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Beccacece L, Pallotti S, Li Y, Huang J, Pasotti L, Napolioni V. Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture. BMC Genomics 2025; 26:524. [PMID: 40410671 PMCID: PMC12102845 DOI: 10.1186/s12864-025-11702-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Accepted: 05/12/2025] [Indexed: 05/25/2025] Open
Abstract
BACKGROUND The Anterior Cruciate Ligament (ACL) plays a critical role in maintaining the musculoskeletal stability of the knee. Its injury has been linked to an increased risk of developing osteoarthritis. This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. Differential gene expression analysis was performed for each dataset, producing a genome-wide transcriptional signature of fold-change significance for individual genes. Stouffer's method was used to integrate the results, identifying genes significantly deregulated across all species. Additionally, gene-set enrichment analysis revealed pathways that were consistently upregulated or downregulated. RESULTS A positive correlation in expression was observed between human and the other three species (r2 = 0.177-0.305, p-value ≤ 2.7 × 10- 113), identifying 210 genes as the most consistently up- and down-regulated in response to ACL rupture (p-adjusted ≤ 1.27 × 10- 23). These genes are primarily involved in cellular mitosis, collagen pathways, and cartilage development. Furthermore, 60 pathways were found to be significantly up- or down-regulated across all species (p-adjusted ≤ 4.57 × 10- 4). Among these, the upregulation of inhibition of bone mineralization (p-adjusted ≤ 2.99 × 10- 6) aligns with previous findings on the reduction of subchondral bone mineral density following ACL rupture. CONCLUSIONS This study highlights that distinct species exhibit common molecular responses to ACL rupture, underscoring the value of mice, dogs, and rabbits as potential translational model organisms for ACL rupture research. Furthermore, the identified genes and pathways highlight the molecular mechanisms underlying ACL rupture.
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Affiliation(s)
- Livia Beccacece
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile da Varano III, Camerino, 62032, Italy
| | - Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile da Varano III, Camerino, 62032, Italy
| | - Yiyun Li
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile da Varano III, Camerino, 62032, Italy
| | - Jie Huang
- School of Public Health and Emergency Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Leonardo Pasotti
- Complex Orthopedics and Traumatology Unit, AST Macerata, Camerino Hospital, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile da Varano III, Camerino, 62032, Italy.
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Hicks SM, Frias JA, Mishra SK, Scotti M, Muscato DR, Valero MC, Adams LM, Cleary JD, Nakamori M, Wang E, Berglund JA. Alternative splicing dysregulation across tissue and therapeutic approaches in a mouse model of myotonic dystrophy type 1. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102338. [PMID: 39391766 PMCID: PMC11465180 DOI: 10.1016/j.omtn.2024.102338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024]
Abstract
Myotonic dystrophy type 1 (DM1), the leading cause of adult-onset muscular dystrophy, is caused by a CTG repeat expansion. Expression of the repeat causes widespread alternative splicing (AS) defects and downstream pathogenesis, including significant skeletal muscle impacts. The HSA LR mouse model plays a significant role in therapeutic development. This mouse model features a transgene composed of approximately 220 interrupted CTG repeats, which results in skeletal muscle pathology that mirrors DM1. To better understand this model and the growing number of therapeutic approaches developed with it, we performed a meta-analysis of publicly available RNA sequencing data for AS changes across three widely examined skeletal muscles: quadriceps, gastrocnemius, and tibialis anterior. Our analysis demonstrated that transgene expression correlated with the extent of splicing dysregulation across these muscles from gastrocnemius (highest), quadriceps (medium), to tibialis anterior (lowest). We identified 95 splicing events consistently dysregulated across all examined datasets. Comparison of splicing rescue across seven therapeutic approaches showed a range of rescue across the 95 splicing events from the three muscle groups. This analysis contributes to our understanding of the HSA LR model and the growing number of therapeutic approaches currently in preclinical development for DM1.
