Dystrophy Association (MDA USA), and the King Baudouin Foundation. S.E. and H.H. were supported by an MRC strategic award to establish an International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD) MR/S005021/1. B.V. was supported by the Deutsche Forschungsgemeinschaft (DFG) DFG VO 2138/7-1 grant 469177153. J.S. is supported by Cancer Research UK and University College London. A.F. and S.C. were supported by Health & Care Research Wales, Epilepsy Research UK, and Swansea University PhD funding.
Issue: 5
Start Page: 1117
End Page: 1138

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