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Piasecka A, Szcześniak MW, Sekrecki M, Kajdasz A, Sznajder ŁJ, Baud A, Sobczak K. MBNL splicing factors regulate the microtranscriptome of skeletal muscles. Nucleic Acids Res 2024:gkae774. [PMID: 39258536 DOI: 10.1093/nar/gkae774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 08/07/2024] [Accepted: 08/23/2024] [Indexed: 09/12/2024] Open
Abstract
Muscleblind like splicing regulators (MBNLs) govern various RNA-processing steps, including alternative splicing, polyadenylation, RNA stability and mRNA intracellular localization. In myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, MBNLs are sequestered on toxic RNA containing expanded CUG repeats, which leads to disruption of MBNL-regulated processes and disease features of DM1. Herein, we show the significance of MBNLs in regulating microtranscriptome dynamics during the postnatal development of skeletal muscles and in microRNA (miRNA) misregulation observed in mouse models and patients with DM1. We identify multiple miRNAs sensitive to MBNL proteins insufficiency and reveal that many of them were postnatally regulated, which correlates with increases in the activity of these proteins during this process. In adult Mbnl1-knockout mice, miRNA expression exhibited an adult-to-newborn shift. We hypothesize that Mbnl1 deficiency influences miRNA levels through a combination of mechanisms. First, the absence of Mbnl1 protein results in alterations to the levels of pri-miRNAs. Second, MBNLs affect miRNA biogenesis by regulating the alternative splicing of miRNA primary transcripts. We propose that the expression of miR-23b, miR-27b and miR-24-1, produced from the same cluster, depends on the MBNL-sensitive inclusion of alternative exons containing miRNA sequences. Our findings suggest that MBNL sequestration in DM1 is partially responsible for altered miRNA activity. This study provides new insights into the biological roles and functions of MBNL proteins as regulators of miRNA expression in skeletal muscles.
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Affiliation(s)
- Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Michał W Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Michał Sekrecki
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Arkadiusz Kajdasz
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704Poznań, Poland
| | - Łukasz J Sznajder
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Anna Baud
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
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2
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Bao N, Wang Z, Fu J, Dong H, Jin Y. RNA structure in alternative splicing regulation: from mechanism to therapy. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034824 DOI: 10.3724/abbs.2024119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.
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3
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Recinos Y, Bao S, Wang X, Phillips BL, Yeh YT, Weyn-Vanhentenryck SM, Swanson MS, Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain. CELL GENOMICS 2024; 4:100563. [PMID: 38772368 PMCID: PMC11228892 DOI: 10.1016/j.xgen.2024.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/22/2024] [Accepted: 04/23/2024] [Indexed: 05/23/2024]
Abstract
Divergence of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is widespread in mammals, including primates, but the underlying mechanisms and functional impact are poorly understood. Here, we modeled cassette exon inclusion in primate brains as a quantitative trait and identified 1,170 (∼3%) exons with lineage-specific splicing shifts under stabilizing selection. Among them, microtubule-associated protein tau (MAPT) exons 2 and 10 underwent anticorrelated, two-step evolutionary shifts in the catarrhine and hominoid lineages, leading to their present inclusion levels in humans. The developmental-stage-specific divergence of exon 10 splicing, whose dysregulation can cause frontotemporal lobar degeneration (FTLD), is mediated by divergent distal intronic MBNL-binding sites. Competitive binding of these sites by CRISPR-dCas13d/gRNAs effectively reduces exon 10 inclusion, potentially providing a therapeutically compatible approach to modulate tau isoform expression. Our data suggest adaptation of MAPT function and, more generally, a role for AS in the evolutionary expansion of the primate brain.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Brittany L Phillips
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, FL 32610, USA; Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Aya F, Valcárcel J. Shaping human brain development and vulnerability through alternative splicing. CELL GENOMICS 2024; 4:100584. [PMID: 38870907 PMCID: PMC11228946 DOI: 10.1016/j.xgen.2024.100584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Alternative splicing contributes to shaping lineage-specific gene expression and phenotypes. In this issue of Cell Genomics, Recinos, Bao, Wang, et al.1 report that the balance between splicing isoforms of the microtubule-associated protein Tau in the brain is differentially regulated among primates by the RNA-binding protein MBNL2, with consequences for protein aggregation and neurodegeneration in humans.
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Affiliation(s)
- Francisco Aya
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Medical Oncology, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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5
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Lin J, Liu C, Hu E. Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes. Front Immunol 2024; 15:1381765. [PMID: 38919616 PMCID: PMC11196417 DOI: 10.3389/fimmu.2024.1381765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Background Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood. Methods The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses. Results The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis. Conclusion In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.
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Affiliation(s)
- Junhan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Changyuan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Ende Hu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
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Kubota N, Chen L, Zheng S. Shiba: A unified computational method for robust identification of differential RNA splicing across platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596331. [PMID: 38895326 PMCID: PMC11185541 DOI: 10.1101/2024.05.30.596331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a robust method integrating transcript assembly, splicing event identification, read counting, and statistical analysis, to efficiently quantify exon splicing levels across various types of RNA-seq datasets. Compared to existing pipelines, Shiba excels in capturing both annotated and unannotated or cryptic differential splicing events with superior accuracy, sensitivity, and reproducibility. Furthermore, Shiba's unique consideration of junction read imbalance and exon-body read coverage reduces false positives, essential for downstream functional analyses. We have further developed scShiba for single-cell/nucleus (sc/sn) RNA-seq data, enabling the exploration of splicing variations in heterogeneous cell populations. Both simulated and real data demonstrate Shiba's robustness across multiple sample sizes, including n=1 datasets and individual cell clusters from scRNA-seq. Application of Shiba on single replicates of RNA-seq identified new AS-NMD targets, and scShiba on snRNA-seq revealed intricate temporal AS regulation in dopaminergic neurons. Both Shiba and scShiba are provided in Docker/Singularity containers and Snakemake pipeline, enhancing accessibility and reproducibility. The comprehensive capabilities of Shiba and scShiba allow systematic and robust quantification of alternative splicing events, laying a solid foundation for mechanistic exploration of functional complexity in RNA splicing.
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Affiliation(s)
- Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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Yoshizumi K, Nishi M, Igeta M, Nakamori M, Inoue K, Matsumura T, Fujimura H, Jinnai K, Kimura T. Analysis of splicing abnormalities in the white matter of myotonic dystrophy type 1 brain using RNA sequencing. Neurosci Res 2024; 200:48-56. [PMID: 37806497 DOI: 10.1016/j.neures.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by the genomic expansion of CTG repeats, in which RNA-binding proteins, such as muscleblind-like protein, are sequestered in the nucleus, and abnormal splicing is observed in various genes. Although abnormal splicing occurs in the brains of patients with DM1, its relation to central nervous system symptoms is unknown. Several imaging studies have indicated substantial white matter defects in patients with DM1. Here, we performed RNA sequencing and analysis of CTG repeat lengths in the frontal lobe of patients with DM1, separating the gray matter and white matter, to investigate splicing abnormalities in the DM1 brain, especially in the white matter. Several genes showed similar levels of splicing abnormalities in both gray and white matter, with an observable trend toward an increased number of repeats in the gray matter. These findings suggest that white matter defects in DM1 stem from aberrant RNA splicing in both gray and white matter. Notably, several of the genes displaying abnormal splicing are recognized as being dominantly expressed in astrocytes and oligodendrocytes, leading us to hypothesize that splicing defects in the white matter may be attributed to abnormal RNA splicing in glial cells.
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Affiliation(s)
- Kazuki Yoshizumi
- Department of Neurology, Hyogo Medical University, Nishinomiya, 663-8501 Hyogo, Japan
| | - Masamitsu Nishi
- Department of Neurology, Hyogo Medical University, Nishinomiya, 663-8501 Hyogo, Japan
| | - Masataka Igeta
- Department of Biostatistics, Hyogo Medical University, Nishinomiya, 663-8501 Hyogo, Japan
| | - Masayuki Nakamori
- Department of Neurology, Yamaguchi University Graduate School of Medicine, Yamaguchi, 755-8505 Yamaguchi, Japan
| | - Kimiko Inoue
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, 560-8552 Osaka, Japan
| | - Tsuyoshi Matsumura
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, 560-8552 Osaka, Japan
| | - Harutoshi Fujimura
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, 560-8552 Osaka, Japan
| | - Kenji Jinnai
- Department of Neurology, National Hospital Organization Hyogo-Chuo Hospital, Sanda, 669-1515 Hyogo, Japan
| | - Takashi Kimura
- Department of Neurology, Hyogo Medical University, Nishinomiya, 663-8501 Hyogo, Japan.
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Yadava RS, Mandal M, Mahadevan MS. Studying the Effect of MBNL1 and MBNL2 Loss in Skeletal Muscle Regeneration. Int J Mol Sci 2024; 25:2687. [PMID: 38473933 PMCID: PMC10931579 DOI: 10.3390/ijms25052687] [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: 02/05/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Loss of function of members of the muscleblind-like (MBNL) family of RNA binding proteins has been shown to play a key role in the spliceopathy of RNA toxicity in myotonic dystrophy type 1 (DM1), the most common muscular dystrophy affecting adults and children. MBNL1 and MBNL2 are the most abundantly expressed members in skeletal muscle. A key aspect of DM1 is poor muscle regeneration and repair, leading to dystrophy. We used a BaCl2-induced damage model of muscle injury to study regeneration and effects on skeletal muscle satellite cells (MuSCs) in Mbnl1∆E3/∆E3 and Mbnl2∆E2/∆E2 knockout mice. Similar experiments have previously shown deleterious effects on these parameters in mouse models of RNA toxicity. Muscle regeneration in Mbnl1 and Mbnl2 knockout mice progressed normally with no obvious deleterious effects on MuSC numbers or increased expression of markers of fibrosis. Skeletal muscles in Mbnl1∆E3/∆E3/ Mbnl2∆E2/+ mice showed increased histopathology but no deleterious reductions in MuSC numbers and only a slight increase in collagen deposition. These results suggest that factors beyond the loss of MBNL1/MBNL2 and the associated spliceopathy are likely to play a key role in the defects in skeletal muscle regeneration and deleterious effects on MuSCs that are seen in mouse models of RNA toxicity due to expanded CUG repeats.
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Affiliation(s)
| | | | - Mani S. Mahadevan
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA; (R.S.Y.)