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Affiliation(s)
- Sawyer M. Hicks
- Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jesus A. Frias
- Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Subodh K. Mishra
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Marina Scotti
- Center for NeuroGenetics and Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Derek R. Muscato
- Center for NeuroGenetics and Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - M. Carmen Valero
- Center for NeuroGenetics and Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Leanne M. Adams
- Center for NeuroGenetics and Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - John D. Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Eric Wang
- Center for NeuroGenetics and Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - J. Andrew Berglund
- Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, USA
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Xie X, Zhang G, Liu N. Comprehensive analysis of abnormal methylation modification differential expression mRNAs between low-grade and high-grade intervertebral disc degeneration and its correlation with immune cells. Ann Med 2024; 56:2357742. [PMID: 38819022 PMCID: PMC11146251 DOI: 10.1080/07853890.2024.2357742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IDD) is an important cause of low back pain. The aim of this study is to identify the potential molecular mechanism of abnormal methylation-modified DNA in the progression of IDD, hoping to contribute to the diagnosis and management of IDD. METHODS Low-grade IDD (grade I-II) and high-grade IDD (grade III-V) data were downloaded from GSE70362 and GSE129789 datasets. The abnormally methylated modified differentially expressed mRNAs (DEmRNAs) were identified by differential expression analysis (screening criteria were p < .05 and |logFC| > 1) and differential methylation analysis (screening criteria were p < .05 and |δβ| > 0.1). The classification models were constructed, and the receiver operating characteristic analysis was also carried out. In addition, functional enrichment analysis and immune correlation analysis were performed and the miRNAs targeted for the abnormally methylated DEmRNAs were predicted. Finally, expression validation was performed using real-time PCR. RESULTS Compared with low-grade IDD, seven abnormal methylation-modified DEmRNAs (AOX1, IBSP, QDPR, ABLIM1, CRISPLD2, ACTC1 and EMILIN1) were identified in high-grade IDD, and the classification models of random forests (RF) and support vector machine (SVM) were constructed. Moreover, seven abnormal methylation-modified DEmRNAs and classification models have high diagnostic accuracy (area under the curve [AUC] > 0.8). We also found that AUC values of single abnormal methylation-modified DEmRNA were all lower than those of RF and SVM classification models. Pearson correlation analysis found that macrophages M2 and EMILIN1 had significant negative correlation, while macrophages M2 and IBSP had significant positive correlation. In addition, four targeted relationship pairs (hsa-miR-4728-5p-QDPR, hsa-miR-4533-ABLIM1, hsa-miR-4728-5p-ABLIM1 and hsa-miR-4534-CRISPLD2) and multiple signalling pathways (for example, PI3K-AKT signalling pathway, osteoclast differentiation and calcium signalling pathway) were also identified that may be involved in the progression of IDD. CONCLUSION The identification of abnormal methylation-modified DEmRNAs and the construction of classification models in this study were helpful for the diagnosis and management of IDD progression.
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Affiliation(s)
- Xuehu Xie
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Guoqiang Zhang
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Ning Liu
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
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4
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Qin WJ, Shi JJ, Chen RY, Li CY, Liu YJ, Lu JF, Yang GJ, Cao JF, Chen J. Curriculum vitae of CUG binding protein 1 (CELF1) in homeostasis and diseases: a systematic review. Cell Mol Biol Lett 2024; 29:32. [PMID: 38443798 PMCID: PMC10916161 DOI: 10.1186/s11658-024-00556-y] [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: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
RNA-binding proteins (RBPs) are kinds of proteins with either singular or multiple RNA-binding domains (RBDs), and they can assembly into ribonucleic acid-protein complexes, which mediate transportation, editing, splicing, stabilization, translational efficiency, or epigenetic modifications of their binding RNA partners, and thereby modulate various physiological and pathological processes. CUG-BP, Elav-like family 1 (CELF1) is a member of the CELF family of RBPs with high affinity to the GU-rich elements in mRNA, and thus exerting control over critical processes including mRNA splicing, translation, and decay. Mounting studies support that CELF1 is correlated with occurrence, genesis and development and represents a potential therapeutical target for these malignant diseases. Herein, we present the structure and function of CELF1, outline its role and regulatory mechanisms in varieties of homeostasis and diseases, summarize the identified CELF1 regulators and their structure-activity relationships, and prospect the current challenges and their solutions during studies on CELF1 functions and corresponding drug discovery, which will facilitate the establishment of a targeted regulatory network for CELF1 in diseases and advance CELF1 as a potential drug target for disease therapy.
