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Kaur R, Batra J, Stuchlik O, Reed MS, Pohl J, Sambhara S, Lal SK. Heterogeneous Ribonucleoprotein A1 (hnRNPA1) Interacts with the Nucleoprotein of the Influenza a Virus and Impedes Virus Replication. Viruses 2022; 14:v14020199. [PMID: 35215793 PMCID: PMC8880450 DOI: 10.3390/v14020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), like other viruses, depends on the host cellular machinery for replication and production of progeny. The relationship between a virus and a host is complex, shaped by many spatial and temporal interactions between viral and host proteome, ultimately dictating disease outcome. Therefore, it is imperative to identify host-virus interactions as crucial determinants of disease pathogenies. Heterogeneous ribonucleoprotein A1 (hnRNPA1) is an RNA binding protein involved in the life cycle of many DNA and RNA viruses; however, its role in IAV remains undiscovered. Here we report that human hnRNPA1 physically interacts with the nucleoprotein (NP) of IAV in mammalian cells at different time points of the viral replication cycle. Temporal distribution studies identify hnRNPA1 and NP co-localize in the same cellular milieu in both nucleus and mitochondria in NP-transfected and IAV-infected mammalian cells. Interestingly, hnRNPA1 influenced NP gene expression and affected viral replication. Most importantly, hnRNPA1 knockdown caused a significant increase in NP expression and enhanced viral replication (93.82%) in IAV infected A549 cells. Conversely, hnRNPA1 overexpression reduced NP expression at the mRNA and protein levels and impeded virus replication by (60.70%), suggesting antagonistic function. Taken together, results from this study demonstrate that cellular hnRNPA1 plays a protective role in the host hitherto unknown and may hold potential as an antiviral target to develop host-based therapeutics against IAV.
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Affiliation(s)
- Ramandeep Kaur
- School of Science, Monash University, Selangor 47500, Malaysia; (R.K.); (J.B.)
| | - Jyoti Batra
- School of Science, Monash University, Selangor 47500, Malaysia; (R.K.); (J.B.)
| | - Olga Stuchlik
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (O.S.); (M.S.R.); (J.P.)
| | - Matthew S. Reed
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (O.S.); (M.S.R.); (J.P.)
| | - Jan Pohl
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (O.S.); (M.S.R.); (J.P.)
| | - Suryaprakash Sambhara
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (O.S.); (M.S.R.); (J.P.)
- Correspondence: (S.S.); (S.K.L.)
| | - Sunil Kumar Lal
- School of Science, Monash University, Selangor 47500, Malaysia; (R.K.); (J.B.)
- Tropical Medicine & Biology Platform, Monash University, Selangor 47500, Malaysia
- Correspondence: (S.S.); (S.K.L.)
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102
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Odeh HM, Fare CM, Shorter J. Nuclear-Import Receptors Counter Deleterious Phase Transitions in Neurodegenerative Disease. J Mol Biol 2022; 434:167220. [PMID: 34464655 PMCID: PMC8748273 DOI: 10.1016/j.jmb.2021.167220] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 01/17/2023]
Abstract
Nuclear-import receptors (NIRs) engage nuclear-localization signals (NLSs) of polypeptides in the cytoplasm and transport these cargo across the size-selective barrier of the nuclear-pore complex into the nucleoplasm. Beyond this canonical role in nuclear transport, NIRs operate in the cytoplasm to chaperone and disaggregate NLS-bearing clients. Indeed, NIRs can inhibit and reverse functional and deleterious phase transitions of their cargo, including several prominent neurodegenerative disease-linked RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as TDP-43, FUS, EWSR1, TAF15, hnRNPA1, and hnRNPA2. Importantly, elevated NIR expression can mitigate degenerative phenotypes connected to aberrant cytoplasmic aggregation of RBPs with PrLDs. Here, we review recent discoveries that NIRs can also antagonize aberrant interactions and toxicity of arginine-rich, dipeptide-repeat proteins that are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) caused by G4C2 hexanucleotide repeat expansions in the first intron of C9ORF72. We also highlight recent findings that multiple NIR family members can prevent and reverse liquid-liquid phase separation of specific clients bearing RGG motifs in an NLS-independent manner. Finally, we discuss strategies to enhance NIR activity or expression, which could have therapeutic utility for several neurodegenerative disorders, including ALS, FTD, multisystem proteinopathy, limbic-predominant age-related TDP-43 encephalopathy, tauopathies, and related diseases.