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Nowzari ZR, Hale M, Ellis J, Biaesch S, Vangaveti S, Reddy K, Chen AA, Berglund JA. Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574689. [PMID: 38260517 PMCID: PMC10802415 DOI: 10.1101/2024.01.08.574689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) of Exon 11 of the Insulin Receptor ( INSR ) is highly regulated and disrupted in several human disorders. To better understand INSR exon 11 AS regulation, splicing activity of an INSR exon 11 minigene reporter was measured across a gradient of the AS regulator muscleblind-like 1 protein (MBNL1). The RNA-binding protein Fox-1 (RBFOX1) was added to determine its impact on MBNL1-regulated splicing. The role of the RBFOX1 UGCAUG binding site within intron 11 was assessed across the MBNL1 gradient. Mutating the UGCAUG motif inhibited RBFOX1 regulation of exon 11 and had the unexpected effect of reducing MBNL1 regulation of this exon. Molecular dynamics simulations showed that exon 11 and the adjacent RNA adopts a dynamically stable conformation. Mutation of the RBFOX1 binding site altered RNA structure and dynamics, while a mutation that created an optimal MBNL1 binding site at the RBFOX1 site shifted the RNA back to wild type. An antisense oligonucleotide (ASO) was used to confirm the structure in this region of the pre-mRNA. This example of intronic mutations shifting pre-mRNA structure and dynamics to modulate splicing suggests RNA structure and dynamics should be taken into consideration for AS regulation and therapeutic interventions targeting pre-mRNA.
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He L, Guo H, Wang H, Zhu K, Li D, Zhang C, Ai Y, Yang JJ. Rbfox1 regulates alternative splicing of Nrcam in primary sensory neurons to mediate peripheral nerve injury-induced neuropathic pain. Neurotherapeutics 2024; 21:e00309. [PMID: 38241164 PMCID: PMC10903086 DOI: 10.1016/j.neurot.2023.e00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The primary sensory neurons of the dorsal root ganglia (DRG) are subject to transcriptional alterations following peripheral nerve injury. These alterations are believed to play a pivotal role in the genesis of neuropathic pain. Alternative RNA splicing is a process that generates multiple transcript variants from a single gene, significantly contributing to the complexity of the transcriptome. However, little is known about the functional significance and control of alternative RNA splicing in injured DRG after spinal nerve ligation (SNL). In our study, we conducted a comprehensive transcriptome profiling and bioinformatic analysis to approach and identified a neuron-specific isoform of an RNA splicing regulator, RNA-binding Fox1 (Rbfox1, also known as A2BP1), as a crucial regulator of alternative RNA splicing in injured DRG after SNL. Notably, Rbfox1 expression is markedly reduced in injured DRG following peripheral nerve injury. Restoring this reduction effectively mitigates nociceptive hypersensitivity. Conversely, mimicking the downregulation of Rbfox1 expression generates neuropathic pain symptoms. Mechanistically, we uncovered that Rbfox1 may be a key factor influencing alternative RNA splicing of neuron-glial related cell adhesion molecule (NrCAM), a key neuronal cell adhesion molecule. In injured DRG after SNL, the downregulation of Rbfox1amplifies the insertion of exon 10 in Nrcam transcripts, leading to an increase in long Nrcam variants (L-Nrcam) and a corresponding decrease in short Nrcam variants (S-Nrcam) within injured DRG. In summary, our study supports the essential role of Rbfox1 in neuropathic pain within DRG, probably via the regulation of Nrcam splicing. These findings suggest that Rbfox1 could be a potential target for neuropathic pain therapy.
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Affiliation(s)
- Long He
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Haoyu Guo
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China; Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Hongwei Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Kuicheng Zhu
- Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Da Li
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Chaofan Zhang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Yanqiu Ai
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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González-Martínez I, Cerro-Herreros E, Moreno N, García-Rey A, Espinosa-Espinosa J, Carrascosa-Sàez M, Piqueras-Losilla D, Arzumanov A, Seoane-Miraz D, Jad Y, Raz R, Wood MJ, Varela MA, Llamusí B, Artero R. Peptide-conjugated antimiRs improve myotonic dystrophy type 1 phenotypes by promoting endogenous MBNL1 expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102024. [PMID: 37744174 PMCID: PMC10514136 DOI: 10.1016/j.omtn.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by a CTG repeat expansion in the DMPK gene that generates toxic RNA with a myriad of downstream alterations in RNA metabolism. A key consequence is the sequestration of alternative splicing regulatory proteins MBNL1/2 by expanded transcripts in the affected tissues. MBNL1/2 depletion interferes with a developmental alternative splicing switch that causes the expression of fetal isoforms in adults. Boosting the endogenous expression of MBNL proteins by inhibiting the natural translational repressors miR-23b and miR-218 has previously been shown to be a promising therapeutic approach. We designed antimiRs against both miRNAs with a phosphorodiamidate morpholino oligonucleotide (PMO) chemistry conjugated to cell-penetrating peptides (CPPs) to improve delivery to affected tissues. In DM1 cells, CPP-PMOs significantly increased MBNL1 levels. In some candidates, this was achieved using concentrations less than two orders of magnitude below the median toxic concentration, with up to 5.38-fold better therapeutic window than previous antagomiRs. In HSALR mice, intravenous injections of CPP-PMOs improve molecular, histopathological, and functional phenotypes, without signs of toxicity. Our findings place CPP-PMOs as promising antimiR candidates to overcome the treatment delivery challenge in DM1 therapy.
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Affiliation(s)
- Irene González-Martínez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Estefanía Cerro-Herreros
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Nerea Moreno
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Andrea García-Rey
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
- Group of Emerging and Neglected Diseases, Ecoepidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito 170521, Ecuador
| | - Marc Carrascosa-Sàez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Diego Piqueras-Losilla
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Andrey Arzumanov
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - David Seoane-Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Yahya Jad
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Richard Raz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Matthew J. Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Miguel A. Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Beatriz Llamusí
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
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13
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Kwon HC, Bae Y, Lee SJV. The Role of mRNA Quality Control in the Aging of Caenorhabditis elegans. Mol Cells 2023; 46:664-671. [PMID: 37968980 PMCID: PMC10654458 DOI: 10.14348/molcells.2023.0103] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 11/17/2023] Open
Abstract
The proper maintenance of mRNA quality that is regulated by diverse surveillance pathways is essential for cellular homeostasis and is highly conserved among eukaryotes. Here, we review findings regarding the role of mRNA quality control in the aging and longevity of Caenorhabditis elegans, an outstanding model for aging research. We discuss the recently discovered functions of the proper regulation of nonsense-mediated mRNA decay, ribosome-associated quality control, and mRNA splicing in the aging of C. elegans. We describe how mRNA quality control contributes to longevity conferred by various regimens, including inhibition of insulin/insulin-like growth factor 1 (IGF-1) signaling, dietary restriction, and reduced mechanistic target of rapamycin signaling. This review provides valuable information regarding the relationship between the mRNA quality control and aging in C. elegans, which may lead to insights into healthy longevity in complex organisms, including humans.
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Affiliation(s)
- Hyunwoo C. Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yunkyu Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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14
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Xiao C, M’Angale PG, Wang S, Lemieux A, Thomson T. Identifying new players in structural synaptic plasticity through dArc1 interrogation. iScience 2023; 26:108048. [PMID: 37876812 PMCID: PMC10590816 DOI: 10.1016/j.isci.2023.108048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/28/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The formation, expansion, and pruning of synapses, known as structural synaptic plasticity, is needed for learning and memory, and perturbation of plasticity is associated with many neurological disorders and diseases. Previously, we observed that the Drosophila homolog of Activity-regulated cytoskeleton-associated protein (dArc1), forms a capsid-like structure, associates with its own mRNA, and is transported across synapses. We demonstrated that this transfer is needed for structural synaptic plasticity. To identify mRNAs that are modified by dArc1 in presynaptic neuron and postsynaptic muscle, we disrupted the expression of dArc1 and performed genomic analysis with deep sequencing. We found that dArc1 affects the expression of genes involved in metabolism, phagocytosis, and RNA-splicing. Through immunoprecipitation we also identified potential mRNA cargos of dArc1 capsids. This study suggests that dArc1 acts as a master regulator of plasticity by affecting several distinct and highly conserved cellular processes.
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Affiliation(s)
- Cong Xiao
- Department of Neurobiology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - P. Githure M’Angale
- Department of Neurobiology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Shuhao Wang
- Department of Neurobiology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Adrienne Lemieux
- Department of Neurobiology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Travis Thomson
- Department of Neurobiology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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15
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Ikenoshita S, Matsuo K, Yabuki Y, Kawakubo K, Asamitsu S, Hori K, Usuki S, Hirose Y, Bando T, Araki K, Ueda M, Sugiyama H, Shioda N. A cyclic pyrrole-imidazole polyamide reduces pathogenic RNA in CAG/CTG triplet repeat neurological disease models. J Clin Invest 2023; 133:e164792. [PMID: 37707954 PMCID: PMC10645379 DOI: 10.1172/jci164792] [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: 08/24/2022] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Expansion of CAG and CTG (CWG) triplet repeats causes several inherited neurological diseases. The CWG repeat diseases are thought to involve complex pathogenic mechanisms through expanded CWG repeat-derived RNAs in a noncoding region and polypeptides in a coding region, respectively. However, an effective therapeutic approach has not been established for the CWG repeat diseases. Here, we show that a CWG repeat DNA-targeting compound, cyclic pyrrole-imidazole polyamide (CWG-cPIP), suppressed the pathogenesis of coding and noncoding CWG repeat diseases. CWG-cPIP bound to the hairpin form of mismatched CWG DNA, interfering with transcription elongation by RNA polymerase through a preferential activity toward repeat-expanded DNA. We found that CWG-cPIP selectively inhibited pathogenic mRNA transcripts from expanded CWG repeats, reducing CUG RNA foci and polyglutamine accumulation in cells from patients with myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Treatment with CWG-cPIP ameliorated behavioral deficits in adeno-associated virus-mediated CWG repeat-expressing mice and in a genetic mouse model of HD, without cytotoxicity or off-target effects. Together, we present a candidate compound that targets expanded CWG repeat DNA independently of its genomic location and reduces both pathogenic RNA and protein levels. CWG-cPIP may be used for the treatment of CWG repeat diseases and improvement of clinical outcomes.
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Affiliation(s)
- Susumu Ikenoshita
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Department of Neurology, Graduate School of Medical Sciences
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Kosuke Kawakubo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis and
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
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16
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Taylor K, Piasecka A, Kajdasz A, Brzęk A, Polay Espinoza M, Bourgeois CF, Jankowski A, Borowiak M, Raczyńska KD, Sznajder ŁJ, Sobczak K. Modulatory role of RNA helicases in MBNL-dependent alternative splicing regulation. Cell Mol Life Sci 2023; 80:335. [PMID: 37882878 PMCID: PMC10602967 DOI: 10.1007/s00018-023-04927-0] [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: 01/31/2023] [Revised: 07/14/2023] [Accepted: 08/17/2023] [Indexed: 10/27/2023]
Abstract
Muscleblind-like splicing regulators (MBNLs) activate or repress the inclusion of alternative splicing (AS) events, enabling the developmental transition of fetal mRNA splicing isoforms to their adult forms. Herein, we sought to elaborate the mechanism by which MBNLs mediate AS related to biological processes. We evaluated the functional role of DEAD-box (DDX) RNA helicases, DDX5 and DDX17 in MBNL-dependent AS regulation. Whole-transcriptome analysis and validation approaches revealed a handful of MBNLs-dependent AS events to be affected by DDX5 and DDX17 in mostly an opposite manner. The opposite expression patterns of these two groups of factors during muscle development and coordination of fetal-to-adult splicing transition indicate the importance of these proteins at early stages of development. The identified pathways of how the helicases modulate MBNL splicing activity include DDX5 and DDX17-dependent changes in the ratio of MBNL splicing isoforms and most likely changes in accessibility of MBNL-binding sites. Another pathway involves the mode of action of the helicases independent of MBNL activity. These findings lead to a deeper understanding of the network of interdependencies between RNA-binding proteins and constitute a valuable element in the discussion on developmental homeostasis and pathological states in which the studied protein factors play a significant role.