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Affiliation(s)
- Wan-Jia Qin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jin-Jin Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Ru-Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jia-Feng Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Yoon YM, Velez TE, Upadhyay V, Vazquez SE, Lee CT, Selvan KC, Law CS, Blaine KM, Hollinger MK, Decker DC, Clark MR, Strek ME, Guzy RD, Adegunsoye A, Noth I, Wolters PJ, Anderson M, DeRisi JL, Shum AK, Sperling AI. Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.08.23289640. [PMID: 37214861 PMCID: PMC10197719 DOI: 10.1101/2023.05.08.23289640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Interstitial lung diseases (ILD) are heterogeneous conditions that may lead to progressive fibrosis and death of affected individuals. Despite diversity in clinical manifestations, enlargement of lung-associated lymph nodes (LLN) in fibrotic ILD patients predicts worse survival. Herein, we revealed a common adaptive immune landscape in LLNs of all ILD patients, characterized by highly activated germinal centers and antigen-activated T cells including regulatory T cells (Tregs). In support of these findings, we identified serum reactivity to 17 candidate auto-antigens in ILD patients through a proteome-wide screening using phage immunoprecipitation sequencing. Autoantibody responses to actin binding LIM protein 1 (ABLIM1), a protein highly expressed in aberrant basaloid cells of fibrotic lungs, were correlated with LLN frequencies of T follicular helper cells and Tregs in ILD patients. Together, we demonstrate that end-stage ILD patients have converging immune mechanisms, in part driven by antigen-specific immune responses, which may contribute to disease progression.
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Affiliation(s)
- Young me Yoon
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Tania E. Velez
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Vaibhav Upadhyay
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Sara E. Vazquez
- University of California San Francisco and Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Cathryn T. Lee
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | | | - Christopher S. Law
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Kelly M. Blaine
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Maile K. Hollinger
- University of Chicago, Department of Medicine, Chicago, IL 60637
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Donna C. Decker
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Marcus R. Clark
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Mary E. Strek
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Robert D. Guzy
- University of Wisconsin at Madison, Department of Medicine, Madison, WI 53792
| | | | - Imre Noth
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Paul J. Wolters
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Mark Anderson
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Joseph L. DeRisi
- University of California San Francisco and Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Anthony K. Shum
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Anne I. Sperling
- University of Chicago, Department of Medicine, Chicago, IL 60637
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
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6
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Actin-Binding LIM 1 (ABLIM1) Inhibits Glioblastoma Progression and Serves as a Novel Prognostic Biomarker. DISEASE MARKERS 2022; 2022:9516808. [PMID: 36583064 PMCID: PMC9794427 DOI: 10.1155/2022/9516808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Background Glioma is the most prevalent malignant brain tumor in adult humans, and glioblastoma (GBM) is the most malignant type. The actin-binding LIM 1 (ABLIM1) protein can modulate actin polymerization, which is essential for the cell proliferation and migration. We aim to investigate ABLIM1 expression, function, and clinical significance in GBM. Methods The ABLIM1 mRNA level was extracted from the TCGA and GTEx online databases. The ABLIM1 protein expression level was explored using immunohistochemistry staining in a GBM cohort enrolled in our hospital (n = 104). The patient survival and prognostic factors were determined using the Kaplan-Meier method and multivariate Cox hazard proportional analysis, respectively. Two human GBM cell lines, U87 and U251 cells, were utilized for ABLIM1 overexpression and cell proliferation analyses. A subcutaneous xenograft model was generated using nude mice to validate the tumor-related effect of ABLIM1 in vivo. Results ABLIM1 exhibited a significantly lower mRNA level in GBM than in other glioma or normal brain tissues. Higher ABLIM1 protein level was correlated with smaller GBM tumor size and better cancer-specific survival (CSS). Multivariate analysis identified ABLIM1 as a novel independent prognostic factor for GBM prognosis. ABLIM1 overexpression significantly inhibits U87 and U251 cell proliferation and colony formation. Consistently, ABLIM1 exerted tumor-suppressing functions in mice models. Conclusion ABLIM1 plays antitumor roles in GBM progression and could be served as a novel biomarker to help predict GBM prognosis.