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Affiliation(s)
- Hana M Odeh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/CharlotteFare
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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103
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Benson BC, Shaw PJ, Azzouz M, Highley JR, Hautbergue GM. Proteinopathies as Hallmarks of Impaired Gene Expression, Proteostasis and Mitochondrial Function in Amyotrophic Lateral Sclerosis. Front Neurosci 2022; 15:783624. [PMID: 35002606 PMCID: PMC8733206 DOI: 10.3389/fnins.2021.783624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/26/2021] [Indexed: 01/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset neurodegenerative disease characterized by progressive degeneration of upper and lower motor neurons. As with the majority of neurodegenerative diseases, the pathological hallmarks of ALS involve proteinopathies which lead to the formation of various polyubiquitylated protein aggregates in neurons and glia. ALS is a highly heterogeneous disease, with both familial and sporadic forms arising from the convergence of multiple disease mechanisms, many of which remain elusive. There has been considerable research effort invested into exploring these disease mechanisms and in recent years dysregulation of RNA metabolism and mitochondrial function have emerged as of crucial importance to the onset and development of ALS proteinopathies. Widespread alterations of the RNA metabolism and post-translational processing of proteins lead to the disruption of multiple biological pathways. Abnormal mitochondrial structure, impaired ATP production, dysregulation of energy metabolism and calcium homeostasis as well as apoptosis have been implicated in the neurodegenerative process. Dysfunctional mitochondria further accumulate in ALS motor neurons and reflect a wider failure of cellular quality control systems, including mitophagy and other autophagic processes. Here, we review the evidence for RNA and mitochondrial dysfunction as some of the earliest critical pathophysiological events leading to the development of ALS proteinopathies, explore their relative pathological contributions and their points of convergence with other key disease mechanisms. This review will focus primarily on mutations in genes causing four major types of ALS (C9ORF72, SOD1, TARDBP/TDP-43, and FUS) and in protein homeostasis genes (SQSTM1, OPTN, VCP, and UBQLN2) as well as sporadic forms of the disease. Finally, we will look to the future of ALS research and how an improved understanding of central mechanisms underpinning proteinopathies might inform research directions and have implications for the development of novel therapeutic approaches.
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Affiliation(s)
- Bridget C Benson
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
| | - J Robin Highley
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
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104
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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105
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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106
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Meneses A, Koga S, O’Leary J, Dickson DW, Bu G, Zhao N. TDP-43 Pathology in Alzheimer’s Disease. Mol Neurodegener 2021; 16:84. [PMID: 34930382 PMCID: PMC8691026 DOI: 10.1186/s13024-021-00503-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/21/2021] [Indexed: 12/05/2022] Open
Abstract
Transactive response DNA binding protein of 43 kDa (TDP-43) is an intranuclear protein encoded by the TARDBP gene that is involved in RNA splicing, trafficking, stabilization, and thus, the regulation of gene expression. Cytoplasmic inclusion bodies containing phosphorylated and truncated forms of TDP-43 are hallmarks of amyotrophic lateral sclerosis (ALS) and a subset of frontotemporal lobar degeneration (FTLD). Additionally, TDP-43 inclusions have been found in up to 57% of Alzheimer’s disease (AD) cases, most often in a limbic distribution, with or without hippocampal sclerosis. In some cases, TDP-43 deposits are also found in neurons with neurofibrillary tangles. AD patients with TDP-43 pathology have increased severity of cognitive impairment compared to those without TDP-43 pathology. Furthermore, the most common genetic risk factor for AD, apolipoprotein E4 (APOE4), is associated with increased frequency of TDP-43 pathology. These findings provide strong evidence that TDP-43 pathology is an integral part of multiple neurodegenerative conditions, including AD. Here, we review the biology and pathobiology of TDP-43 with a focus on its role in AD. We emphasize the need for studies on the mechanisms that lead to TDP-43 pathology, especially in the setting of age-related disorders such as AD.
