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Hayward B, Kumari D, Santra S, van Karnebeek CDM, van Kuilenburg ABP, Usdin K. All three MutL complexes are required for repeat expansion in a human stem cell model of CAG-repeat expansion mediated glutaminase deficiency. Sci Rep 2024; 14:13772. [PMID: 38877099 PMCID: PMC11178883 DOI: 10.1038/s41598-024-64480-z] [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: 01/09/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
The Repeat Expansion Diseases (REDs) arise from the expansion of a disease-specific short tandem repeat (STR). Different REDs differ with respect to the repeat involved, the cells that are most expansion prone and the extent of expansion. Furthermore, whether these diseases share a common expansion mechanism is unclear. To date, expansion has only been studied in a limited number of REDs. Here we report the first studies of the expansion mechanism in induced pluripotent stem cells derived from a patient with a form of the glutaminase deficiency disorder known as Global Developmental Delay, Progressive Ataxia, And Elevated Glutamine (GDPAG; OMIM# 618412) caused by the expansion of a CAG-STR in the 5' UTR of the glutaminase (GLS) gene. We show that alleles with as few as ~ 120 repeats show detectable expansions in culture despite relatively low levels of R-loops formed at this locus. Additionally, using a CRISPR-Cas9 knockout approach we show that PMS2 and MLH3, the constituents of MutLα and MutLγ, the 2 mammalian MutL complexes known to be involved in mismatch repair (MMR), are essential for expansion. Furthermore, PMS1, a component of a less well understood MutL complex, MutLβ, is also important, if not essential, for repeat expansion in these cells. Our results provide insights into the factors important for expansion and lend weight to the idea that, despite some differences, the same mechanism is responsible for expansion in many, if not all, REDs.
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Affiliation(s)
- Bruce Hayward
- Section On Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daman Kumari
- Section On Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Saikat Santra
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B15 2TG, UK
| | - Clara D M van Karnebeek
- Emma Center for Personalized Medicine, Departments of Pediatrics and Human Genetics, Amsterdam Gastro-Enterology Endocrinology and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- United for Metabolic Diseases, Amsterdam, The Netherlands
| | - André B P van Kuilenburg
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Karen Usdin
- Section On Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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Hwang YH, Hayward BE, Zafarullah M, Kumar J, Durbin Johnson B, Holmans P, Usdin K, Tassone F. Both cis and trans-acting genetic factors drive somatic instability in female carriers of the FMR1 premutation. Sci Rep 2022; 12:10419. [PMID: 35729184 PMCID: PMC9213438 DOI: 10.1038/s41598-022-14183-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
The fragile X mental retardation (FMR1) gene contains an expansion-prone CGG repeat within its 5' UTR. Alleles with 55-200 repeats are known as premutation (PM) alleles and confer risk for one or more of the FMR1 premutation (PM) disorders that include Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-Associated Neuropsychiatric Disorders (FXAND). PM alleles expand on intergenerational transmission, with the children of PM mothers being at risk of inheriting alleles with > 200 CGG repeats (full mutation FM) alleles) and thus developing Fragile X Syndrome (FXS). PM alleles can be somatically unstable. This can lead to individuals being mosaic for multiple size alleles. Here, we describe a detailed evaluation of somatic mosaicism in a large cohort of female PM carriers and show that 94% display some evidence of somatic instability with the presence of a series of expanded alleles that differ from the next allele by a single repeat unit. Using two different metrics for instability that we have developed, we show that, as with intergenerational instability, there is a direct relationship between the extent of somatic expansion and the number of CGG repeats in the originally inherited allele and an inverse relationship with the number of AGG interruptions. Expansions are progressive as evidenced by a positive correlation with age and by examination of blood samples from the same individual taken at different time points. Our data also suggests the existence of other genetic or environmental factors that affect the extent of somatic expansion. Importantly, the analysis of candidate single nucleotide polymorphisms (SNPs) suggests that two DNA repair factors, FAN1 and MSH3, may be modifiers of somatic expansion risk in the PM population as observed in other repeat expansion disorders.
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Affiliation(s)
- Ye Hyun Hwang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Bruce Eliot Hayward
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Jay Kumar
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Blythe Durbin Johnson
- Department of Public Health Sciences, University of California, Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Karen Usdin
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA. .,MIND Institute, University of California Davis Medical Center, Sacramento, CA, 95817, USA.
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Dolskiy AA, Yarushkin AA, Grishchenko IV, Lemskaya NA, Pindyurin AV, Boldyreva LV, Pustylnyak VO, Yudkin DV. miRNA expression and interaction with the 3'UTR of FMR1 in FRAXopathy pathogenesis. Noncoding RNA Res 2021; 6:1-7. [PMID: 33426406 PMCID: PMC7781359 DOI: 10.1016/j.ncrna.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/19/2020] [Accepted: 11/28/2020] [Indexed: 12/20/2022] Open
Abstract
FRAXopathies are caused by the expansion of the CGG repeat in the 5'UTR of the FMR1 gene, which encodes the protein responsible for the synthesis of FMRP. This mutation leads to dramatic changes in FMRP expression at both the mRNA and protein levels. Evidence is emerging that changes in FMR1 mRNA expression can lead to the dysregulation of the miRNAs that target its 3'UTR. In the present work, B-lymphocyte cell lines obtained from patients with FRAXopathies were used, and a wide variety of FMR1 gene activities were observed, allowing the identification of the relationships between FMR1 dysregulation and miRNA activity. We studied the expression levels of eight miRNAs that target the FMR1 gene. To prove the interaction of the studied miRNAs with FMR1, a plasmid was constructed that possesses three primary structures: the miRNA gene, with expression driven by an inducible promoter; a constitutively expressed FusionRed reporter; and an eGFP reporter followed by the 3'UTR of the FMR1 gene. We evaluated changes in miRNA expression in response to alterations in FMR1 gene activity in a model cell line as well as interactions with some miRNAs with the FMR1 3'UTR.
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Affiliation(s)
- Alexander A. Dolskiy
- State Research Center of Virology and Biotechnology “Vector”, Federal
Service for Surveillance on Consumer Rights Protection and Human Well-being
(FBRI SRC VB “Vector”, Rospotrebnadzor), Koltsovo, Novosibirsk Region,
Russia
| | - Andrey A. Yarushkin
- Federal Research Center of Fundamental and Translational Medicine,
Novosibirsk, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Novosibirsk Region,
Russia
| | - Irina V. Grishchenko
- State Research Center of Virology and Biotechnology “Vector”, Federal
Service for Surveillance on Consumer Rights Protection and Human Well-being
(FBRI SRC VB “Vector”, Rospotrebnadzor), Koltsovo, Novosibirsk Region,
Russia
| | - Natalya A. Lemskaya
- State Research Center of Virology and Biotechnology “Vector”, Federal
Service for Surveillance on Consumer Rights Protection and Human Well-being
(FBRI SRC VB “Vector”, Rospotrebnadzor), Koltsovo, Novosibirsk Region,
Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the
Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, Russia
| | - Alexey V. Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the
Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the
Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, Russia
| | - Vladimir O. Pustylnyak
- Federal Research Center of Fundamental and Translational Medicine,
Novosibirsk, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Novosibirsk Region,
Russia
| | - Dmitry V. Yudkin
- State Research Center of Virology and Biotechnology “Vector”, Federal
Service for Surveillance on Consumer Rights Protection and Human Well-being
(FBRI SRC VB “Vector”, Rospotrebnadzor), Koltsovo, Novosibirsk Region,
Russia
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