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Kim EK, Lee SY, Kim Y, Ahn SM, Jang HH. Peroxiredoxin 1 post-transcriptionally regulates snoRNA expression. Free Radic Biol Med 2019; 141:1-9. [PMID: 31158443 DOI: 10.1016/j.freeradbiomed.2019.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 11/28/2022]
Abstract
Peroxiredoxin 1 (Prx1) is a member of the Prx family that detoxifies various peroxide substrates through conserved catalytic cysteine residues with the use of reducing equivalents. In addition to this well-known role of Prx1, we have previously demonstrated that Prx1 also has RNA-binding properties, but its function as an RNA-binding protein (RBP) remains unknown. To characterize the role of Prx1 as an RBP, we pulled down Prx1-RNA complexes and sequenced the target RNAs of Prx1. Through sequencing and further validation studies, we revealed that Prx1 binds to a specific subset of small nucleolar RNAs (snoRNAs) and regulates these molecules at the post-transcriptional level. We also found that active cysteine residues provide a structural and functional link between these two distinct functions of Prx1 (i.e., ROS scavenging and RNA-binding activities). Prx1 functions as a snoRNA-binding protein in its reduced state, and post-transcriptionally regulates the expression of a set of snoRNAs. However, when the active cysteine residues are oxidized, Prx1 loses its activity as a snoRNA-binding protein. This study is the first report describing the novel role of Prx1 as a post-transcriptional regulator of snoRNAs.
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Affiliation(s)
- Eun-Kyung Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea
| | - Sun Young Lee
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Yosup Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, 21999, Republic of Korea
| | - Sung-Min Ahn
- Department of Genome Medicine and Science, College of Medicine, Gachon University, Incheon, 21936, Republic of Korea; Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, 21565, Republic of Korea.
| | - Ho Hee Jang
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea; Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, 21999, Republic of Korea.
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2
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Transcriptional analysis reveals distinct subtypes in amyotrophic lateral sclerosis: implications for personalized therapy. Future Med Chem 2016; 7:1335-59. [PMID: 26144267 DOI: 10.4155/fmc.15.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable disease, caused by the loss of the upper and lower motor neurons. The lack of therapeutic progress is mainly due to the insufficient understanding of complexity and heterogeneity underlying the pathogenic mechanisms of ALS. Recently, we analyzed whole-genome expression profiles of motor cortex of sporadic ALS patients, classifying them into two subgroups characterized by differentially expressed genes and pathways. Some of the deregulated genes encode proteins, which are primary targets of drugs currently in preclinical or clinical studies for several clinical conditions, including neurodegenerative diseases. In this review, we discuss in-depth the potential role of these candidate targets in ALS pathogenesis, highlighting their possible relevance for personalized ALS treatments.
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3
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RNA-Binding Proteins Associated Molecular Mechanisms of Motor Neuron Degeneration Pathogenesis. Mol Biotechnol 2014; 56:779-86. [DOI: 10.1007/s12033-014-9785-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ricketts T, McGoldrick P, Fratta P, de Oliveira HM, Kent R, Phatak V, Brandner S, Blanco G, Greensmith L, Acevedo-Arozena A, Fisher EMC. A nonsense mutation in mouse Tardbp affects TDP43 alternative splicing activity and causes limb-clasping and body tone defects. PLoS One 2014; 9:e85962. [PMID: 24465814 PMCID: PMC3897576 DOI: 10.1371/journal.pone.0085962] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 12/03/2013] [Indexed: 12/11/2022] Open
Abstract
Mutations in TARDBP, encoding Tar DNA binding protein-43 (TDP43), cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Attempts to model TDP43 dysfunction in mice have used knockouts or transgenic overexpressors, which have revealed the difficulties of manipulating TDP43, whose level is tightly controlled by auto-regulation. In a complementary approach, to create useful mouse models for the dissection of TDP43 function and pathology, we have identified a nonsense mutation in the endogenous mouse Tardbp gene through screening an N-ethyl-N-nitrosourea (ENU) mutant mouse archive. The mutation is predicted to cause a Q101X truncation in TDP43. We have characterised Tardbp(Q101X) mice to investigate this mutation in perturbing TDP43 biology at endogenous expression levels. We found the Tardbp(Q101X) mutation is homozygous embryonic lethal, highlighting the importance of TDP43 in early development. Heterozygotes (Tardbp(+/Q101X) ) have abnormal levels of mutant transcript, but we find no evidence of the truncated protein and mice have similar full-length TDP43 protein levels as wildtype littermates. Nevertheless, Tardbp(+/Q101X) mice have abnormal alternative splicing of downstream gene targets, and limb-clasp and body tone phenotypes. Thus the nonsense mutation in Tardbp causes a mild loss-of-function phenotype and behavioural assessment suggests underlying neurological abnormalities. Due to the role of TDP43 in ALS, we investigated potential interactions with another known causative gene, mutant superoxide dismutase 1 (SOD1). Tardbp(+/Q101X) mice were crossed with the SOD1(G93Adl) transgenic mouse model of ALS. Behavioural and physiological assessment did not reveal modifying effects on the progression of ALS-like symptoms in the double mutant progeny from this cross. In summary, the Tardbp(Q101X) mutant mice are a useful tool for the dissection of TDP43 protein regulation, effects on splicing, embryonic development and neuromuscular phenotypes. These mice are freely available to the community.