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107
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Distinct roles of hnRNPH1 low-complexity domains in splicing and transcription. Proc Natl Acad Sci U S A 2021; 118:2109668118. [PMID: 34873036 PMCID: PMC8685725 DOI: 10.1073/pnas.2109668118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 12/21/2022] Open
Abstract
Phase separation of low-complexity (LC) domains appended to most RNA-binding proteins (RBPs) emerges as a principle underlying spatiotemporal protein recruitment. Yet, how LC domains regulate the function of RBPs in cells remains unclear. An alternative-splicing regulator, hnRNPH1, contains two LC domains (LC1 and LC2). Here, we show that phase separation of the LC1 can exert control over hnRNPH1 function in RNA-splicing possibly by facilitating interactions between hnRNPH1 and a variety of RBPs. In contrast, the LC2 lacking in vitro phase properties, is required for aberrant transcriptional activation in the context of fusion oncoproteins. These results have broad implications for understanding how phase separation contributes to distinct roles of LC domains in control of physiological as well as oncogenic functions. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins that control key events in RNA biogenesis under both normal and diseased cellular conditions. The low-complexity (LC) domain of hnRNPs can become liquid-like droplets or reversible amyloid-like polymers by phase separation. Yet, whether phase separation of the LC domains contributes to physiological functions of hnRNPs remains unclear. hnRNPH1 contains two LC domains, LC1 and LC2. Here, we show that reversible phase separation of the LC1 domain is critical for both interaction with different kinds of RNA-binding proteins and control of the alternative-splicing activity of hnRNPH1. Interestingly, although not required for phase separation, the LC2 domain contributes to the robust transcriptional activation of hnRNPH1 when fused to the DNA-binding domain, as found recently in acute lymphoblastic leukemia. Our data suggest that the ability of the LC1 domain to phase-separate into reversible polymers or liquid-like droplets is essential for function of hnRNPH1 as an alternative RNA-splicing regulator, whereas the LC2 domain may contribute to the aberrant transcriptional activity responsible for cancer transformation.
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108
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Taylor NC, Nikić-Spiegel I. Film-like organelles equip cells with multiple genetic codes. Trends Biochem Sci 2021; 47:369-371. [PMID: 34895957 DOI: 10.1016/j.tibs.2021.11.006] [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: 11/14/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 10/19/2022]
Abstract
The simultaneous incorporation of distinct noncanonical amino acids into different proteins within eukaryotic cells remains challenging. This new study by Reinkemeier and Lemke demonstrates how 2D phase separation can be used to engineer spatially separated organelles. These film-like organelles translate proteins independently from each other and the canonical genetic code.
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Affiliation(s)
- Neil C Taylor
- Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076 Tübingen, Germany
| | - Ivana Nikić-Spiegel
- Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076 Tübingen, Germany. @cin.uni-tuebingen.de
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109
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TDP-43 and HERV-K Envelope-Specific Immunogenic Epitopes Are Recognized in ALS Patients. Viruses 2021; 13:v13112301. [PMID: 34835107 PMCID: PMC8623164 DOI: 10.3390/v13112301] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 01/10/2023] Open
Abstract
The human endogenous retrovirus-K (HERV-K) and TAR DNA-binding protein 43 (TDP-43) have been associated with the pathophysiology of amyotrophic lateral sclerosis (ALS). Given these findings, we investigated the humoral response against HERV-K envelope surface (env-su) glycoprotein antigens and TDP-43 in the plasma of ALS patients and healthy controls (HCs). The measured levels of Abs against the different epitopes’ fragments were significantly elevated in ALS patients, both in long-survivor (LS) and newly diagnosed (ND) patients, compared to HCs. We observed a positive correlation between HERV-K and TDP-43 antibodies (Abs) levels, which seemed to strengthen with disease progression, that was not found in HCs. The TDP-43 and HERV-K epitopes identified in this study are highly immunogenic and recognized by the humoral response of ALS patients. Increased circulating levels of Abs directed against specific HERV-K- and TDP-43-derived epitopes could serve as possible biomarkers.