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7
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In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLoS Comput Biol 2022; 18:e1009918. [PMID: 35226669 PMCID: PMC8912908 DOI: 10.1371/journal.pcbi.1009918] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/10/2022] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.
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Disrupting the Molecular Pathway in Myotonic Dystrophy. Int J Mol Sci 2021; 22:ijms222413225. [PMID: 34948025 PMCID: PMC8708683 DOI: 10.3390/ijms222413225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/26/2023] Open
Abstract
Myotonic dystrophy is the most common muscular dystrophy in adults. It consists of two forms: type 1 (DM1) and type 2 (DM2). DM1 is associated with a trinucleotide repeat expansion mutation, which is transcribed but not translated into protein. The mutant RNA remains in the nucleus, which leads to a series of downstream abnormalities. DM1 is widely considered to be an RNA-based disorder. Thus, we consider three areas of the RNA pathway that may offer targeting opportunities to disrupt the production, stability, and degradation of the mutant RNA.
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Poulin H, Mercier A, Djemai M, Pouliot V, Deschenes I, Boutjdir M, Puymirat J, Chahine M. iPSC-derived cardiomyocytes from patients with myotonic dystrophy type 1 have abnormal ion channel functions and slower conduction velocities. Sci Rep 2021; 11:2500. [PMID: 33510259 PMCID: PMC7844414 DOI: 10.1038/s41598-021-82007-8] [Citation(s) in RCA: 6] [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: 03/20/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Cardiac complications such as electrical abnormalities including conduction delays and arrhythmias are the main cause of death in individuals with Myotonic Dystrophy type 1 (DM1). We developed a disease model using iPSC-derived cardiomyocytes (iPSC-CMs) from a healthy individual and two DM1 patients with different CTG repeats lengths and clinical history (DM1-1300 and DM1-300). We confirmed the presence of toxic RNA foci and mis-spliced MBNL1/2 transcripts in DM1 iPSC-CMs. In DM1-1300, we identified a switch in the cardiac sodium channel SCN5A from the adult to the neonatal isoform. The down-regulation of adult SCN5A isoforms is consistent with a shift in the sodium current activation to depolarized potentials observed in DM1-1300. L-type calcium current density was higher in iPSC-CMs from DM1-1300, which is correlated with the overexpression of the CaV1.2 transcript and proteins. Importantly, INa and ICaL dysfunctions resulted in prolonged action potentials duration, slower velocities, and decreased overshoots. Optical mapping analysis revealed a slower conduction velocity in DM1-1300 iPSC-CM monolayers. In conclusion, our data revealed two distinct ions channels perturbations in DM1 iPSC-CM from the patient with cardiac dysfunction, one affecting Na+ channels and one affecting Ca2+ channels. Both have an impact on cardiac APs and ultimately on heart conduction.
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Affiliation(s)
- Hugo Poulin
- CERVO Brain Research Centre, Quebec, QC, Canada
| | | | | | | | - Isabelle Deschenes
- Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, USA
| | - Mohamed Boutjdir
- Cardiovascular Research Program, VA New York Harbor Healthcare System, Brooklyn, New York, NY, USA
- Department of Medicine, Cell Biology and Pharmacology, State University of New York Downstate Medical Center, New York, NY, USA
- Depatrment of Medicine, NYU School of Medicine, New York, NY, USA
| | - Jack Puymirat
- Unit of Human Genetics, Hôpital de l'Enfant-Jésus, CHU Research Center, Quebec, QC, Canada
| | - Mohamed Chahine
- CERVO Brain Research Centre, Quebec, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec, QC, Canada.