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Affiliation(s)
- Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Agnieszka Piasecka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Arkadiusz Kajdasz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Brzęk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Micaela Polay Espinoza
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Artur Jankowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Małgorzata Borowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Katarzyna D Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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17
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Nutter CA, Kidd BM, Carter HA, Hamel JI, Mackie PM, Kumbkarni N, Davenport ML, Tuyn DM, Gopinath A, Creigh PD, Sznajder ŁJ, Wang ET, Ranum LPW, Khoshbouei H, Day JW, Sampson JB, Prokop S, Swanson MS. Choroid plexus mis-splicing and altered cerebrospinal fluid composition in myotonic dystrophy type 1. Brain 2023; 146:4217-4232. [PMID: 37143315 PMCID: PMC10545633 DOI: 10.1093/brain/awad148] [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: 01/23/2023] [Revised: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
Myotonic dystrophy type 1 is a dominantly inherited multisystemic disease caused by CTG tandem repeat expansions in the DMPK 3' untranslated region. These expanded repeats are transcribed and produce toxic CUG RNAs that sequester and inhibit activities of the MBNL family of developmental RNA processing factors. Although myotonic dystrophy is classified as a muscular dystrophy, the brain is also severely affected by an unusual cohort of symptoms, including hypersomnia, executive dysfunction, as well as early onsets of tau/MAPT pathology and cerebral atrophy. To address the molecular and cellular events that lead to these pathological outcomes, we recently generated a mouse Dmpk CTG expansion knock-in model and identified choroid plexus epithelial cells as particularly affected by the expression of toxic CUG expansion RNAs. To determine if toxic CUG RNAs perturb choroid plexus functions, alternative splicing analysis was performed on lateral and hindbrain choroid plexi from Dmpk CTG knock-in mice. Choroid plexus transcriptome-wide changes were evaluated in Mbnl2 knockout mice, a developmental-onset model of myotonic dystrophy brain dysfunction. To determine if transcriptome changes also occurred in the human disease, we obtained post-mortem choroid plexus for RNA-seq from neurologically unaffected (two females, three males; ages 50-70 years) and myotonic dystrophy type 1 (one female, three males; ages 50-70 years) donors. To test that choroid plexus transcriptome alterations resulted in altered CSF composition, we obtained CSF via lumbar puncture from patients with myotonic dystrophy type 1 (five females, five males; ages 35-55 years) and non-myotonic dystrophy patients (three females, four males; ages 26-51 years), and western blot and osmolarity analyses were used to test CSF alterations predicted by choroid plexus transcriptome analysis. We determined that CUG RNA induced toxicity was more robust in the lateral choroid plexus of Dmpk CTG knock-in mice due to comparatively higher Dmpk and lower Mbnl RNA levels. Impaired transitions to adult splicing patterns during choroid plexus development were identified in Mbnl2 knockout mice, including mis-splicing previously found in Dmpk CTG knock-in mice. Whole transcriptome analysis of myotonic dystrophy type 1 choroid plexus revealed disease-associated RNA expression and mis-splicing events. Based on these RNA changes, predicted alterations in ion homeostasis, secretory output and CSF composition were confirmed by analysis of myotonic dystrophy type 1 CSF. Our results implicate choroid plexus spliceopathy and concomitant alterations in CSF homeostasis as an unappreciated contributor to myotonic dystrophy type 1 CNS pathogenesis.
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Affiliation(s)
- Curtis A Nutter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Benjamin M Kidd
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Helmut A Carter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Johanna I Hamel
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Philip M Mackie
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nayha Kumbkarni
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Mackenzie L Davenport
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Dana M Tuyn
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Adithya Gopinath
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Peter D Creigh
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Laura P W Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, McKnight Brain Institute and the Fixel Institute for Neurological Diseases, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Habibeh Khoshbouei
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John W Day
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jacinda B Sampson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Stefan Prokop
- Department of Pathology, Immunology, and Laboratory Medicine, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute and the Fixel Institute for Neurological Diseases, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
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18
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Sznajder L, Khan M, Tadross M, Ciesiołka A, Nutter C, Taylor K, Pearson C, Sobczak K, Lewis M, Swanson M, Yuen R. Autistic traits in myotonic dystrophy type 1 due to MBNL inhibition and RNA mis-splicing. RESEARCH SQUARE 2023:rs.3.rs-3221704. [PMID: 37645891 PMCID: PMC10462192 DOI: 10.21203/rs.3.rs-3221704/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tandem repeat expansions are enriched in autism spectrum disorder, including CTG expansion in the DMPK gene that underlines myotonic muscular dystrophy type 1. Although the clinical connection of autism to myotonic dystrophy is corroborated, the molecular links remained unknown. Here, we show a mechanistic path of autism via repeat expansion in myotonic dystrophy. We found that inhibition of muscleblind-like (MBNL) splicing factors by expanded CUG RNAs alerts the splicing of autism-risk genes during brain development especially a class of autism-relevant microexons. To provide in vivo evidence that the CTG expansion and MBNL inhibition axis leads to the presentation of autistic traits, we demonstrate that CTG expansion and MBNL-null mouse models recapitulate autism-relevant mis-splicing profiles and demonstrate social deficits. Our findings indicate that DMPK CTG expansion-associated autism arises from developmental mis-splicing. Understanding this pathomechanistic connection provides an opportunity for greater in-depth investigations of mechanistic threads in autism.
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19
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Puri D, Sharma S, Samaddar S, Ravivarma S, Banerjee S, Ghosh-Roy A. Muscleblind-1 interacts with tubulin mRNAs to regulate the microtubule cytoskeleton in C. elegans mechanosensory neurons. PLoS Genet 2023; 19:e1010885. [PMID: 37603562 PMCID: PMC10470942 DOI: 10.1371/journal.pgen.1010885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 08/31/2023] [Accepted: 07/26/2023] [Indexed: 08/23/2023] Open
Abstract
Regulation of the microtubule cytoskeleton is crucial for the development and maintenance of neuronal architecture, and recent studies have highlighted the significance of regulated RNA processing in the establishment and maintenance of neural circuits. In a genetic screen conducted using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1/mbl-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. Our findings demonstrate that mbl-1 is required cell-autonomously for axon growth and proper synapse positioning in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 leads to increased microtubule dynamics and mixed orientation of microtubules in the anterior neurite of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and reduction of gentle touch sensation in mbl-1 mutant. Our data also revealed that mbl-1 is genetically epistatic to mec-7 (β tubulin) and mec-12 (α tubulin) in regulating axon growth. Furthermore, mbl-1 is epistatic to sad-1, an ortholog of BRSK/Brain specific-serine/threonine kinase and a known regulator of synaptic machinery, for synapse formation at the correct location of the PLM neurite. Notably, the immunoprecipitation of MBL-1 resulted in the co-purification of mec-7, mec-12, and sad-1 mRNAs, suggesting a direct interaction between MBL-1 and these transcripts. Additionally, mbl-1 mutants exhibited reduced levels and stability of mec-7 and mec-12 transcripts. Our study establishes a previously unknown link between RNA-binding proteins and cytoskeletal machinery, highlighting their crucial roles in the development and maintenance of the nervous system.
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Affiliation(s)
- Dharmendra Puri
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sunanda Sharma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sarbani Samaddar
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sruthy Ravivarma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sourav Banerjee
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
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20
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Sebastian R, Jin K, Pavon N, Bansal R, Potter A, Song Y, Babu J, Gabriel R, Sun Y, Aronow B, Pak C. Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids. Nat Commun 2023; 14:3770. [PMID: 37355690 PMCID: PMC10290702 DOI: 10.1038/s41467-023-39420-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how NRXN1 deletions impact cortical development in a cell type-specific manner and disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying NRXN1 heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single-cell transcriptomic analysis over the course of brain organoid development from 3 weeks to 3.5 months. Intriguingly, while both deletions similarly impacted molecular pathways associated with ubiquitin-proteasome system, alternative splicing, and synaptic signaling in maturing glutamatergic and GABAergic neurons, SCZ-NRXN1 deletions specifically perturbed developmental trajectories of early neural progenitors and accumulated disease-specific transcriptomic signatures. Using calcium imaging, we found that both deletions led to long-lasting changes in spontaneous and synchronous neuronal networks, implicating synaptic dysfunction. Our study reveals developmental-timing- and cell-type-dependent actions of NRXN1 deletions in unique genetic contexts.
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Affiliation(s)
- Rebecca Sebastian
- Graduate Program in Neuroscience & Behavior, UMass Amherst, Amherst, MA, 01003, USA
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Narciso Pavon
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Ruby Bansal
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Andrew Potter
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Yoonjae Song
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Juliana Babu
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA, 01003, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45256, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA.
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21
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Porquet F, Weidong L, Jehasse K, Gazon H, Kondili M, Blacher S, Massotte L, Di Valentin E, Furling D, Gillet NA, Klein AF, Seutin V, Willems L. Specific DMPK-promoter targeting by CRISPRi reverses myotonic dystrophy type 1-associated defects in patient muscle cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:857-871. [PMID: 37273786 PMCID: PMC10238591 DOI: 10.1016/j.omtn.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disease that originates from an expansion of CTG microsatellites in the 3' untranslated region of the DMPK gene, thus leading to the expression of transcripts containing expanded CUG repeats (CUGexp). The pathophysiology is explained by a toxic RNA gain of function where CUGexp RNAs form nuclear aggregates that sequester and alter the function of MBNL splicing factors, triggering splicing misregulation linked to the DM1 symptoms. There is currently no cure for DM1, and most therapeutic strategies aim at eliminating CUGexp-DMPK transcripts. Here, we investigate a DMPK-promoter silencing strategy using CRISPR interference as a new alternative approach. Different sgRNAs targeting the DMPK promoter are evaluated in DM1 patient muscle cells. The most effective guides allowed us to reduce the level of DMPK transcripts and CUGexp-RNA aggregates up to 80%. The CUGexp-DMPK repression corrects the overall transcriptome, including spliceopathy, and reverses a physiological parameter in DM1 muscle cells. Its action is specific and restricted to the DMPK gene, as confirmed by genome-wide expression analysis. Altogether, our findings highlight DMPK-promoter silencing by CRISPRi as a promising therapeutic approach for DM1.
