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Lin X, Wang W, Yang M, Damseh N, de Sousa MML, Jacob F, Lång A, Kristiansen E, Pannone M, Kissova M, Almaas R, Kuśnierczyk A, Siller R, Shahrour M, Al-Ashhab M, Abu-Libdeh B, Tang W, Slupphaug G, Elpeleg O, Bøe SO, Eide L, Sullivan GJ, Rinholm JE, Song H, Ming GL, van Loon B, Edvardson S, Ye J, Bjørås M. A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial-temporal regulation of histone arginine methylation in neurodevelopment. Genome Biol 2023; 24:216. [PMID: 37773136 PMCID: PMC10540402 DOI: 10.1186/s13059-023-03037-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/04/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Oxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pathways, cell cycle, neuronal protection, and arginine methylation. In 2019, five patients from three families carrying four biallelic loss-of-function variants in OXR1 were reported to be associated with cerebellar atrophy. However, the impact of OXR1 on cellular functions and molecular mechanisms in the human brain is largely unknown. Notably, no human disease models are available to explore the pathological impact of OXR1 deficiency. RESULTS We report a novel loss-of-function mutation in the TLDc domain of the human OXR1 gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generate patient-derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identify that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1-dependent mechanisms regulating gene expression during neurodevelopment. We model the function of OXR1 in early human brain development using patient-derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions. CONCLUSIONS This study provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency in patients.
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Affiliation(s)
- Xiaolin Lin
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, 0373, Oslo, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Mingyi Yang
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, 0373, Oslo, Norway
- Norwegian Centre for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Nadirah Damseh
- Department of Pediatrics, Makassed Hospital and Al-Quds University, East Jerusalem, Palestine
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Fadi Jacob
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anna Lång
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Elise Kristiansen
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, 0373, Oslo, Norway
| | - Marco Pannone
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Miroslava Kissova
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Runar Almaas
- Department of Pediatric Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Anna Kuśnierczyk
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- The Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Richard Siller
- Norwegian Centre for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Maher Shahrour
- Department of Pediatrics, Makassed Hospital and Al-Quds University, East Jerusalem, Palestine
- Department of Newborn and Developmental Paediatrics, Toronto, ON, Canada
| | - Motee Al-Ashhab
- Department of Pediatrics, Makassed Hospital and Al-Quds University, East Jerusalem, Palestine
| | - Bassam Abu-Libdeh
- Department of Pediatrics, Makassed Hospital and Al-Quds University, East Jerusalem, Palestine
| | - Wannan Tang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Geir Slupphaug
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- The Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Orly Elpeleg
- Department of Genetics, Hadassah University Hospital, Jerusalem, Israel
| | - Stig Ove Bøe
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Lars Eide
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gareth J Sullivan
- Norwegian Centre for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Johanne Egge Rinholm
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- The Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Barbara van Loon
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Simon Edvardson
- Department of Genetics, Hadassah University Hospital, Jerusalem, Israel.
| | - Jing Ye
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway.
- Department of Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway.
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
- Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, 0373, Oslo, Norway.
- Norwegian Centre for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway.
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Pawar T, Bjørås M, Klungland A, Eide L. Metabolism and DNA repair shape a specific modification pattern in mitochondrial DNA. Mitochondrion 2017; 40:16-28. [PMID: 28893634 DOI: 10.1016/j.mito.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial DNA (mtDNA) resides in the vicinity of energy-rich reactions. Thus, chemical modifications of mtDNA might mirror mitochondrial processes and could serve as biomarkers of metabolic processes in the mitochondria. This hypothesis was tested by assessing modifications at 17 different sites in the mtDNA as a function of cell type, oxidative stress and mitochondrial activity. Two mouse mutants with a metabolic phenotype were compared to wild-type (WT) mice: the ogg1-/- mouse that lacks the 8-oxoguanine DNA glycosylase (OGG1), and the alkbh7-/- mouse missing the ALKBH7 protein that has been implicated in fatty acid oxidation. It was found that cell type, oxidative stress and mitochondrial complex activity shaped distinct modification patterns in mtDNA, and that OGG1 and ALKBH7 independently modulated these modification patterns. The modifications included ribonucleotides, which also accumulated in mtDNA with age. Interestingly, this age-dependent accumulation most likely involves DNA repair, as mtDNA from ogg1-/- mice did not accumulate modifications with age. On the other hand, alkbh7-/- mtDNA accumulated more modifications with age than WT mtDNA. Our results show that mtDNA is dynamically modified with metabolic activity and imply a novel synergy between metabolism and mtDNA repair proteins.
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Affiliation(s)
- Tina Pawar
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway; Department of clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
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