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 DOI: 10.1101/401604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/24/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3' UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3-5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3' UTR in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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11
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 PMCID: PMC7780154 DOI: 10.1016/j.celrep.2020.108531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3′ UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3–5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3′ UTR in vivo. Rieger et al. assay the function of the RNA-binding protein CELF6 by defining its targets in the brain. They show that CELF6 largely binds 3′ UTRs of synaptic mRNAs. Using a massively parallel reporter assay, they further show that CELF6 and other CELFs are associated with lower mRNA abundance and that targets are derepressed in Celf6-knockout mice in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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12
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Chen M, Yan J, Han Q, Luo J, Zhang Q. Identification of hub-methylated differentially expressed genes in patients with gestational diabetes mellitus by multi-omic WGCNA basing epigenome-wide and transcriptome-wide profiling. J Cell Biochem 2019; 121:3173-3184. [PMID: 31886571 DOI: 10.1002/jcb.29584] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022]
Abstract
Gestational diabetes mellitus (GDM), defined as dysglycaemia that is detected during pregnancy for the first time, has become a global health burden. GDM was found to be correlated to epigenetic changes, which would cause abnormal expression of placental genes. In the present study, we performed multi-omic weighted gene coexpression network analysis (WGCNA) to systematically identify the hub genes for GDM using both epigenome- and transcriptome-wide microarray data. Two microarray datasets (GSE70493 and GSE70494) were downloaded from the Gene Expression Omnibus (GEO) database. GEO2R was used to screen differentially expressed genes (DEGs) and differentially methylated genes (DMGs) between normal and GDM samples, separately. The results of WGCNA found that 15 modules were identified and the MEblack module had a significantly negative correlation with GDM (r = -.28, P = .03). GO enrichment analysis by BinGO of the MEblack module showed that genes were primarily enriched for the presentation of antigen processing, regulation of interferon-α production and interferon-γ-mediated signaling pathway. By comparing the DEGs, DMGs and hub genes in the coexpression network, we identified five hypermethylated, lowly expressed genes (ABLIM1, GRHL1, HLA-F, NDRG1, and SASH1) and one hypomethylated, highly expressed gene (EIF3F) as GDM-related hub DMGs. Moreover, the expression levels of ABLIM1, GRHL1, HLA-F, NDRG1, and SASH11 in the GDM patients and healthy controls were validated by a real-time quantitative polymerase chain reaction. Finally, gene set enrichment analysis showed that the biological function of cardiac muscle contraction was enriched for four GDM-related hub DMGs (ABLIM1, GRHL1, NDRG1, and SASH1). Analysis of this study revealed that dysmethylated hub genes in GDM placentas might affect the placental function and thus, take part in GDM pathogenesis and fetal cardiac development.
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Affiliation(s)
- Min Chen
- Department of Obstetrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jianying Yan
- Department of Obstetrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Qing Han
- Department of Obstetrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jinying Luo
- Department of Obstetrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Qinjian Zhang
- Department of Obstetrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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13
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Wang T, Liu Q, Duan L. MBNL1 regulates resistance of HeLa cells to cisplatin via Nrf2. Biochem Biophys Res Commun 2019; 522:763-769. [PMID: 31791583 DOI: 10.1016/j.bbrc.2019.11.162] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/24/2019] [Indexed: 12/30/2022]
Abstract
Chemotherapy is an important method in the treatment of cervical cancer, but some patients will face drug resistance, which often indicates a poor prognosis. Moreover, there is no complete solution at present. Therefore, it is urgent to study the drug resistance mechanism of cervical cancer. Based on sequencing data mining, we predicted that MBNL1 might be involved in the occurrence and poor prognosis of cervical cancer, and verifed that MBNL1 could regulate the resistance of HeLa cells to cisplatin via Nrf2. In addition, we demonstrated that MBNL1 up regulated the degradation of Nrf2 protein by increasing the mRNA stability of Cul3. These results can provide theoretical basis for clinical development of new diagnosis and treatment targets for cisplatin resistance.
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Affiliation(s)
- Ting Wang
- Obstetrics and Gynecology Department, Yuncheng County People's Hospital, Shandong Province, China
| | - Qiong Liu
- Clinical Laboratory, Hubei University Hospital, Hubei Province, China
| | - Lian Duan
- Surgery, Hubei University Hospital, Hubei Province, China.