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Affiliation(s)
- Florent Porquet
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Lin Weidong
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Kévin Jehasse
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Maria Kondili
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Silvia Blacher
- Laboratory of Biology of Tumor and Development, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Laurent Massotte
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | | | - Denis Furling
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Nicolas Albert Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, 5000 Namur, Belgium
| | - Arnaud François Klein
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Vincent Seutin
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
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22
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Hildebrandt RP, Moss KR, Janusz-Kaminska A, Knudson LA, Denes LT, Saxena T, Boggupalli DP, Li Z, Lin K, Bassell GJ, Wang ET. Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes. Nat Commun 2023; 14:3427. [PMID: 37296096 PMCID: PMC10256740 DOI: 10.1038/s41467-023-38923-6] [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: 08/23/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
RNA binding proteins (RBPs) act as critical facilitators of spatially regulated gene expression. Muscleblind-like (MBNL) proteins, implicated in myotonic dystrophy and cancer, localize RNAs to myoblast membranes and neurites through unknown mechanisms. We find that MBNL forms motile and anchored granules in neurons and myoblasts, and selectively associates with kinesins Kif1bα and Kif1c through its zinc finger (ZnF) domains. Other RBPs with similar ZnFs associate with these kinesins, implicating a motor-RBP specificity code. MBNL and kinesin perturbation leads to widespread mRNA mis-localization, including depletion of Nucleolin transcripts from neurites. Live cell imaging and fractionation reveal that the unstructured carboxy-terminal tail of MBNL1 allows for anchoring at membranes. An approach, termed RBP Module Recruitment and Imaging (RBP-MRI), reconstitutes kinesin- and membrane-recruitment functions using MBNL-MS2 coat protein fusions. Our findings decouple kinesin association, RNA binding, and membrane anchoring functions of MBNL while establishing general strategies for studying multi-functional, modular domains of RBPs.
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Affiliation(s)
- Ryan P Hildebrandt
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kathryn R Moss
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Luke A Knudson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lance T Denes
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Tanvi Saxena
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Devi Prasad Boggupalli
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Zhuangyue Li
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kun Lin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
- Myology Institute, University of Florida, Gainesville, FL, USA.
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23
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Botta S, de Prisco N, Chemiakine A, Brandt V, Cabaj M, Patel P, Doron‐Mandel E, Treadway CJ, Jovanovic M, Brown NG, Soni RK, Gennarino VA. Dosage sensitivity to Pumilio1 variants in the mouse brain reflects distinct molecular mechanisms. EMBO J 2023; 42:e112721. [PMID: 37070548 PMCID: PMC10233381 DOI: 10.15252/embj.2022112721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/19/2023] Open
Abstract
Different mutations in the RNA-binding protein Pumilio1 (PUM1) cause divergent phenotypes whose severity tracks with dosage: a mutation that reduces PUM1 levels by 25% causes late-onset ataxia, whereas haploinsufficiency causes developmental delay and seizures. Yet PUM1 targets are derepressed to equal degrees in both cases, and the more severe mutation does not hinder PUM1's RNA-binding ability. We therefore considered the possibility that the severe mutation might disrupt PUM1 interactions, and identified PUM1 interactors in the murine brain. We find that mild PUM1 loss derepresses PUM1-specific targets, but the severe mutation disrupts interactions with several RNA-binding proteins and the regulation of their targets. In patient-derived cell lines, restoring PUM1 levels restores these interactors and their targets to normal levels. Our results demonstrate that dosage sensitivity does not always signify a linear relationship with protein abundance but can involve distinct mechanisms. We propose that to understand the functions of RNA-binding proteins in a physiological context will require studying their interactions as well as their targets.
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Affiliation(s)
- Salvatore Botta
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
- Department of Translational Medical ScienceUniversity of Campania Luigi VanvitelliCasertaItaly
| | - Nicola de Prisco
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Alexei Chemiakine
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Vicky Brandt
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Maximilian Cabaj
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Purvi Patel
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | | | - Colton J Treadway
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Marko Jovanovic
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Vincenzo A Gennarino
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
- Departments of NeurologyColumbia University Irving Medical CenterNew YorkNYUSA
- Columbia Stem Cell InitiativeColumbia University Irving Medical CenterNew YorkNYUSA
- Initiative for Columbia Ataxia and TremorColumbia University Irving Medical CenterNew YorkNYUSA
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24
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Khandelwal A, Cushman J, Choi J, Zhuravka I, Rajbhandari A, Valiulahi P, Li X, Zhou C, Comai L, Reddy S. Mbnl2 loss alters novel context processing and impairs object recognition memory. iScience 2023; 26:106732. [PMID: 37216102 PMCID: PMC10193234 DOI: 10.1016/j.isci.2023.106732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Patients with myotonic dystrophy type I (DM1) demonstrate visuospatial dysfunction and impaired performance in tasks requiring recognition or memory of figures and objects. In DM1, CUG expansion RNAs inactivate the muscleblind-like (MBNL) proteins. We show that constitutive Mbnl2 inactivation in Mbnl2ΔE2/ΔE2 mice selectively impairs object recognition memory in the novel object recognition test. When exploring the context of a novel arena in which the objects are later encountered, the Mbnl2ΔE2/ΔE2 dorsal hippocampus responds with a lack of enrichment for learning and memory-related pathways, mounting instead transcriptome alterations predicted to impair growth and neuron viability. In Mbnl2ΔE2/ΔE2 mice, saturation effects may prevent deployment of a functionally relevant transcriptome response during novel context exploration. Post-novel context exploration alterations in genes implicated in tauopathy and dementia are observed in the Mbnl2ΔE2/ΔE2 dorsal hippocampus. Thus, MBNL2 inactivation in patients with DM1 may alter novel context processing in the dorsal hippocampus and impair object recognition memory.
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Affiliation(s)
- Abinash Khandelwal
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse Cushman
- UCLA Behavioral Testing Core, University of California Los Angeles, Los Angeles, CA 90095-1563, USA
| | - Jongkyu Choi
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Irina Zhuravka
- UCLA Behavioral Testing Core, University of California Los Angeles, Los Angeles, CA 90095-1563, USA
| | - Abha Rajbhandari
- UCLA Behavioral Testing Core, University of California Los Angeles, Los Angeles, CA 90095-1563, USA
| | - Parvin Valiulahi
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xiandu Li
- . Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chenyu Zhou
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lucio Comai
- . Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sita Reddy
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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25
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Montañés-Agudo P, Pinto YM, Creemers EE. Splicing factors in the heart: Uncovering shared and unique targets. J Mol Cell Cardiol 2023; 179:72-79. [PMID: 37059416 DOI: 10.1016/j.yjmcc.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/29/2023] [Accepted: 04/09/2023] [Indexed: 04/16/2023]
Abstract
Alternative splicing generates specialized protein isoforms that allow the heart to adapt during development and disease. The recent discovery that mutations in the splicing factor RNA-binding protein 20 (RBM20) cause a severe form of familial dilated cardiomyopathy has sparked a great interest in alternative splicing in the field of cardiology. Since then, identification of splicing factors controlling alternative splicing in the heart has grown at a rapid pace. Despite the intriguing observation that a certain overlap exists between the targets of some splicing factors, an integrated and systematic analysis of their splicing networks is missing. Here, we compared the splicing networks of individual splicing factors by re-analyzing original RNA-sequencing data from eight previously published mouse models, in which a single splicing factor has been genetically deleted (i.e. HNRNPU, MBNL1/2, QKI, RBM20, RBM24, RBPMS, SRSF3, SRSF4). We show that key splicing events in Camk2d, Ryr2, Tpm1, Tpm2 and Pdlim5 require the combined action of the majority of these splicing factors. Additionally, we identified common targets and pathways among splicing factors, with the largest overlap between the splicing networks of MBNL, QKI and RBM24. We also re-analyzed a large-scale RNA-sequencing study on hearts of 128 heart failure patients. Here, we observed that MBNL1, QKI and RBM24 expression varied greatly. This variation in expression correlated with differential splicing of their downstream targets as found in mice, suggesting that aberrant splicing by MBNL1, QKI and RBM24 might contribute to the disease mechanism in heart failure.
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Affiliation(s)
- Pablo Montañés-Agudo
- Experimental Cardiology, Room K2-112, Amsterdam UMC Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Yigal M Pinto
- Experimental Cardiology, Room K2-104, Amsterdam UMC, location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Esther E Creemers
- Experimental Cardiology, Room K2-104-2, Amsterdam UMC, Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
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26
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He C, Li Y, Chen ZY, Huang CK. Crosstalk of renal cell carcinoma cells and tumor-associated macrophages aggravates tumor progression by modulating muscleblind-like protein 2/B-cell lymphoma 2/beclin 1-mediated autophagy. Cytotherapy 2023; 25:298-309. [PMID: 36244911 DOI: 10.1016/j.jcyt.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND AIMS M2-polarized tumor-associated macrophages contribute to the development of multiple human cancers, including renal cell carcinoma (RCC). However, the crosstalk mechanism between M2 macrophages and RCC remains unclear. METHODS The authors constructed a co-culture system of M2 macrophages differentiated from THP-1 and RCC cells. Microscopic examination and quantitative real‑time polymerase chain reaction (qRT-PCR) validated the morphology and types of macrophages. The proliferation, migration and invasion of RCC cells were assessed by Cell Counting Kit 8 (Dojindo Molecular Technologies, Inc, Santa Clara, CA, USA) and Transwell assay (Corning, Corning, NY, USA). Messenger RNA (mRNA) and protein expression of target molecules was detected by qRT‑PCR and western blotting. Expression of Ki-67, E-cadherin and N-cadherin was measured by immunofluorescence staining or immunohistochemistry. Molecular interaction was evaluated by RNA pull-down, RNA immunoprecipitation and co-immunoprecipitation. A xenograft model was established to determine tumor growth in vivo. RESULTS RCC cells triggered the activation of M2 macrophages. Functionally, M2-polarized macrophages facilitated the growth, migration, invasion and epithelial-mesenchymal transition of RCC cells by suppressing autophagy, whereas rapamycin, an activator of autophagy, significantly counteracted the tumor-promoting effects of M2 macrophages. Mechanistically, M2 macrophage-derived C-C motif chemokine 2 (CCL2) enhanced modulation of muscleblind-like protein 2 (MBNL2) expression. MBNL2 raised the stability of B-cell lymphoma 2 (Bcl-2) by directly binding to Bcl-2 mRNA, which endowed RCC cells with malignant properties via inhibition of beclin 1-dependent autophagy. CONCLUSIONS RCC-induced M2-polarized macrophages secrete CCL2 to promote the growth and metastasis of RCC cells via inhibition of MBNL2/Bcl-2/beclin 1-mediated autophagy, which provide a novel perspective for the development of a therapeutic strategy for -RCC.
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Affiliation(s)
- Cheng He
- Department of Urology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yang Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Zhi-Yong Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Chang-Kun Huang
- Department of Urology, The Second Xiangya Hospital, Central South University, 410011 Changsha, Hunan China..