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110
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Hackman P, Rusanen SM, Johari M, Vihola A, Jonson PH, Sarparanta J, Donner K, Lahermo P, Koivunen S, Luque H, Soininen M, Mahjneh I, Auranen M, Arumilli M, Savarese M, Udd B. Dominant Distal Myopathy 3 (MPD3) Caused by a Deletion in the HNRNPA1 Gene. NEUROLOGY-GENETICS 2021; 7:e632. [PMID: 34722876 PMCID: PMC8552285 DOI: 10.1212/nxg.0000000000000632] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/27/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
Background and Objectives To determine the genetic cause of the disease in the previously reported family with adult-onset autosomal dominant distal myopathy (myopathy, distal, 3; MPD3). Methods Continued clinical evaluation including muscle MRI and muscle pathology. A linkage analysis with single nucleotide polymorphism arrays and genome sequencing were used to identify the genetic defect, which was verified by Sanger sequencing. RNA sequencing was used to investigate the transcriptional effects of the identified genetic defect. Results Small hand muscles (intrinsic, thenar, and hypothenar) were first involved with spread to the lower legs and later proximal muscles. Dystrophic changes with rimmed vacuoles and cytoplasmic inclusions were observed in muscle biopsies at advanced stage. A single nucleotide polymorphism array confirmed the previous microsatellite-based linkage to 8p22-q11 and 12q13-q22. Genome sequencing of three affected family members combined with structural variant calling revealed a small heterozygous deletion of 160 base pairs spanning the second last exon 10 of the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) gene, which is in the linked region on chromosome 12. Segregation of the mutation with the disease was confirmed by Sanger sequencing. RNA sequencing showed that the mutant allele produces a shorter mutant mRNA transcript compared with the wild-type allele. Immunofluorescence studies on muscle biopsies revealed small p62 and larger TDP-43 inclusions. Discussion A small exon 10 deletion in the gene HNRNPA1 was identified as the cause of MPD3 in this family. The new HNRNPA1-related phenotype, upper limb presenting distal myopathy, was thus confirmed, and the family displays the complexities of gene identification.
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Affiliation(s)
- Peter Hackman
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Salla M Rusanen
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Mridul Johari
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Anna Vihola
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Jaakko Sarparanta
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Kati Donner
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Päivi Lahermo
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Sampo Koivunen
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Helena Luque
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Merja Soininen
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Ibrahim Mahjneh
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Mari Auranen
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Meharji Arumilli
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Marco Savarese
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
| | - Bjarne Udd
- Folkhälsan Research Center (P.H., S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S., B.U.); University of Helsinki (S.M.R., M.J., A.V., P.H.J., J.S., S.K., H.L., M.S., M.A., M.S.), Helsinki; Finnish Neuromuscular Center, Fimlab Laboratories and Tampere University (A.V.); Institute for Molecular Medicine Finland (FIMM), University of Helsinki (K.D., P.L.); MRC, University of Oulu, Oulu (I.M.); Pietarsaari Hospital, Pietarsaari, Finland (I.M.); Clinical Neurosciences, Neurology, Helsinki University Hospital (M.A.); Vaasa Central Hospital (B.U.), Vaasa, Finland
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Lenard AJ, Hutten S, Zhou Q, Usluer S, Zhang F, Bourgeois BMR, Dormann D, Madl T. Phosphorylation Regulates CIRBP Arginine Methylation, Transportin-1 Binding and Liquid-Liquid Phase Separation. Front Mol Biosci 2021; 8:689687. [PMID: 34738012 PMCID: PMC8562343 DOI: 10.3389/fmolb.2021.689687] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
Arginine-glycine(-glycine) (RG/RGG) regions are highly abundant in RNA-binding proteins and involved in numerous physiological processes. Aberrant liquid-liquid phase separation (LLPS) and stress granule (SGs) association of RG/RGG regions in the cytoplasm have been implicated in several neurodegenerative disorders. LLPS and SG association of these proteins is regulated by the interaction with nuclear import receptors, such as transportin-1 (TNPO1), and by post-translational arginine methylation. Strikingly, many RG/RGG proteins harbour potential phosphorylation sites within or close to their arginine methylated regions, indicating a regulatory role. Here, we studied the role of phosphorylation within RG/RGG regions on arginine methylation, TNPO1-binding and LLPS using the cold-inducible RNA-binding protein (CIRBP) as a paradigm. We show that the RG/RGG region of CIRBP is in vitro phosphorylated by serine-arginine protein kinase 1 (SRPK1), and discovered two novel phosphorylation sites in CIRBP. SRPK1-mediated phosphorylation of the CIRBP RG/RGG region impairs LLPS and binding to TNPO1 in vitro and interferes with SG association in cells. Furthermore, we uncovered that arginine methylation of the CIRBP RG/RGG region regulates in vitro phosphorylation by SRPK1. In conclusion, our findings indicate that LLPS and TNPO1-mediated chaperoning of RG/RGG proteins is regulated through an intricate interplay of post-translational modifications.