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Affiliation(s)
- Thomas Ricketts
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Philip McGoldrick
- Sobell Department of Motor Neuroscience and Movement Disorders and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Pietro Fratta
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | | | - Rosie Kent
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
| | - Vinaya Phatak
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
| | - Sebastian Brandner
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Gonzalo Blanco
- Biology Department, University of York, York, United Kingdom
| | - Linda Greensmith
- Sobell Department of Motor Neuroscience and Movement Disorders and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
| | - Abraham Acevedo-Arozena
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
| | - Elizabeth M. C. Fisher
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
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Baralle FE, Buratti E. RNA and splicing regulation in neurodegeneration. Mol Cell Neurosci 2013; 56:404-5. [PMID: 24090657 DOI: 10.1016/j.mcn.2013.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 08/01/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022] Open
Affiliation(s)
- Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB) 34149 Trieste, Italy; Padriciano 99, 34149 Trieste, Italy.
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Buratti E, Romano M, Baralle FE. TDP-43 high throughput screening analyses in neurodegeneration: advantages and pitfalls. Mol Cell Neurosci 2013; 56:465-74. [PMID: 23500590 DOI: 10.1016/j.mcn.2013.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/22/2013] [Accepted: 03/01/2013] [Indexed: 12/13/2022] Open
Abstract
Dysfunctions in RNA processing and in particular the aberrant regulation of RNA binding proteins (RBPs) have recently been shown to play a fundamental role in the pathogenesis of neurodegenerative diseases. Understanding the pathogenic mechanisms involved will require the elucidation of the role(s) played by these RBPs in the general cell metabolism and neuronal survival in particular. In the past, the preferred approach has been to determine first of all the functional properties of the factor(s) of interest and then use this knowledge to determine targets in biologically relevant events. More recently, novel experimental approaches such as microarrays, RNA-seq and CLIP-seq have also become very popular to study RBPs. The advantage of these approaches, collectively known as high throughput screening (HTS), is their ability to determine gene expression changes or RNA/protein targets at a global cellular level. In theory, HTS strategies should be ideal for uncovering novel functional roles/targets of any RBP inside the cell. In practice, however, there are still difficulties in getting a coherent picture from all the huge amount of data they generate, frequently not validated experimentally and thus of unknown value. They may even act unfavorably towards a specific increase of knowledge of RBP functions, as the incomplete results are taken as solid data. In this work we will illustrate as an example the use of the HTS methodologies to characterize the interactions of a specific RBP: TDP-43. The multiple functions of this protein in RNA processing and its involvement in the pathogenesis of several forms of amyotrophic lateral sclerosis, frontotemporal lobar degeneration and other neurodegenerative diseases make it an excellent substrate for our analysis of the various advantages and limitations of different HTS experimental approaches.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB) 34012 Trieste, Italy
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Vanden Broeck L, Naval-Sánchez M, Adachi Y, Diaper D, Dourlen P, Chapuis J, Kleinberger G, Gistelinck M, Van Broeckhoven C, Lambert JC, Hirth F, Aerts S, Callaerts P, Dermaut B. TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila. Cell Rep 2013; 3:160-72. [PMID: 23333275 DOI: 10.1016/j.celrep.2012.12.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 10/29/2012] [Accepted: 12/19/2012] [Indexed: 02/08/2023] Open
Abstract
TDP-43 proteinopathy is strongly implicated in the pathogenesis of amyotrophic lateral sclerosis and related neurodegenerative disorders. Whether TDP-43 neurotoxicity is caused by a novel toxic gain-of-function mechanism of the aggregates or by a loss of its normal function is unknown. We increased and decreased expression of TDP-43 (dTDP-43) in Drosophila. Although upregulation of dTDP-43 induced neuronal ubiquitin and dTDP-43-positive inclusions, both up- and downregulated dTDP-43 resulted in selective apoptosis of bursicon neurons and highly similar transcriptome alterations at the pupal-adult transition. Gene network analysis and genetic validation showed that both up- and downregulated dTDP-43 directly and dramatically increased the expression of the neuronal microtubule-associated protein Map205, resulting in cytoplasmic accumulations of the ecdysteroid receptor (EcR) and a failure to switch EcR-dependent gene programs from a pupal to adult pattern. We propose that dTDP-43 neurotoxicity is caused by a loss of its normal function.
