1
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Beard DC, Zhang X, Wu DY, Martin JR, Erickson A, Boua JV, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Palmer CW, Fuhler NA, Lawrence AB, Hill CA, Papouin T, Noguchi KK, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. Cell Rep 2023; 42:113411. [PMID: 37952155 PMCID: PMC10843706 DOI: 10.1016/j.celrep.2023.113411] [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: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNA methyltransferase 3A (DNMT3A), a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a Dnmt3aP900L/+ mouse mimicking a mutation with mild to moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes that may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.
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Affiliation(s)
- Diana C Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jane Valeriane Boua
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA; Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cory W Palmer
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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2
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Townley BA, Buerer L, Tsao N, Bacolla A, Mansoori F, Rusanov T, Clark N, Goodarzi N, Schmidt N, Srivatsan SN, Sun H, Sample RA, Brickner JR, McDonald D, Tsai MS, Walter MJ, Wozniak DF, Holehouse AS, Pena V, Tainer JA, Fairbrother WG, Mosammaparast N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 2023; 83:2258-2275.e11. [PMID: 37369199 PMCID: PMC10483886 DOI: 10.1016/j.molcel.2023.06.011] [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: 06/20/2022] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.
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Affiliation(s)
- Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ning Tsao
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Fadhel Mansoori
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timur Rusanov
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathanial Clark
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Negar Goodarzi
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - Nicolas Schmidt
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Hua Sun
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Reilly A Sample
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew McDonald
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David F Wozniak
- Department of Psychiatry, Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alex S Holehouse
- Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Vladimir Pena
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI 02912, USA.
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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Beard DC, Zhang X, Wu DY, Martin JR, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Lawrence AB, Hill CA, Papouin T, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530041. [PMID: 36909558 PMCID: PMC10002657 DOI: 10.1101/2023.02.27.530041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
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Affiliation(s)
- Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y. Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R. Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G. Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B. McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B. Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A. Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R. Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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4
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Minakova E, Mikati MO, Madasu MK, Conway SM, Baldwin JW, Swift RG, McCullough KB, Dougherty JD, Maloney SE, Al-Hasani R. Perinatal oxycodone exposure causes long-term sex-dependent changes in weight trajectory and sensory processing in adult mice. Psychopharmacology (Berl) 2022; 239:3859-3873. [PMID: 36269379 DOI: 10.1007/s00213-022-06257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]
Abstract
RATIONALE In utero opioid exposure is associated with lower weight and a neonatal opioid withdrawal syndrome (NOWS) at birth, along with longer-term adverse neurodevelopmental outcomes and mood disorders. While NOWS is sometimes treated with continued opioids, clinical studies have not addressed if long-term neurobehavioral outcomes are worsened with continued postnatal exposure to opioids. In addition, pre-clinical studies comparing in utero only opioid exposure to continued post-natal opioid administration for withdrawal mitigation are lacking. OBJECTIVES Here, we sought to understand the impact of continued postnatal opioid exposure on long term behavioral consequences. METHODS We implemented a rodent perinatal opioid exposure model of oxycodone (Oxy) exposure that included Oxy exposure until birth (short Oxy) and continued postnatal opioid exposure (long Oxy) spanning gestation through birth and lactation. RESULTS Short Oxy exposure was associated with a sex-specific increase in weight gain trajectory in adult male mice. Long Oxy exposure caused an increased weight gain trajectory in adult males and alterations in nociceptive processing in females. Importantly, there was no evidence of long-term social behavioral deficits, anxiety, hyperactivity, or memory deficits following short or long Oxy exposure. CONCLUSIONS Our findings suggest that offspring with prolonged opioid exposure experienced some long-term sequelae compared to pups with opioid cessation at birth. These results highlight the potential long-term consequences of opioid administration as a mitigation strategy for clinical NOWS symptomology and suggest alternatives should be explored.
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Affiliation(s)
- Elena Minakova
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwa O Mikati
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8232, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.,Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.,Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA.,Washington University Pain Management Center, Washington University School of Medicine, St. Louis, MO, USA.,Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis, St. Louis, MO, USA
| | - Manish K Madasu
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA.,Washington University Pain Management Center, Washington University School of Medicine, St. Louis, MO, USA.,Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis, St. Louis, MO, USA
| | - Sineadh M Conway
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA.,Washington University Pain Management Center, Washington University School of Medicine, St. Louis, MO, USA.,Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis, St. Louis, MO, USA
| | - Justin W Baldwin
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.,Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Raylynn G Swift
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8232, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katherine B McCullough
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8232, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8232, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8232, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA. .,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Ream Al-Hasani
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA. .,Washington University Pain Management Center, Washington University School of Medicine, St. Louis, MO, USA. .,Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis, St. Louis, MO, USA.