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27
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Tajima Y, Ito K, Yuan Y, Frank MO, Saito Y, Darnell RB. NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons. Cell Rep 2023; 42:112050. [PMID: 36716149 PMCID: PMC10382602 DOI: 10.1016/j.celrep.2023.112050] [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: 09/13/2022] [Revised: 11/12/2022] [Accepted: 01/15/2023] [Indexed: 01/30/2023] Open
Abstract
We describe a patient haploinsufficient for the neuronal RNA binding protein NOVA1 who developed a behavioral motor hyperactivity disorder, suggesting a role of NOVA1 in postnatal motor inhibition. To investigate Nova1's action in adult Gad2+ inhibitory neurons, we generated a conditional Nova1-null mouse (Nova1-cKOGad2-cre). Strikingly, the phenotypes of these mice show many similarities to the NOVA1 haploinsufficient patient and identify a function of Nova1 in the hypothalamus. Molecularly, Nova1 loss in Gad2-positive neurons alters downstream expression of Impact mRNA, along with a subset of RNAs encoding electron transport chain-related factors and ribosomal proteins. NOVA1 stabilizes Impact mRNA by binding its 3' UTR, antagonizing the actions of miR-138 and miR-124. Together, these studies demonstrate actions of NOVA1 in adult hypothalamic neurons, mechanisms by which it functions in translation and metabolism, including through direct binding to Impact mRNA, and illuminate its role in human neurologic disease.
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Affiliation(s)
- Yoko Tajima
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yuan Yuan
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mayu O Frank
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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28
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Nitschke L, Hu RC, Miller A, Lucas L, Cooper T. Alternative splicing mediates the compensatory upregulation of MBNL2 upon MBNL1 loss-of-function. Nucleic Acids Res 2023; 51:1245-1259. [PMID: 36617982 PMCID: PMC9943662 DOI: 10.1093/nar/gkac1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Loss of gene function can be compensated by paralogs with redundant functions. An example of such compensation are the paralogs of the Muscleblind-Like (MBNL) family of RNA-binding proteins that are sequestered and lose their function in Myotonic Dystrophy Type 1 (DM1). Loss of MBNL1 increases the levels of its paralog MBNL2 in tissues where Mbnl2 expression is low, allowing MBNL2 to functionally compensate for MBNL1 loss. Here, we show that loss of MBNL1 increases the inclusion of Mbnl2 exon 6 and exon 9. We find that inclusion of Mbnl2 exon 6 increases the translocation of MBNL2 to the nucleus, while the inclusion of Mbnl2 exon 9 shifts the reading frame to an alternative C-terminus. We show that the C-terminus lacking exon 9 contains a PEST domain which causes proteasomal degradation. Loss of MBNL1 increases the inclusion of exon 9, resulting in an alternative C-terminus lacking the PEST domain and the increase of MBNL2. We further find that the compensatory mechanism is active in a mouse DM1 model. Together, this study uncovers the compensatory mechanism by which loss of MBNL1 upregulates its paralog MBNL2 and highlights a potential role of the compensatory mechanism in DM1.
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Affiliation(s)
- Larissa Nitschke
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rong-Chi Hu
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew N Miller
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lathan Lucas
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Chemical, Physical & Structural Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas A Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Tahraoui-Bories J, Mérien A, González-Barriga A, Lainé J, Leteur C, Polvèche H, Carteron A, De Lamotte JD, Nicoleau C, Polentes J, Jarrige M, Gomes-Pereira M, Ventre E, Poydenot P, Furling D, Schaeffer L, Legay C, Martinat C. MBNL-dependent impaired development within the neuromuscular system in myotonic dystrophy type 1. Neuropathol Appl Neurobiol 2023; 49:e12876. [PMID: 36575942 PMCID: PMC10107781 DOI: 10.1111/nan.12876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/29/2022]
Abstract
AIMS Myotonic dystrophy type I (DM1) is one of the most frequent muscular dystrophies in adults. Although DM1 has long been considered mainly a muscle disorder, growing evidence suggests the involvement of peripheral nerves in the pathogenicity of DM1 raising the question of whether motoneurons (MNs) actively contribute to neuromuscular defects in DM1. METHODS By using micropatterned 96-well plates as a coculture platform, we generated a functional neuromuscular model combining DM1 and muscleblind protein (MBNL) knock-out human-induced pluripotent stem cells-derived MNs and human healthy skeletal muscle cells. RESULTS This approach led to the identification of presynaptic defects which affect the formation or stability of the neuromuscular junction at an early developmental stage. These neuropathological defects could be reproduced by the loss of RNA-binding MBNL proteins, whose loss of function in vivo is associated with muscular defects associated with DM1. These experiments indicate that the functional defects associated with MNs can be directly attributed to MBNL family proteins. Comparative transcriptomic analyses also revealed specific neuronal-related processes regulated by these proteins that are commonly misregulated in DM1. CONCLUSIONS Beyond the application to DM1, our approach to generating a robust and reliable human neuromuscular system should facilitate disease modelling studies and drug screening assays.
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Affiliation(s)
| | - Antoine Mérien
- INSERM/UEVE UMR 861, Université Paris Saclay, I-STEM, Corbeil-Essonnes, France
| | - Anchel González-Barriga
- INSERM, Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, Paris, France
| | - Jeanne Lainé
- INSERM, Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, Paris, France
| | | | | | | | | | | | | | | | - Mário Gomes-Pereira
- INSERM, Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, Paris, France
| | | | | | - Denis Furling
- INSERM, Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, Paris, France
| | - Laurent Schaeffer
- INMG, INSERM U1217, CNRS UMR5310, Université Lyon 1, Université de Lyon, Hospices Civils de Lyon, Lyon, France
| | - Claire Legay
- CNRS, SPINN-Saint-Pères Paris Institute for the Neurosciences, Université Paris Cité, Paris, France
| | - Cécile Martinat
- INSERM/UEVE UMR 861, Université Paris Saclay, I-STEM, Corbeil-Essonnes, France
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Golini E, Rigamonti M, Raspa M, Scavizzi F, Falcone G, Gourdon G, Mandillo S. Excessive rest time during active phase is reliably detected in a mouse model of myotonic dystrophy type 1 using home cage monitoring. Front Behav Neurosci 2023; 17:1130055. [PMID: 36935893 PMCID: PMC10017452 DOI: 10.3389/fnbeh.2023.1130055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited neuromuscular disease caused by the abnormal expansion of CTG-repeats in the 3'-untranslated region of the Dystrophia Myotonica Protein Kinase (DMPK) gene, characterized by multisystemic symptoms including muscle weakness, myotonia, cardio-respiratory problems, hypersomnia, cognitive dysfunction and behavioral abnormalities. Sleep-related disturbances are among the most reported symptoms that negatively affect the quality of life of patients and that are present in early and adult-onset forms of the disease. DMSXL mice carry a mutated human DMPK transgene containing >1,000 CTGrepeats, modeling an early onset, severe form of DM1. They exhibit a pathologic neuromuscular phenotype and also synaptic dysfunction resulting in neurological and behavioral deficits similar to those observed in patients. Additionally, they are underweight with a very high mortality within the first month after birth presenting several welfare issues. To specifically explore sleep/rest-related behaviors of this frail DM1 mouse model we used an automated home cage-based system that allows 24/7 monitoring of their activity non-invasively. We tested male and female DMSXL mice and their wild-type (WT) littermates in Digital Ventilated Cages (DVCR) assessing activity and rest parameters on day and night for 5 weeks. We demonstrated that DMSXL mice show reduced activity and regularity disruption index (RDI), higher percentage of zero activity per each hour and longer periods of rest during the active phase compared to WT. This novel rest-related phenotype in DMSXL mice, assessed unobtrusively, could be valuable to further explore mechanisms and potential therapeutic interventions to alleviate the very common symptom of excessive daytime sleepiness in DM1 patients.
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Affiliation(s)
- Elisabetta Golini
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, Italy
| | - Mara Rigamonti
- Tecniplast S.p.A., Buguggiate, Italy
- *Correspondence: Mara Rigamonti,
| | - Marcello Raspa
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, Italy
| | - Ferdinando Scavizzi
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, Italy
| | - Germana Falcone
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, Italy
| | - Genevieve Gourdon
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, Italy
- Silvia Mandillo,
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31
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Suárez-Sánchez R, Ávila-Avilés RD, Hernández-Hernández JM, Sánchez-Celis D, Azotla-Vilchis CN, Gómez-Macías ER, Leyva-García N, Ortega A, Magaña JJ, Cisneros B, Hernández-Hernández O. RNA Foci Formation in a Retinal Glial Model for Spinocerebellar Ataxia Type 7. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010023. [PMID: 36675972 PMCID: PMC9861853 DOI: 10.3390/life13010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder characterized by cerebellar ataxia and retinopathy. SCA7 is caused by a CAG expansion in the ATXN7 gene, which results in an extended polyglutamine (polyQ) tract in the encoded protein, the ataxin-7. PolyQ expanded ataxin-7 elicits neurodegeneration in cerebellar Purkinje cells, however, its impact on the SCA7-associated retinopathy remains to be addressed. Since Müller glial cells play an essential role in retinal homeostasis, we generate an inducible model for SCA7, based on the glial Müller MIO-M1 cell line. The SCA7 pathogenesis has been explained by a protein gain-of-function mechanism, however, the contribution of the mutant RNA to the disease cannot be excluded. In this direction, we found nuclear and cytoplasmic foci containing mutant RNA accompanied by subtle alternative splicing defects in MIO-M1 cells. RNA foci were also observed in cells from different lineages, including peripheral mononuclear leukocytes derived from SCA7 patient, suggesting that this molecular mark could be used as a blood biomarker for SCA7. Collectively, our data showed that our glial cell model exhibits the molecular features of SCA7, which makes it a suitable model to study the RNA toxicity mechanisms, as well as to explore therapeutic strategies aiming to alleviate glial dysfunction.