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14
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Liu Z, Han S, Shen X, Wang Y, Cui C, He H, Chen Y, Zhao J, Li D, Zhu Q, Yin H. The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. Int J Biol Sci 2019; 15:1404-1418. [PMID: 31337971 PMCID: PMC6643139 DOI: 10.7150/ijbs.35073] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/26/2019] [Indexed: 12/27/2022] Open
Abstract
Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
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15
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Belanger K, Nutter CA, Li J, Yu P, Kuyumcu-Martinez MN. A developmentally regulated spliced variant of PTBP1 is upregulated in type 1 diabetic hearts. Biochem Biophys Res Commun 2018; 509:384-389. [PMID: 30594394 DOI: 10.1016/j.bbrc.2018.12.150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 01/09/2023]
Abstract
Alternative splicing (AS) is dysregulated in Type 1 diabetic (T1D) hearts but mechanisms responsible are unclear. Here, we provide evidence that the RNA binding protein (RBP) PTBP1 is modulated in adult T1D hearts contributing to AS changes. We show that a spliced variant of PTBP1 that is highly expressed in normal newborn mouse hearts is aberrantly expressed in adult T1D mouse hearts. Comparing known PTBP1-target datasets to our T1D mouse transcriptome datasets, we discovered a group of genes with PTBP1 binding sites in their pre-mRNAs that are differentially spliced in T1D mouse hearts. We demonstrated that inducible expression of diabetes-induced PTBP1 spliced variant has less repressive splicing function. Notably, PTBP1 regulates AS of some of its targets antagonistically to RBFOX2. In sum, our results indicate that diabetic conditions disrupt developmental regulation of PTBP1 leading to differential AS of PTBP1 target genes. Identification of PTBP1 and PTBP1-regulated RNA networks can provide RNA-based therapies for the treatment of diabetes cardiac complications.
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Affiliation(s)
- KarryAnne Belanger
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Curtis A Nutter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jin Li
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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16
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Belanger K, Nutter CA, Li J, Tasnim S, Liu P, Yu P, Kuyumcu-Martinez MN. CELF1 contributes to aberrant alternative splicing patterns in the type 1 diabetic heart. Biochem Biophys Res Commun 2018; 503:3205-3211. [PMID: 30158053 DOI: 10.1016/j.bbrc.2018.08.126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 08/20/2018] [Indexed: 12/20/2022]
Abstract
Dysregulated alternative splicing (AS) that contributes to diabetes pathogenesis has been identified, but little is known about the RNA binding proteins (RBPs) involved. We have previously found that the RBP CELF1 is upregulated in the diabetic heart; however, it is unclear if CELF1 contributes to diabetes-induced AS changes. Utilizing genome wide approaches, we identified extensive changes in AS patterns in Type 1 diabetic (T1D) mouse hearts. We discovered that many aberrantly spliced genes in T1D hearts have CELF1 binding sites. CELF1-regulated AS affects key genes within signaling pathways relevant to diabetes pathogenesis. Disruption of CELF1 binding sites impairs AS regulation by CELF1. In sum, our results indicate that CELF1 target RNAs are aberrantly spliced in the T1D heart leading to abnormal gene expression. These discoveries pave the way for targeting RBPs and their RNA networks as novel therapies for cardiac complications of diabetes.
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Affiliation(s)
- KarryAnne Belanger
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Curtis A Nutter
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jin Li
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Sadia Tasnim
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Peiru Liu
- Ball High School, Galveston, TX, 77555, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Department of Neuroscience,Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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17
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Narahara H, Sakai E, Yamaguchi Y, Narahara S, Iwatake M, Okamoto K, Yoshida N, Tsukuba T. Actin binding LIM 1 (abLIM1) negatively controls osteoclastogenesis by regulating cell migration and fusion. J Cell Physiol 2018; 234:486-499. [PMID: 29904924 DOI: 10.1002/jcp.26605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/16/2018] [Indexed: 12/22/2022]
Abstract
Actin binding LIM 1 (abLIM1) is a cytoskeletal actin-binding protein that has been implicated in interactions between actin filaments and cytoplasmic targets. Previous biochemical and cytochemical studies have shown that abLIM1 interacts and co-localizes with F-actin in the retina and muscle. However, whether abLIM1 regulates osteoclast differentiation has not yet been elucidated. In this study, we examined the role of abLIM1 in osteoclast differentiation and function. We found that abLIM1 expression was upregulated during receptor activator of nuclear factor kappa-B ligand (RANKL)-induced osteoclast differentiation, and that a novel transcript of abLIM1 was exclusively expressed in osteoclasts. Overexpression of abLIM1 in the murine monocytic cell line, RAW-D suppressed osteoclast differentiation and decreased expression of several osteoclast-marker genes. By contrast, small interfering RNA-induced knockdown of abLIM1 enhanced the formation of multinucleated osteoclasts and markedly increased the expression of the osteoclast-marker genes. Mechanistically, abLIM1 regulated the localization of tubulin, migration, and fusion in osteoclasts. Thus, these results indicate that abLIM1 negatively controls osteoclast differentiation by regulating cell migration and fusion mediated via actin formation.