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Affiliation(s)
- Aneta J. Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Saskia Hutten
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany
- BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany
| | - Qishun Zhou
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin M. R. Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dorothee Dormann
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany
- BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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112
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Xia RM, Liu T, Li WG, Xu XQ. RNA-binding protein RBM24 represses colorectal tumourigenesis by stabilising PTEN mRNA. Clin Transl Med 2021; 11:e383. [PMID: 34709758 PMCID: PMC8506628 DOI: 10.1002/ctm2.383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA-binding motif protein 24 (RBM24) functions as a splicing regulator, which is critical for organ development and is dysregulated in human cancers. Here, we aim to uncover the biological function of RBM24 in colorectal tumourigenesis. METHODS Xenograft tumour model, Rbm24 knockout and Apcmin/+ mouse models were utilised. Colorectal cancer cells overexpressing or silencing RBM24 were established. RNA immunoprecipitation (RIP) assay was conducted to detect protein-RNA associations. Gene expression was measured by immunohistochemistry, western blotting, or quantitative PCR (qPCR). RESULTS Rbm24-knockout mice developed spontaneous colorectal adenomas with lower expression of phosphatase and tensin homolog (PTEN). Immunohistochemical staining for the proliferation markers Ki-67 and pHH3 and BrdU assay showed intestinal hyperplasia in Rbm24-knockout mice compared to wild-type mice. RBM24 expression in colorectal adenoma tissues of Apcmin/+ mouse was downregulated compared with adjacent normal samples and was positively correlated with PTEN expression. In vitro, RBM24 overexpression suppressed cell proliferation, migration, invasion and increased sensitivity to 5-FU or cisplatin in CRC cells. Mechanistically, RBM24 maintained PTEN mRNA stability by directly binding to the GT-rich region at positions 8101-8251 in the 3'-UTR of PTEN mRNA, prolonging the half-life of PTEN mRNA, thereby increasing PTEN expression. Hence, low expression of RBM24 downregulated PTEN mRNA, causing the activation of PI3K-Akt signalling in CRC cells. Furthermore, RBM24 expression in CRC tissues was lower than adjacent normal samples. RBM24 expression was positively correlated with PTEN expression and negatively correlated with Ki-67 level. CRC patients with high RBM24 expression had a favourable outcome. CONCLUSIONS Taken together, RBM24 expression is markedly lower in colorectal tumours than in para-carcinoma tissues. Rbm24-knockout mice develop spontaneous colorectal adenomas. RBM24 directly binds and stabilises PTEN mRNA, which could cause the suppression of CRC cell proliferation, migration and invasion, thereby repressing colorectal tumourigenesis. These findings support the tumour-suppressive role of RBM24. Targeting RBM24 holds strong promise for the diagnosis and treatment of CRC.