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Affiliation(s)
- Rocío Suárez-Sánchez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
| | - Rodolfo Daniel Ávila-Avilés
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - J. Manuel Hernández-Hernández
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Daniel Sánchez-Celis
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Cuauhtli N. Azotla-Vilchis
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Enue R. Gómez-Macías
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Norberto Leyva-García
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
| | - Arturo Ortega
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del, Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
- Escuela de Ingeniería y Ciencias, Departamento de Bioingeniería, Tecnológico de Monterrey-Campus Ciudad de México, Ciudad de México 14380, Mexico
| | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Oscar Hernández-Hernández
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
- Correspondence: or ; Tel.: +52-(55)-5999-1000 (ext. 14710)
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32
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Ait Benichou S, Jauvin D, De Serres-Bérard T, Pierre M, Ling KK, Bennett CF, Rigo F, Gourdon G, Chahine M, Puymirat J. Antisense oligonucleotides as a potential treatment for brain deficits observed in myotonic dystrophy type 1. Gene Ther 2022; 29:698-709. [PMID: 35075265 PMCID: PMC9750879 DOI: 10.1038/s41434-022-00316-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023]
Abstract
Myotonic dystrophy, or dystrophia myotonica type 1 (DM1), is a multi-systemic disorder and is the most common adult form of muscular dystrophy. It affects not only muscles but also many organs, including the brain. Cerebral impairments include cognitive deficits, daytime sleepiness, and loss of visuospatial and memory functions. The expression of mutated transcripts with CUG repeats results in a gain of toxic mRNA function. The antisense oligonucleotide (ASO) strategy to treat DM1 brain deficits is limited by the fact that ASOs do not cross the blood-brain barrier after systemic administration, indicating that other methods of delivery should be considered. ASO technology has emerged as a powerful tool for developing potential new therapies for a wide variety of human diseases, and its potential has been proven in a recent clinical trial. Targeting DMPK mRNA in neural cells derived from human induced pluripotent stem cells obtained from a DM1 patient with the IONIS 486178 ASO abolished CUG-expanded foci, enabled nuclear redistribution of MBNL1/2, and corrected aberrant splicing. Intracerebroventricular injection of the IONIS 486178 ASO in DMSXL mice decreased the levels of mutant DMPK mRNAs by up to 70% throughout different brain regions. It also reversed behavioral abnormalities following neonatal administration. The present study indicated that the IONIS 486178 ASO targets mutant DMPK mRNAs in the brain and strongly supports the feasibility of a therapy for DM1 patients based on the intrathecal injection of an ASO.
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Affiliation(s)
- Siham Ait Benichou
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
| | - Dominic Jauvin
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
- CERVO Research Center, Institut universitaire en santé mentale de Québec, Quebec City, QC, Canada
| | - Thiéry De Serres-Bérard
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
- CERVO Research Center, Institut universitaire en santé mentale de Québec, Quebec City, QC, Canada
| | - Marion Pierre
- CERVO Research Center, Institut universitaire en santé mentale de Québec, Quebec City, QC, Canada
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Genevieve Gourdon
- Sorbonne Université, Inserm, Association Institut de Myologie, Centre de recherche en Myologie, Paris, France
| | - Mohamed Chahine
- CERVO Research Center, Institut universitaire en santé mentale de Québec, Quebec City, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
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33
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Stoodley J, Miraz DS, Jad Y, Fischer M, Wood MJA, Varela MA. Peptide-Conjugated PMOs for the Treatment of Myotonic Dystrophy. Methods Mol Biol 2022; 2587:209-237. [PMID: 36401033 DOI: 10.1007/978-1-0716-2772-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Antisense oligonucleotides (ASOs) have shown great therapeutic potential in the treatment of many neuromuscular diseases including myotonic dystrophy 1 (DM1). However, systemically delivered ASOs display poor biodistribution and display limited penetration into skeletal muscle. The conjugation of cell-penetrating peptides (CPPs) to phosphorodiamidate morpholino oligonucleotides (PMOs), a class of ASOs with a modified backbone, can be used to enhance ASO skeletal muscle penetration. Peptide-PMOs (P-PMOs) have been shown to be highly effective in correcting the DM1 skeletal muscle phenotype in both murine and cellular models of DM1 and at a molecular and functional level. Here we describe the synthesis and conjugation of P-PMOs and methods for analyzing their biodistribution and toxicity in the HSA-LR DM1 mouse model and their efficacy both in vitro and in vivo using FISH and RT-PCR splicing analysis.
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Affiliation(s)
- Jessica Stoodley
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - David Seoane Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Yahya Jad
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Mathieu Fischer
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Matthew J A Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Miguel A Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Oxford, UK. .,MDUK Oxford Neuromuscular Centre, Oxford, UK.
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34
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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35
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Altered Behavioral Responses Show GABA Sensitivity in Muscleblind-Like 2-Deficient Mice: Implications for CNS Symptoms in Myotonic Dystrophy. eNeuro 2022; 9:ENEURO.0218-22.2022. [PMID: 36150891 PMCID: PMC9557336 DOI: 10.1523/eneuro.0218-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 01/17/2023] Open
Abstract
Considerable evidence from mouse models and human postmortem brain suggests loss of Muscleblind-like protein 2 (MBNL2) function in brain is a major driver of CNS symptoms in Myotonic dystrophy type 1 (DM1). Increased hypersomnia, fatigue, and surgical complications associated with general anesthesia suggest possible sensitivity to GABAergic inhibition in DM1. To test the hypothesis that MBNL2 depletion leads to behavioral sensitivity to GABAA receptor (GABAA-R) modulation, Mbnl2 knock-out (KO) and wild-type (WT) littermates were treated with the anesthetic sevoflurane, the benzodiazepine diazepam, the imidazopyridine zolpidem, and the benzodiazepine rescue agent, flumazenil (Ro 15-1788), and assessed for various behavioral metrics. Mbnl2 KO mice exhibited delayed recovery following sevoflurane, delayed emergence and recovery from zolpidem, and enhanced sleep time at baseline that was modulated by flumazenil. A significantly higher proportion of Mbnl2 KO mice also loss their righting reflex [loss of righting reflex (LORR)] from a standard diazepam dose. We further examined whether MBNL2 depletion affects total GABAA-R mRNA subunit levels and validated RNA-sequencing data of mis-spliced Gabrg2, whose isoform ratios are known to regulate GABA sensitivity and associated behaviors. While no other GABAA-R subunit mRNA levels tested were altered in Mbnl2 KO mouse prefrontal cortex, Gabrg2S/L mRNA ratio levels were significantly altered. Taken together, our findings indicate that loss of MBNL2 function affects GABAergic function in a mouse model of myotonic dystrophy (DM1).
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36
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Rhine K, Al-Azzam N, Yu T, Yeo GW. Aging RNA granule dynamics in neurodegeneration. Front Mol Biosci 2022; 9:991641. [PMID: 36188213 PMCID: PMC9523239 DOI: 10.3389/fmolb.2022.991641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Disordered RNA-binding proteins and repetitive RNA sequences are the main genetic causes of several neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington's disease. Importantly, these components also seed the formation of cytoplasmic liquid-like granules, like stress granules and P bodies. Emerging evidence demonstrates that healthy granules formed via liquid-liquid phase separation can mature into solid- or gel-like inclusions that persist within the cell. These solidified inclusions are a precursor to the aggregates identified in patients, demonstrating that dysregulation of RNA granule biology is an important component of neurodegeneration. Here, we review recent literature highlighting how RNA molecules seed proteinaceous granules, the mechanisms of healthy turnover of RNA granules in cells, which biophysical properties underly a transition to solid- or gel-like material states, and why persistent granules disrupt the cellular homeostasis of neurons. We also identify various methods that will illuminate the contributions of disordered proteins and RNAs to neurodegeneration in ongoing research efforts.
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Affiliation(s)
- Kevin Rhine
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Norah Al-Azzam
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
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37
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Krueger SB, Zimmerman SC. Dynamic Covalent Template-Guided Screen for Nucleic Acid-Targeting Agents. J Med Chem 2022; 65:12417-12426. [PMID: 36099320 DOI: 10.1021/acs.jmedchem.2c01086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trinucleotide repeat diseases such as myotonic dystrophy type 1 (DM1) and Huntington's disease (HD) are caused by expanded DNA repeats that can be used as templates to synthesize their own inhibitors. Because it would be particularly advantageous to reversibly assemble multivalent nucleic acid-targeting agents in situ, we sought to develop a target-guided screen that uses dynamic covalent chemistry to identify multitarget inhibitors. We report the synthesis of a library of amine- or aldehyde-containing fragments. The assembly of these fragments led to a diverse set of hit combinations that was confirmed by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) in the presence of DM1 and HD repeat sequences. Of interest for both diseases, the resulting hit combinations inhibited transcription selectively and in a cooperative manner in vitro, with inhibitory concentration (IC50) values in the micromolar range. This dynamic covalent library and screening approach could be applied to identify compounds that reversibly assemble on other nucleic acid targets.
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Affiliation(s)
- Sarah B Krueger
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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38
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Krueger SB, Lanzendorf AN, Jeon HH, Zimmerman SC. Selective and Reversible Ligand Assembly on the DNA and RNA Repeat Sequences in Myotonic Dystrophy. Chembiochem 2022; 23:e202200260. [PMID: 35790065 PMCID: PMC9733911 DOI: 10.1002/cbic.202200260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/03/2022] [Indexed: 02/06/2023]
Abstract
Small molecule targeting of DNA and RNA sequences has come into focus as a therapeutic strategy for diseases such as myotonic dystrophy type 1 (DM1), a trinucleotide repeat disease characterized by RNA gain-of-function. Herein, we report a novel template-selected, reversible assembly of therapeutic agents in situ via aldehyde-amine condensation. Rationally designed small molecule targeting agents functionalized with either an aldehyde or an amine were synthesized and screened against the target nucleic acid sequence. The assembly of fragments was confirmed by MALDI-MS in the presence of DM1-relevant nucleic acid sequences. The resulting hit combinations of aldehyde and amine inhibited the formation of r(CUG)exp in vitro in a cooperative manner at low micromolar levels and rescued mis-splicing defects in DM1 model cells. This reversible template-selected assembly is a promising approach to achieve cell permeable and multivalent targeting via in situ synthesis and could be applied to other nucleic acid targets.
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Affiliation(s)
- Sarah B Krueger
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Amie N Lanzendorf
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Hyoeun Heather Jeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
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39
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Buen Abad Najar CF, Burra P, Yosef N, Lareau LF. Identifying cell state-associated alternative splicing events and their coregulation. Genome Res 2022; 32:1385-1397. [PMID: 35858747 PMCID: PMC9341514 DOI: 10.1101/gr.276109.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing shapes the transcriptome and contributes to each cell's unique identity, but single-cell RNA sequencing (scRNA-seq) has struggled to capture the impact of alternative splicing. We previously showed that low recovery of mRNAs from single cells led to erroneous conclusions about the cell-to-cell variability of alternative splicing. Here, we present a method, Psix, to confidently identify splicing that changes across a landscape of single cells, using a probabilistic model that is robust against the data limitations of scRNA-seq. Its autocorrelation-inspired approach finds patterns of alternative splicing that correspond to patterns of cell identity, such as cell type or developmental stage, without the need for explicit cell clustering, labeling, or trajectory inference. Applying Psix to data that follow the trajectory of mouse brain development, we identify exons whose alternative splicing patterns cluster into modules of coregulation. We show that the exons in these modules are enriched for binding by distinct neuronal splicing factors and that their changes in splicing correspond to changes in expression of these splicing factors. Thus, Psix reveals cell type-dependent splicing patterns and the wiring of the splicing regulatory networks that control them. Our new method will enable scRNA-seq analysis to go beyond transcription to understand the roles of post-transcriptional regulation in determining cell identity.