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5
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Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process. Cell Rep 2022; 41:111474. [PMID: 36261025 PMCID: PMC9624251 DOI: 10.1016/j.celrep.2022.111474] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 06/16/2022] [Accepted: 09/19/2022] [Indexed: 01/07/2023] Open
Abstract
Within eukaryotic cells, translation is regulated independent of transcription, enabling nuanced, localized, and rapid responses to stimuli. Neurons respond transcriptionally and translationally to synaptic activity. Although transcriptional responses are documented in astrocytes, here we test whether astrocytes have programmed translational responses. We show that seizure activity rapidly changes the transcripts on astrocyte ribosomes, some predicted to be downstream of BDNF signaling. In acute slices, we quantify the extent to which cues of neuronal activity activate translation in astrocytes and show that this translational response requires the presence of neurons, indicating that the response is non-cell autonomous. We also show that this induction of new translation extends into the periphery of astrocytes. Finally, synaptic proteomics show that new translation is required for changes that occur in perisynaptic astrocyte protein composition after fear conditioning. Regulation of translation in astrocytes by neuronal activity suggests an additional mechanism by which astrocytes may dynamically modulate nervous system functioning.
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6
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Chen J, Lambo ME, Ge X, Dearborn JT, Liu Y, McCullough KB, Swift RG, Tabachnick DR, Tian L, Noguchi K, Garbow JR, Constantino JN, Gabel HW, Hengen KB, Maloney SE, Dougherty JD. A MYT1L syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation. Neuron 2021; 109:3775-3792.e14. [PMID: 34614421 PMCID: PMC8668036 DOI: 10.1016/j.neuron.2021.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/07/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023]
Abstract
Human genetics have defined a new neurodevelopmental syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes intellectual disability, autism, ADHD, obesity, and brain anomalies is unknown. Here, we developed a Myt1l haploinsufficient mouse model that develops obesity, white-matter thinning, and microcephaly, mimicking common clinical phenotypes. During brain development we discovered disrupted gene expression, mediated in part by loss of Myt1l gene-target activation, and identified precocious neuronal differentiation as the mechanism for microcephaly. In contrast, in adults we discovered that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. Myt1l haploinsufficiency also results in behavioral anomalies, including hyperactivity, muscle weakness, and social alterations, with more severe phenotypes in males. Overall, our findings provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.
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Affiliation(s)
- Jiayang Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary E Lambo
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO USA
| | - Joshua T Dearborn
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Katherine B McCullough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Raylynn G Swift
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Dora R Tabachnick
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucy Tian
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA; Alvin J Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO USA
| | - John N Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Keith B Hengen
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
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7
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Smith AM, LaValle TA, Shinawi M, Ramakrishnan SM, Abel HJ, Hill CA, Kirkland NM, Rettig MP, Helton NM, Heath SE, Ferraro F, Chen DY, Adak S, Semenkovich CF, Christian DL, Martin JR, Gabel HW, Miller CA, Ley TJ. Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome. Nat Commun 2021; 12:4549. [PMID: 34315901 PMCID: PMC8316576 DOI: 10.1038/s41467-021-24800-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
Germline pathogenic variants in DNMT3A were recently described in patients with overgrowth, obesity, behavioral, and learning difficulties (DNMT3A Overgrowth Syndrome/DOS). Somatic mutations in the DNMT3A gene are also the most common cause of clonal hematopoiesis, and can initiate acute myeloid leukemia (AML). Using whole genome bisulfite sequencing, we studied DNA methylation in peripheral blood cells of 11 DOS patients and found a focal, canonical hypomethylation phenotype, which is most severe with the dominant negative DNMT3AR882H mutation. A germline mouse model expressing the homologous Dnmt3aR878H mutation phenocopies most aspects of the human DOS syndrome, including the methylation phenotype and an increased incidence of spontaneous hematopoietic malignancies, suggesting that all aspects of this syndrome are caused by this mutation.
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Affiliation(s)
- Amanda M Smith
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Taylor A LaValle
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sai M Ramakrishnan
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Haley J Abel
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Michael P Rettig
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nichole M Helton
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon E Heath
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Ferraro
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy J Ley
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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8
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Nygaard KR, Swift RG, Glick RM, Wagner RE, Maloney SE, Gould GG, Dougherty JD. Oxytocin receptor activation does not mediate associative fear deficits in a Williams Syndrome model. GENES, BRAIN, AND BEHAVIOR 2021; 21:e12750. [PMID: 33978321 PMCID: PMC8842878 DOI: 10.1111/gbb.12750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022]
Abstract
Williams Syndrome results in distinct behavioral phenotypes, which include learning deficits, anxiety, increased phobias and hypersociability. While the underlying mechanisms driving this subset of phenotypes is unknown, oxytocin (OT) dysregulation is hypothesized to be involved as some studies have shown elevated blood OT and altered OT receptor expression in patients. A "Complete Deletion" (CD) mouse, modeling the hemizygous deletion in Williams Syndrome, recapitulates many of the phenotypes present in humans. These CD mice also exhibit impaired fear responses in the conditioned fear task. Here, we address whether OT dysregulation is responsible for this impaired associative fear memory response. We show direct delivery of an OT receptor antagonist to the central nervous system did not rescue the attenuated contextual or cued fear memory responses in CD mice. Thus, increased OT signaling is not acutely responsible for this phenotype. We also evaluated OT receptor and serotonin transporter availability in regions related to fear learning, memory and sociability using autoradiography in wild type and CD mice. While no differences withstood correction, we identified regions that may warrant further investigation. There was a nonsignificant decrease in OT receptor expression in the lateral septal nucleus and nonsignificant lowered serotonin transporter availability in the striatum and orbitofrontal cortex. Together, these data suggest the fear conditioning anomalies in the Williams Syndrome mouse model are independent of any alterations in the oxytocinergic system caused by deletion of the Williams locus.