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Affiliation(s)
- Haruna Narahara
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Eiko Sakai
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yu Yamaguchi
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Shun Narahara
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Mayumi Iwatake
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kuniaki Okamoto
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Noriaki Yoshida
- Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takayuki Tsukuba
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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18
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 PMCID: PMC11323716 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D. Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J. Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S. Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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19
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Lee YH, Jhuang YL, Chen YL, Jeng YM, Yuan RH. Paradoxical overexpression of MBNL2 in hepatocellular carcinoma inhibits tumor growth and invasion. Oncotarget 2018; 7:65589-65601. [PMID: 27564110 PMCID: PMC5323177 DOI: 10.18632/oncotarget.11577] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/12/2016] [Indexed: 01/18/2023] Open
Abstract
Pre-mRNA alternative splicing is an essential step in the process of gene expression. It provides cells with the opportunity to create various protein isoforms. Disruptions of alternative splicing are associated with various diseases, including cancer. The muscleblind-like (MBNL) protein is a splicing regulatory protein. Overexpression of MBNL proteins in embryonic stem cells promotes differentiated cell-like alternative splicing patterns. We examined the expression level of MBNL2 in 143 resected HCCs using immunohistochemistry. MBNL2 was overexpressed in 51 (35.7%) HCCs. The overexpression of MBNL2 correlated with smaller tumor size (≤ 3 cm, P = 0.0108) and low tumor stage (Stage I, P = 0.0026), indicating that MBNL2 expression was lost in the late stage of HCC development. Furthermore, patients with MBNL2-positive HCCs had a borderline better 5-year overall survival (P = 0.0579). In non-cancerous liver parenchyma, MBNL2 was stained on the Canals of Hering and hepatocytes newly derived from hepatic progenitor cells. The overexpression of MBNL2 in Hep-J5 cells suppressed proliferation, tumorsphere formation, migration, and in vitro invasion, and also reduced in vivo tumor growth in NOD/SCID mice. In contrast, MBNL2 depletion with RNA interference in Huh7 cells increased in vitro migration and invasion, but did not enhance tumor growth. These results indicate that MBNL2 is a tumor suppressor in hepatocarcinogenesis.
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Affiliation(s)
- Yu-Hsin Lee
- Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Lin Jhuang
- Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Ling Chen
- Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yung-Ming Jeng
- Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Pathology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ray-Hwang Yuan
- Department of Surgery, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Integrated Diagnostics and Therapeutics, National Taiwan University Hospital, Taipei 10051, Taiwan
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20
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Novel Splicing Mutation in B3GAT3 Associated with Short Stature, GH Deficiency, Hypoglycaemia, Developmental Delay, and Multiple Congenital Anomalies. Case Rep Genet 2017; 2017:3941483. [PMID: 29318063 PMCID: PMC5727645 DOI: 10.1155/2017/3941483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 01/26/2023] Open
Abstract
B3GAT3, encoding β-1,3-glucuronyltransferase 3, has an important role in proteoglycan biosynthesis. Homozygous B3GAT3 mutations have been associated with short stature, skeletal deformities, and congenital heart defects. We describe for the first time a novel heterozygous splice site mutation in B3GAT3 contributing to severe short stature, growth hormone (GH) deficiency, recurrent ketotic hypoglycaemia, facial dysmorphism, and congenital heart defects. A female infant, born at 34 weeks' gestation to nonconsanguineous Caucasian parents with a birth weight of 1.9 kg, was noted to have cloacal abnormality, ventricular septal defect, pulmonary stenosis, and congenital sensorineural deafness. At 4 years of age, she was diagnosed with GH deficiency due to her short stature (height < 2.5 SD). MRI of the pituitary gland revealed a small anterior pituitary. She has multiple dysmorphic features: anteverted nares, small upturned nose, hypertelorism, slight frontal bossing, short proximal bones, hypermobile joints, and downslanting palpebral fissures. Whole exome sequencing (WES) was performed on the genomic DNA from the patient and biological mother. A heterozygous mutation in B3GAT3 (c.888+262T>G) in the invariant “GT” splice donor site was identified. This variant is considered to be pathogenic as it decreases the splicing efficiency in the mRNA.