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Affiliation(s)
- Lies Vanden Broeck
- Laboratory of Behavioral and Developmental Genetics, Center of Human Genetics, University of Leuven, B3000 Leuven, Belgium
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Budini M, Romano V, Avendaño-Vázquez SE, Bembich S, Buratti E, Baralle FE. Role of selected mutations in the Q/N rich region of TDP-43 in EGFP-12xQ/N-induced aggregate formation. Brain Res 2012; 1462:139-50. [PMID: 22406069 DOI: 10.1016/j.brainres.2012.02.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/02/2012] [Accepted: 02/03/2012] [Indexed: 02/08/2023]
Abstract
The overview of TDP 43 functions immediately disclose a number of open questions regarding its pathological role. The formation of TDP-43 aggregates is one of the major distinguishing features of TDP-43 proteinopathies, especially in patients affected by Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar degeneration (FTLD). At the moment, however, very little is known regarding the biological processes that underlie TDP-43 aggregation and, most importantly, its potential consequences on cellular metabolism. For these reasons, it is particularly important to further investigate this process in order to gain a better understanding of the pathology and to develop novel therapeutic effectors. In this report, we focus on a series of missense mutations associated with disease in the 342-366 region of this protein to examine their ability to affect RNA splicing regulation and to induce aggregate formation. In particular, aggregate formation was assessed in a novel system capable of inducing TDP-43 aggregation in experimental cell lines and primary neuronal cultures. The results of this analysis showed that the presence of two of these missense mutations in the 342-366 region (G348V and N352S) could differentially affect the levels and appearance of TDP-43 aggregation with respect to the wild-type protein. This article is part of a Special Issue entitled RNA-Binding Proteins.
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Affiliation(s)
- Mauricio Budini
- International Centre for Genetic Engineering and Biotechnology (ICGEB) 34012 Trieste, Italy
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Budini M, Buratti E, Stuani C, Guarnaccia C, Romano V, De Conti L, Baralle FE. Cellular model of TAR DNA-binding protein 43 (TDP-43) aggregation based on its C-terminal Gln/Asn-rich region. J Biol Chem 2012; 287:7512-25. [PMID: 22235134 DOI: 10.1074/jbc.m111.288720] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
TDP-43 is one of the major components of the neuronal and glial inclusions observed in several neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. These characteristic aggregates are a "landmark" of the disease, but their role in the pathogenesis is still obscure. In previous works, we have shown that the C-terminal Gln/Asn-rich region (residues 321-366) of TDP-43 is involved in the interaction of this protein with other members of the heterogeneous nuclear ribonucleoprotein protein family. Furthermore, we have shown that the interaction through this region is important for TDP-43 splicing inhibition of cystic fibrosis transmembrane regulator exon 9, and there were indications that it was involved in the aggregation process. Our experiments show that in cell lines and primary rat neuronal cultures, the introduction of tandem repeats carrying the 331-369-residue Gln/Asn region from TDP-43 can trigger the formation of phosphorylated and ubiquitinated aggregates that recapitulate many but not all the characteristics observed in patients. These results establish a much needed cell-based TDP-43 aggregation model useful to investigate the mechanisms involved in the formation of inclusions and the gain- and loss-of-function consequences of TDP-43 aggregation within cells. In addition, it will be a powerful tool to test novel therapeutic strategies/effectors aimed at preventing/reducing this phenomenon.
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Affiliation(s)
- Mauricio Budini
- International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy
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Budini M, Buratti E. TDP-43 autoregulation: implications for disease. J Mol Neurosci 2011; 45:473-9. [PMID: 21681666 DOI: 10.1007/s12031-011-9573-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 06/06/2011] [Indexed: 12/13/2022]
Abstract
TDP-43 is a nuclear protein that has been shown to play a central role in RNA metabolism. In recent years, this protein has become very important in the study of neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration (FTLD). These diseases share, as common feature, the presence of abnormally aggregated, posttranslationally modified, and mislocalized TDP-43 in the cell cytoplasm of both neurons and glial cells. A major question in TDP-43 research is represented by the investigation of the mechanism(s) that trigger this process and its potential consequences. Regarding the first issue, it is likely that relative protein expression levels might play an important role as has been demonstrated for many protein aggregation processes. In fact, the eventual misregulation of TDP-43 expression leading to enhanced protein production might well correlate with enhanced aggregation, and thus results in increasingly harmful gain- or loss-of-function effects on cellular metabolism. For this reason, it is important to determine the mechanisms that act to regulate TDP-43 levels within the cell. In normal conditions, it is now clear that TDP-43 can modulate its own protein levels through a negative feedback loop triggered by binding to its own RNA in the 3'UTR region leading to mRNA degradation. This work discusses how an eventual disruption of this mechanism might affect TDP-43 pathology, focusing in particular on its association with stress granules and intrinsic aggregation properties.
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Affiliation(s)
- Mauricio Budini
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012, Trieste, Italy
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