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Affiliation(s)
- Kayla R. Nygaard
- Department of GeneticsWashington University in St. LouisSt. LouisMissouriUSA,Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA
| | - Raylynn G. Swift
- Department of GeneticsWashington University in St. LouisSt. LouisMissouriUSA,Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA
| | - Rebecca M. Glick
- Department of GeneticsWashington University in St. LouisSt. LouisMissouriUSA,Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA
| | - Rachael E. Wagner
- Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA
| | - Susan E. Maloney
- Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA,Intellectual and Developmental Disabilities Research CenterWashington University in St. LouisSt. LouisMissouriUSA
| | - Georgianna G. Gould
- Department of Cellular and Integrative PhysiologyUniversity of Texas Health San AntonioSan AntonioTexasUSA
| | - Joseph D. Dougherty
- Department of GeneticsWashington University in St. LouisSt. LouisMissouriUSA,Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA,Intellectual and Developmental Disabilities Research CenterWashington University in St. LouisSt. LouisMissouriUSA
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9
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 DOI: 10.1101/401604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/24/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3' UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3-5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3' UTR in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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10
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 PMCID: PMC7780154 DOI: 10.1016/j.celrep.2020.108531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3′ UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3–5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3′ UTR in vivo. Rieger et al. assay the function of the RNA-binding protein CELF6 by defining its targets in the brain. They show that CELF6 largely binds 3′ UTRs of synaptic mRNAs. Using a massively parallel reporter assay, they further show that CELF6 and other CELFs are associated with lower mRNA abundance and that targets are derepressed in Celf6-knockout mice in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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11
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Christian DL, Wu DY, Martin JR, Moore JR, Liu YR, Clemens AW, Nettles SA, Kirkland NM, Papouin T, Hill CA, Wozniak DF, Dougherty JD, Gabel HW. DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders. Cell Rep 2020; 33:108416. [PMID: 33238114 PMCID: PMC7716597 DOI: 10.1016/j.celrep.2020.108416] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/17/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) have been detected in autism and related disorders, but how these mutations disrupt nervous system function is unknown. Here, we define the effects of DNMT3A mutations associated with neurodevelopmental disease. We show that diverse mutations affect different aspects of protein activity but lead to shared deficiencies in neuronal DNA methylation. Heterozygous DNMT3A knockout mice mimicking DNMT3A disruption in disease display growth and behavioral alterations consistent with human phenotypes. Strikingly, in these mice, we detect global disruption of neuron-enriched non-CG DNA methylation, a binding site for the Rett syndrome protein MeCP2. Loss of this methylation leads to enhancer and gene dysregulation that overlaps with models of Rett syndrome and autism. These findings define the effects of DNMT3A haploinsufficiency in the brain and uncover disruption of the non-CG methylation pathway as a convergence point across neurodevelopmental disorders.
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Affiliation(s)
- Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - J Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Yiran R Liu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - David F Wozniak
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.
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12
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Yang X, Zhao L, Pei J, Wang Z, Zhang J, Wang B. CELF6 modulates triple-negative breast cancer progression by regulating the stability of FBP1 mRNA. Breast Cancer Res Treat 2020; 183:71-82. [PMID: 32601971 DOI: 10.1007/s10549-020-05753-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) remains a great challenge in clinical treatment due to a shortage of effective therapeutic targets and acquired chemoresistance. Here, we identified the role of an RNA-binding protein, CUG-BP Elav-like family member 6 (CELF6), in the TNBC development and paclitaxel (PTX) chemoresistance. METHODS Stable CELF6-overexpressing cell lines were established in BT549 and MDA-MB-231 cells. Cell proliferation was determined using cell counting, two-dimensional colony formation, and MTT assay. Meanwhile, cell migration and cell invasion were detected by Transwell assay. Furthermore, the downstream target gene of CELF6 was identified and the direct interaction was further determined by luciferase reporter assay, immunoprecipitation, and RNA pull-down. Additionally, the PTX resistant cell line was established to determine the role of CELF6 in PTX resistance. RESULTS CELF6 overexpression suppressed cell proliferation, cell migration, and cell invasion. Mechanistically, Fructose-Bisphosphatase 1 (FBP1) was identified as the target gene of CELF6 and stabilized by CELF6 via binding 3'UTR. CELF6 overexpression mediated inhibition in TNBC development was dependent on FBP1. Moreover, CELF6 overexpression increased the sensitivity to PTX treatment. CONCLUSION CELF6 functions as a tumor suppressor by upregulating FBP 1 expression via stabilizing its mRNA, and thereby inhibits TNBC progression.
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Affiliation(s)
- Xiaowei Yang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China.
| | - Lu Zhao
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Jing Pei
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Zhaorui Wang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Jingjie Zhang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Benzhong Wang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
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