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Affiliation(s)
| | - Prakruthi Burra
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California 94720, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Liana F Lareau
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
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40
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Hu Y, Rong R, Wang Y, Yan S, Liu S, Wang L. Downregulating EVA1C exerts the potential to promote neuron growth after neonatal hypoxic-ischemic encephalopathy injury associated with alternative splicing. IBRAIN 2022; 8:481-491. [PMID: 37786591 PMCID: PMC10529346 DOI: 10.1002/ibra.12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 10/04/2023]
Abstract
Neonatal hypoxic-ischemic encephalopathy (NHIE) is one of the major diseases in newborns during the perinatal stage, which globally is the main reason for children's morbidity and mortality. However, the mechanism of NHIE still remains poorly clear. In this study, the 7-day-old rats were subjected to hypoxic-ischemia (HI), then brain damage was detected. Afterward, the expression of eva-1 homolog C (EVA1C) was measured in vitro by establishing the oxygen-glucose deprivation (OGD) model in SHSY5Y cells and human fetal neurons. Subsequently, the potential function and mechanism of EVA1C were explored by silencing EVA1C and alternative splicing prediction. As a result, obvious neurobehavioral impairment and brain infarction were detected through Zea-Longa score and TTC staining; meanwhile, neuron injury was tested by HE and Nissl staining post HI. Moreover, it was found that the expression of EVA1C was notably upregulated in SHSY5Y cells and human fetal neurons after OGD. In addition, cell survival and growth were increased after silencing EVA1C, which might be associated with alternative splicing. In conclusion, EVA1C interference exhibited potential in promoting neuron survival and growth, associated with exon skipping with the alternative splicing site in 34613318:34687258, which may provide the basis for the therapeutic target and mechanism research of NHIE.
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Affiliation(s)
- Yue Hu
- Department of Anesthesia OperationThe First People's Hospital of Shuangliu DistrictChengduSichuanChina
| | - Rong Rong
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Yi Wang
- Animal Zoology DepartmentKunming Medical UniversityKunmingYunnanChina
| | - Shan‐Shan Yan
- Animal Zoology DepartmentKunming Medical UniversityKunmingYunnanChina
| | - Su Liu
- Center for Epigenetics and Induced Pluripotent Stem Cells, Kennedy Krieger InstituteJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Lei Wang
- Animal Zoology DepartmentKunming Medical UniversityKunmingYunnanChina
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41
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Dincã DM, Lallemant L, González-Barriga A, Cresto N, Braz SO, Sicot G, Pillet LE, Polvèche H, Magneron P, Huguet-Lachon A, Benyamine H, Azotla-Vilchis CN, Agonizantes-Juárez LE, Tahraoui-Boris J, Martinat C, Hernández-Hernández O, Auboeuf D, Rouach N, Bourgeois CF, Gourdon G, Gomes-Pereira M. Myotonic dystrophy RNA toxicity alters morphology, adhesion and migration of mouse and human astrocytes. Nat Commun 2022; 13:3841. [PMID: 35789154 PMCID: PMC9253038 DOI: 10.1038/s41467-022-31594-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
Brain dysfunction in myotonic dystrophy type 1 (DM1), the prototype of toxic RNA disorders, has been mainly attributed to neuronal RNA misprocessing, while little attention has been given to non-neuronal brain cells. Here, using a transgenic mouse model of DM1 that expresses mutant RNA in various brain cell types (neurons, astroglia, and oligodendroglia), we demonstrate that astrocytes exhibit impaired ramification and polarization in vivo and defects in adhesion, spreading, and migration. RNA-dependent toxicity and phenotypes are also found in human transfected glial cells. In line with the cell phenotypes, molecular analyses reveal extensive expression and accumulation of toxic RNA in astrocytes, which result in RNA spliceopathy that is more severe than in neurons. Astrocyte missplicing affects primarily transcripts that regulate cell adhesion, cytoskeleton, and morphogenesis, and it is confirmed in human brain tissue. Our findings demonstrate that DM1 impacts astrocyte cell biology, possibly compromising their support and regulation of synaptic function. Myotonic dystrophy type 1 (DM1) is characterized by debilitating neurological symptoms. Dinca et al. demonstrate the pronounced impact of DM1 on the morphology and RNA metabolism of astrocytes. Their findings suggest astroglial pathology in DM1 brain dysfunction.
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Affiliation(s)
- Diana M Dincã
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Louison Lallemant
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | | | - Noémie Cresto
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France
| | - Sandra O Braz
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.,Inserm UMR1163, Institut Imagine, Université Paris Cite, 75015, Paris, France
| | - Géraldine Sicot
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Laure-Elise Pillet
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France.,Doctoral School N°562, Paris Descartes University, Paris, 75006, France
| | - Hélène Polvèche
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Paul Magneron
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Aline Huguet-Lachon
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Hélène Benyamine
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Cuauhtli N Azotla-Vilchis
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Luis E Agonizantes-Juárez
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Julie Tahraoui-Boris
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Cécile Martinat
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Oscar Hernández-Hernández
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie, 69364, Lyon, France
| | - Nathalie Rouach
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie, 69364, Lyon, France
| | - Geneviève Gourdon
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.
| | - Mário Gomes-Pereira
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.
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42
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Pharmacotherapy alleviates pathological changes in human direct reprogrammed neuronal cell model of myotonic dystrophy type 1. PLoS One 2022; 17:e0269683. [PMID: 35776705 PMCID: PMC9249217 DOI: 10.1371/journal.pone.0269683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/25/2022] [Indexed: 12/02/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a trinucleotide repeat disorder affecting multiple organs. However, most of the research is focused on studying and treating its muscular symptoms. On the other hand, despite the significant impact of the neurological symptoms on patients’ quality of life, no drug therapy was studied due to insufficient reproducibility in DM1 brain-specific animal models. To establish DM1 neuronal model, human skin fibroblasts were directly converted into neurons by using lentivirus expressing small hairpin RNA (shRNA) against poly-pyrimidine tract binding protein (PTBP). We found faster degeneration in DM1 human induced neurons (DM1 hiNeurons) compared to control human induced neurons (ctrl hiNeurons), represented by lower viability from 10 days post viral-infection (DPI) and abnormal axonal growth at 15 DPI. Nuclear RNA foci were present in most of DM1 hiNeurons at 10 DPI. Furthermore, DM1 hiNeurons modelled aberrant splicing of MBNL1 and 2, MAPT, CSNK1D and MPRIP at 10 DPI. We tested two drugs that were shown to be effective for DM1 in non-neuronal model and found that treatment of DM1 hiNeurons with 100 nM or 200 nM actinomycin D (ACT) for 24 h resulted in more than 50% reduction in the number of RNA foci per nucleus in a dose dependent manner, with 16.5% reduction in the number of nuclei containing RNA foci at 200 nM and treatment with erythromycin at 35 μM or 65 μM for 48 h rescued mis-splicing of MBNL1 exon 5 and MBNL 2 exons 5 and 8 up to 17.5%, 10% and 8.5%, respectively. Moreover, erythromycin rescued the aberrant splicing of MAPT exon 2, CSNK1D exon 9 and MPRIP exon 9 to a maximum of 46.4%, 30.7% and 19.9%, respectively. These results prove that our model is a promising tool for detailed pathogenetic examination and novel drug screening for the nervous system.
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43
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Wang LH, Lin CY, Lin YM, Buée L, Sergeant N, Blum D, Chern Y, Wang GS. Calpain-2 Mediates MBNL2 Degradation and a Developmental RNA Processing Program in Neurodegeneration. J Neurosci 2022; 42:5102-5114. [PMID: 35606145 PMCID: PMC9233439 DOI: 10.1523/jneurosci.2006-21.2022] [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: 10/05/2021] [Revised: 03/24/2022] [Accepted: 05/03/2022] [Indexed: 12/24/2022] Open
Abstract
Increasing loss of structure and function of neurons and decline in cognitive function is commonly seen during the progression of neurologic diseases, although the causes and initial symptoms of individual diseases are distinct. This observation suggests a convergence of common degenerative features. In myotonic dystrophy type 1 (DM1), the expression of expanded CUG RNA induces neurotransmission dysfunction before axon and dendrite degeneration and reduced MBNL2 expression associated with aberrant alternative splicing. The role of loss of function of MBNL2 in the pathogenesis of neurodegeneration and the causal mechanism of neurodegeneration-reduced expression of MBNL2 remain elusive. Here, we show that increased MBNL2 expression is associated with neuronal maturation and required for neuronal morphogenesis and the fetal to adult developmental transition of RNA processing. Neurodegenerative conditions including NMDA receptor (NMDAR)-mediated excitotoxicity and dysregulated calcium homeostasis triggered nuclear translocation of calpain-2, thus resulting in MBNL2 degradation and reversal of MBNL2-regulated RNA processing to developmental patterns. Nuclear expression of calpain-2 resembled its developmental pattern and was associated with MBNL2 degradation. Knock-down of calpain-2 expression or inhibition of calpain-2 nuclear translocation prevented neurodegeneration-reduced MBNL2 expression and dysregulated RNA processing. Increased calpain-2 nuclear translocation associated with reduced MBNL2 expression and aberrant RNA processing occurred in models for DM1 and Alzheimer's disease (AD) including EpA960/CaMKII-Cre mice of either sex and female APP/PS1 and THY-Tau22 mice. Our results identify a regulatory mechanism for MBNL2 downregulation and suggest that calpain-2-mediated MBNL2 degradation accompanied by re-induction of a developmental RNA processing program may be a converging pathway to neurodegeneration.SIGNIFICANCE STATEMENT Neurologic diseases share many features during disease progression, such as cognitive decline and brain atrophy, which suggests a common pathway for developing degenerative features. Here, we show that the neurodegenerative conditions glutamate-induced excitotoxicity and dysregulated calcium homeostasis induced translocation of the cysteine protease calpain-2 into the nucleus, resulting in MBNL2 degradation and reversal of MBNL2-regulated RNA processing to an embryonic pattern. Knock-down or inhibition of nuclear translocation of calpain-2 prevented MBNL2 degradation and maintained MBNL2-regulated RNA processing in the adult pattern. Models of myotonic dystrophy and Alzheimer's disease (AD) also showed calpain-2-mediated MBNL2 degradation and a developmental RNA processing program. Our studies suggest MBNL2 function disrupted by calpain-2 as a common pathway, thus providing an alternative therapeutic strategy for neurodegeneration.