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Affiliation(s)
- Rong Mu Xia
- Institute of Stem Cell and Regenerative MedicineSchool of MedicineXiamen UniversityXiamenFujianPeople's Republic of China
| | - Tao Liu
- Department of Hepatobiliary SurgerySchool of MedicineXiang'an Hospital of Xiamen UniversityXiamen UniversityXiamenFujianPeople's Republic of China
| | - Wen Gang Li
- Institute of Stem Cell and Regenerative MedicineSchool of MedicineXiamen UniversityXiamenFujianPeople's Republic of China
- Department of Hepatobiliary SurgerySchool of MedicineXiang'an Hospital of Xiamen UniversityXiamen UniversityXiamenFujianPeople's Republic of China
| | - Xiu Qin Xu
- Institute of Stem Cell and Regenerative MedicineSchool of MedicineXiamen UniversityXiamenFujianPeople's Republic of China
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Wang Y, Zhang XF, Wang DY, Zhu Y, Chen L, Zhang JJ. Long noncoding RNA SOX2OT promotes pancreatic cancer cell migration and invasion through destabilizing FUS protein via ubiquitination. Cell Death Discov 2021; 7:261. [PMID: 34552054 PMCID: PMC8458496 DOI: 10.1038/s41420-021-00640-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023] Open
Abstract
Pancreatic cancer is a highly aggressive and lethal digestive system malignancy. Our previous studies revealed the correlation of high levels of lncRNA SOX2OT expression with patients’ poor survival outcomes, the promoting role of SOX2OT in proliferation and cycle progression of pancreatic cancer cells, and the in vivo binding of SOX2OT to RNA binding protein FUS, which destabilized the protein expression of FUS. However, the mechanism of SOX2OT binding and inhibiting FUS protein stability remains unclear. In this study, we performed RNA pull-down, cycloheximide-chase, and ubiquitination assays to determine the effect of SOX2OT on FUS ubiquitination, and explored the specific regulatory mechanism of SOX2OT–FUS axis in pancreatic cancer cell migration, invasion, in vivo tumor growth, and metastasis through RNA sequencing. We found that SOX2OT binds to FUS through its 5′ and 3′ regions, resulting in FUS ubiquitination and degradation. The SOX2OT–FUS regulatory axis promotes migration, invasion, tumor growth, and metastasis ability of pancreatic cancer cells. The in-depth elaboration of the SOX2OT–FUS regulatory axis in pancreatic cancer may clarify the mechanism of action of SOX2OT and provide new ideas for pancreatic cancer treatment.
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Affiliation(s)
- Yan Wang
- Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Xiong-Fei Zhang
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China
| | - Dong-Yan Wang
- Department of General Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, People's Republic of China
| | - Yi Zhu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Lei Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Jing-Jing Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China. .,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China. .,Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People's Republic of China.
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Kang SG, Han ZZ, Daude N, McNamara E, Wohlgemuth S, Molina-Porcel L, Safar JG, Mok SA, Westaway D. Pathologic tau conformer ensembles induce dynamic, liquid-liquid phase separation events at the nuclear envelope. BMC Biol 2021; 19:199. [PMID: 34503506 PMCID: PMC8428099 DOI: 10.1186/s12915-021-01132-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023] Open
Abstract
Background The microtubule-associated protein tau forms aggregates in different neurodegenerative diseases called tauopathies. Prior work has shown that a single P301L mutation in tau gene, MAPT, can promote alternative tau folding pathways that correlate with divergent clinical diagnoses. Using progressive chemical denaturation, some tau preparations from the brain featured complex transitions starting at low concentrations of guanidine hydrochloride (GdnHCl) denaturant, indicating an ensemble of differently folded tau species called conformers. On the other hand, brain samples with abundant, tangle-like pathology had simple GdnHCl unfolding profile resembling the profile of fibrillized recombinant tau and suggesting a unitary conformer composition. In studies here we sought to understand tau conformer progression and potential relationships with condensed liquid states, as well as associated perturbations in cell biological processes. Results As starting material, we used brain samples from P301L transgenic mice containing tau conformer ensembles that unfolded at low GdnHCl concentrations and with signatures resembling brain material from P301L subjects presenting with language or memory problems. We seeded reporter cells expressing a soluble form of 4 microtubule-binding repeat tau fused to GFP or YFP reporter moieties, resulting in redistribution of dispersed fluorescence signals into focal assemblies that could fuse together and move within processes between adjacent cells. Nuclear envelope fluorescent tau signals and small fluorescent inclusions behaved as a demixed liquid phase, indicative of liquid-liquid phase separation (LLPS); these droplets exhibited spherical morphology, fusion events and could recover from photobleaching. Moreover, juxtanuclear tau assemblies were associated with disrupted nuclear transport and reduced cell viability in a stable cell line. Staining for thioflavin S (ThS) became more prevalent as tau-derived inclusions attained cross-sectional area greater than 3 μm2, indicating (i) a bipartite composition, (ii) in vivo progression of tau conformers, and (iii) that a mass threshold applying to demixed condensates may drive liquid-solid transitions. Conclusions Tau conformer ensembles characterized by denaturation at low GdnHCl concentration templated the production of condensed droplets in living cells. These species exhibit dynamic changes and develop in vivo, and the larger ThS-positive assemblies may represent a waystation to arrive at intracellular fibrillar tau inclusions seen in end-stage genetic tauopathies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01132-y.