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21
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Abstract
Muscleblind-like (MBNL) proteins bind to hundreds of pre- and mature mRNAs to regulate their alternative splicing, alternative polyadenylation, stability and subcellular localization. Once MBNLs are withheld from transcript regulation, cellular machineries generate products inapt for precise embryonal/adult developmental tasks and myotonic dystrophy, a devastating multi-systemic genetic disorder, develops. We have recently demonstrated that all three MBNL paralogs are capable of fine-tuning cellular content of one of the three MBNL paralogs, MBNL1, by binding to the first coding exon (e1) of its pre-mRNA. Intriguingly, this autoregulatory feedback loop grounded on alternative splicing of e1 appears to play a crucial role in delaying the onset of myotonic dystrophy. Here, we describe this process in the context of other autoregulatory and regulatory loops that maintain the content and diverse functions of MBNL proteins at optimal level in health and disease, thus supporting the overall cellular homeostasis.
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Affiliation(s)
- Patryk Konieczny
- a Department of Gene Expression , Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University , Poland
| | - Ewa Stepniak-Konieczna
- a Department of Gene Expression , Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University , Poland
| | - Krzysztof Sobczak
- a Department of Gene Expression , Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University , Poland
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22
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Russo J, Lee JE, López CM, Anderson J, Nguyen TMP, Heck AM, Wilusz J, Wilusz CJ. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One 2017; 12:e0170680. [PMID: 28129347 PMCID: PMC5271678 DOI: 10.1371/journal.pone.0170680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jerome E. Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina M. López
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - John Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thuy-mi P. Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adam M. Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Nakamura T, Ohsawa-Yoshida N, Zhao Y, Koebis M, Oana K, Mitsuhashi H, Ishiura S. Splicing of human chloride channel 1. Biochem Biophys Rep 2015; 5:63-69. [PMID: 28955807 PMCID: PMC5600464 DOI: 10.1016/j.bbrep.2015.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/28/2015] [Accepted: 11/09/2015] [Indexed: 11/21/2022] Open
Abstract
Expression of chloride channel 1 (CLCN1/ClC-1) in skeletal muscle is driven by alternative splicing, a process regulated in part by RNA-binding protein families MBNL and CELF. Aberrant splicing of CLCN1 produces many mRNAs, which were translated into inactive proteins, resulting in myotonia in myotonic dystrophy (DM), a genetic disorder caused by the expansion of a CTG or CCTG repeat. This increase in abnormal splicing variants containing exons 6B, 7A or the insertion of a TAG stop codon just before exon 7 leads to a decrease in expression of the normal splice pattern. The majority of studies examining splicing in CLCN1 have been performed using mouse Clcn1, as have investigations into the activation and suppression of normal splicing variant expression by MBNL1-3 and CELF3–6, respectively. In contrast, examinations of human CLCN1 have been less common due to the greater complexity of splicing patterns. Here, we constructed a minigene containing CLCN1 exons 5–7 and established a novel assay system to quantify the expression of the normal splicing variant of CLCN1 using real-time RT-PCR. Antisense oligonucleotides could promote normal CLCN1 alternative splicing but the effective sequence was different from that of Clcn1. This result differs from previous reports using Clcn1, highlighting the effect of differences in splicing patterns between mice and humans. Splicing of of human chloride channel 1 (CLCN1) was studied. Abnormal splicing variants were observed. Antisense oligonucleotides could promote normal CLCN1 splicing.
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Affiliation(s)
- Takumi Nakamura
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Natsumi Ohsawa-Yoshida
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yimeng Zhao
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Michinori Koebis
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kosuke Oana
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hiroaki Mitsuhashi
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Shoichi Ishiura
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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