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Affiliation(s)
- Lee-Hsin Wang
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 11529, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Yu Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Mei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Luc Buée
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche-S1172, "Alzheimer & Tauopathies", University of Lille, 59045, Lille, France
| | - Nicolas Sergeant
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche-S1172, "Alzheimer & Tauopathies", University of Lille, 59045, Lille, France
| | - David Blum
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche-S1172, "Alzheimer & Tauopathies", University of Lille, 59045, Lille, France
| | - Yijuang Chern
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 11529, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 11529, Taiwan
| | - Guey-Shin Wang
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 11529, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 11529, Taiwan
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44
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Lee KY, Seah C, Li C, Chen YF, Chen CY, Wu CI, Liao PC, Shyu YC, Olafson HR, McKee KK, Wang ET, Yeh CH, Wang CH. Mice lacking MBNL1 and MBNL2 exhibit sudden cardiac death and molecular signatures recapitulating myotonic dystrophy. Hum Mol Genet 2022; 31:3144-3160. [PMID: 35567413 PMCID: PMC9476621 DOI: 10.1093/hmg/ddac108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/22/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Myotonic dystrophy (DM) is caused by expansions of C(C)TG repeats in the non-coding regions of the DMPK and CNBP genes, and DM patients often suffer from sudden cardiac death due to lethal conduction block or arrhythmia. Specific molecular changes that underlie DM cardiac pathology have been linked to repeat-associated depletion of Muscleblind-like (MBNL) 1 and 2 proteins and upregulation of CUGBP, Elav-like family member 1 (CELF1). Hypothesis solely targeting MBNL1 or CELF1 pathways that could address all the consequences of repeat expansion in heart remained inconclusive, particularly when the direct cause of mortality and results of transcriptome analyses remained undetermined in Mbnl compound knockout (KO) mice with cardiac phenotypes. Here, we develop Myh6-Cre double KO (DKO) (Mbnl1−/−; Mbnl2cond/cond; Myh6-Cre+/−) mice to eliminate Mbnl1/2 in cardiomyocytes and observe spontaneous lethal cardiac events under no anesthesia. RNA sequencing recapitulates DM heart spliceopathy and shows gene expression changes that were previously undescribed in DM heart studies. Notably, immunoblotting reveals a nearly 6-fold increase of Calsequestrin 1 and 50% reduction of epidermal growth factor proteins. Our findings demonstrate that complete ablation of MBNL1/2 in cardiomyocytes is essential for generating sudden death due to lethal cardiac rhythms and reveal potential mechanisms for DM heart pathogenesis.
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Affiliation(s)
- Kuang-Yung Lee
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Carol Seah
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Ching Li
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Yu-Fu Chen
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Chwen-Yu Chen
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Ching-I Wu
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Po-Cheng Liao
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Yu-Chiau Shyu
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan.,Department of Nursing, Chang Gung University of Science and Technology, Taoyuan City, Taiwan
| | - Hailey R Olafson
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL. 32610, USA
| | - Kendra K McKee
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL. 32610, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL. 32610, USA
| | - Chi-Hsiao Yeh
- Department of Thoracic and Cardiovascular Surgery, Chang Gung Memorial Hospital, Linko Branch, Taoyuan, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Chao-Hung Wang
- Division of Cardiology, Department of Internal Medicine, Heart Failure Research Center, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
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45
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The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. PLoS Biol 2022; 20:e3001615. [PMID: 35476669 PMCID: PMC9084524 DOI: 10.1371/journal.pbio.3001615] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 05/09/2022] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process of evolutionary specialization in eutherian mammals resulting in the emergence of a novel placental function for the gene. Mbnl3 belongs to a family of RNA-binding proteins whose members regulate multiple aspects of RNA metabolism. We find that, in eutherians, while both Mbnl3 and its paralog Mbnl2 are strongly expressed in placenta, Mbnl3 expression has been lost from nonplacental tissues in association with the evolution of a novel promoter. Moreover, Mbnl3 has undergone accelerated protein sequence evolution leading to changes in its RNA-binding specificities and cellular localization. While Mbnl2 and Mbnl3 share partially redundant roles in regulating alternative splicing, polyadenylation site usage and, in turn, placenta maturation, Mbnl3 has also acquired novel biological functions. Specifically, Mbnl3 knockout (M3KO) alone results in increased placental growth associated with higher Myc expression. Furthermore, Mbnl3 loss increases fetal resource allocation during limiting conditions, suggesting that location of Mbnl3 on the X chromosome has led to its role in limiting placental growth, favoring the maternal side of the parental genetic conflict.
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46
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Pamudurti NR, Patop IL, Krishnamoorthy A, Bartok O, Maya R, Lerner N, Ashwall-Fluss R, Konakondla JVV, Beatus T, Kadener S. circMbl functions in cis and in trans to regulate gene expression and physiology in a tissue-specific fashion. Cell Rep 2022; 39:110740. [PMID: 35476987 PMCID: PMC9352392 DOI: 10.1016/j.celrep.2022.110740] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 11/03/2022] Open
Abstract
Muscleblind (mbl) is an essential muscle and neuronal splicing regulator. Mbl hosts multiple circular RNAs (circRNAs), including circMbl, which is conserved from flies to humans. Here, we show that mbl-derived circRNAs are key regulators of MBL by cis- and trans-acting mechanisms. By generating fly lines to specifically modulate the levels of all mbl RNA isoforms, including circMbl, we demonstrate that the two major mbl protein isoforms, MBL-O/P and MBL-C, buffer their own levels by producing different types of circRNA isoforms in the eye and fly brain, respectively. Moreover, we show that circMbl has unique functions in trans, as knockdown of circMbl results in specific morphological and physiological phenotypes. In addition, depletion of MBL-C or circMbl results in opposite behavioral phenotypes, showing that they also regulate each other in trans. Together, our results illuminate key aspects of mbl regulation and uncover cis and trans functions of circMbl in vivo.
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Affiliation(s)
| | | | | | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Roni Maya
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Noam Lerner
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Reut Ashwall-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Tsevi Beatus
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sebastian Kadener
- Biology Department, Brandeis University, Waltham, MA 02454, USA; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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47
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Molecular Therapies for Myotonic Dystrophy Type 1: From Small Drugs to Gene Editing. Int J Mol Sci 2022; 23:ijms23094622. [PMID: 35563013 PMCID: PMC9101876 DOI: 10.3390/ijms23094622] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy affecting many different body tissues, predominantly skeletal and cardiac muscles and the central nervous system. The expansion of CTG repeats in the DM1 protein-kinase (DMPK) gene is the genetic cause of the disease. The pathogenetic mechanisms are mainly mediated by the production of a toxic expanded CUG transcript from the DMPK gene. With the availability of new knowledge, disease models, and technical tools, much progress has been made in the discovery of altered pathways and in the potential of therapeutic intervention, making the path to the clinic a closer reality. In this review, we describe and discuss the molecular therapeutic strategies for DM1, which are designed to directly target the CTG genomic tract, the expanded CUG transcript or downstream signaling molecules.
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48
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Degener MJF, van Cruchten RTP, Otero BA, Wang E, Wansink DG, ‘t Hoen PAC. A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. NAR Genom Bioinform 2022; 4:lqac016. [PMID: 35274098 PMCID: PMC8903011 DOI: 10.1093/nargab/lqac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/28/2022] [Accepted: 02/13/2022] [Indexed: 11/14/2022] Open
Abstract
In patients with myotonic dystrophy type 1 (DM1), dysregulation of RNA-binding proteins like MBNL and CELF1 leads to alternative splicing of exons and is thought to induce a return to fetal splicing patterns in adult tissues, including the central nervous system (CNS). To comprehensively evaluate this, we created an atlas of developmentally regulated splicing patterns in the frontal cortex of healthy individuals and DM1 patients, by combining RNA-seq data from BrainSpan, GTEx and DM1 patients. Thirty-four splice events displayed an inclusion pattern in DM1 patients that is typical for the fetal situation in healthy individuals. The regulation of DM1-relevant splicing patterns could partly be explained by changes in mRNA expression of the splice regulators MBNL1, MBNL2 and CELF1. On the contrary, interindividual differences in splicing patterns between healthy adults could not be explained by differential expression of these splice regulators. Our findings lend transcriptome-wide evidence to the previously noted shift to fetal splicing patterns in the adult DM1 brain as a consequence of an imbalance in antagonistic MBNL and CELF1 activities. Our atlas serves as a solid foundation for further study and understanding of the cognitive phenotype in patients.
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Affiliation(s)
- Max J F Degener
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Remco T P van Cruchten
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Brittney A Otero
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, FL 32610-0266 Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, FL 32610-0266 Gainesville, FL, USA
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Peter A C ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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49
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Soltanzadeh P. Myotonic Dystrophies: A Genetic Overview. Genes (Basel) 2022; 13:367. [PMID: 35205411 PMCID: PMC8872148 DOI: 10.3390/genes13020367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
Myotonic dystrophies (DM) are the most common muscular dystrophies in adults, which can affect other non-skeletal muscle organs such as the heart, brain and gastrointestinal system. There are two genetically distinct types of myotonic dystrophy: myotonic dystrophy type 1 (DM1) and myotonic dystrophy type 2 (DM2), both dominantly inherited with significant overlap in clinical manifestations. DM1 results from CTG repeat expansions in the 3'-untranslated region (3'UTR) of the DMPK (dystrophia myotonica protein kinase) gene on chromosome 19, while DM2 is caused by CCTG repeat expansions in intron 1 of the CNBP (cellular nucleic acid-binding protein) gene on chromosome 3. Recent advances in genetics and molecular biology, especially in the field of RNA biology, have allowed better understanding of the potential pathomechanisms involved in DM. In this review article, core clinical features and genetics of DM are presented followed by a discussion on the current postulated pathomechanisms and therapeutic approaches used in DM, including the ones currently in human clinical trial phase.
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Affiliation(s)
- Payam Soltanzadeh
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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Kajdasz A, Niewiadomska D, Sekrecki M, Sobczak K. Distribution of alternative untranslated regions within the mRNA of the CELF1 splicing factor affects its expression. Sci Rep 2022; 12:190. [PMID: 34996980 PMCID: PMC8742084 DOI: 10.1038/s41598-021-03901-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/03/2021] [Indexed: 01/09/2023] Open
Abstract
CUG-binding protein, ELAV-like Family Member 1 (CELF1) plays an important role during the development of different tissues, such as striated muscle and brain tissue. CELF1 is an RNA-binding protein that regulates RNA metabolism processes, e.g., alternative splicing, and antagonizes other RNA-binding proteins, such as Muscleblind-like proteins (MBNLs). Abnormal activity of both classes of proteins plays a crucial role in the pathogenesis of myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults. In this work, we show that alternative splicing of exons forming both the 5' and 3' untranslated regions (UTRs) of CELF1 mRNA is efficiently regulated during development and tissue differentiation and is disrupted in skeletal muscles in the context of DM1. Alternative splicing of the CELF1 5'UTR leads to translation of two potential protein isoforms that differ in the lengths of their N-terminal domains. We also show that the MBNL and CELF proteins regulate the distribution of mRNA splicing isoforms with different 5'UTRs and 3'UTRs and affect the CELF1 expression by changing its sensitivity to specific microRNAs or RNA-binding proteins. Together, our findings show the existence of different mechanisms of regulation of CELF1 expression through the distribution of various 5' and 3' UTR isoforms within CELF1 mRNA.
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Affiliation(s)
- Arkadiusz Kajdasz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Daria Niewiadomska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Michal Sekrecki
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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