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Affiliation(s)
- Sang-Gyun Kang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada
| | - Zhuang Zhuang Han
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada
| | - Emily McNamara
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Serene Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada
| | | | - Jiri G Safar
- Department of Neurology and Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Sue-Ann Mok
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2 M8, Canada. .,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada. .,Division of Neurology, University of Alberta, Edmonton, AB, Canada.
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Salladini E, Gondelaud F, Nilsson JF, Pesce G, Bignon C, Murrali MG, Fabre R, Pierattelli R, Kajava AV, Horvat B, Gerlier D, Mathieu C, Longhi S. Identification of a Region in the Common Amino-terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation. Biomolecules 2021; 11:1324. [PMID: 34572537 PMCID: PMC8471210 DOI: 10.3390/biom11091324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
Henipaviruses are BSL-4 zoonotic pathogens responsible in humans for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We previously showed that the Henipavirus V proteins consist of a long intrinsically disordered N-terminal domain (NTD) and a β-enriched C-terminal domain (CTD). These terminals are critical for V binding to DDB1, which is a cellular protein that is a component of the ubiquitin ligase E3 complex, as well as binding to MDA5 and LGP2, which are two host sensors of viral RNA. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquid-to-hydrogel phase transition and identified the V region responsible for this phenomenon. This region, referred to as PNT3 and encompassing residues 200-310, was further investigated using a combination of biophysical and structural approaches. Congo red binding assays, together with negative-staining transmisison electron microscopy (TEM) studies, show that PNT3 forms amyloid-like fibrils. Fibrillation abilities are dramatically reduced in a rationally designed PNT3 variant in which a stretch of three contiguous tyrosines, falling within an amyloidogenic motif, were replaced by three alanines. Worthy to note, Congo red staining experiments provided hints that these amyloid-like fibrils form not only in vitro but also in cellula after transfection or infection. The present results set the stage for further investigations aimed at assessing the functional role of phase separation and fibrillation by the Henipavirus V proteins.
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Affiliation(s)
- Edoardo Salladini
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Frank Gondelaud
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Juliet F. Nilsson
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Giulia Pesce
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Christophe Bignon
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Maria Grazia Murrali
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Roxane Fabre
- Centre d’Immunologie de Marseille-Luminy (CIML), CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille University, CEDEX 9, 13288 Marseille, France;
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Andrey V. Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, 34293 Montpellier, France;
| | - Branka Horvat
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Denis Gerlier
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Cyrille Mathieu
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
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Hallegger M, Chakrabarti AM, Lee FCY, Lee BL, Amalietti AG, Odeh HM, Copley KE, Rubien JD, Portz B, Kuret K, Huppertz I, Rau F, Patani R, Fawzi NL, Shorter J, Luscombe NM, Ule J. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 2021; 184:4680-4696.e22. [PMID: 34380047 PMCID: PMC8445024 DOI: 10.1016/j.cell.2021.07.018] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 04/12/2021] [Accepted: 07/15/2021] [Indexed: 11/20/2022]
Abstract
Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the specificity and function of protein-RNA complexes remains unclear. We created a series of TDP-43 C-terminal domain (CTD) variants that exhibited a gradient of low to high condensation propensity, as observed in vitro and by nuclear mobility and foci formation. Notably, a capacity for condensation was required for efficient TDP-43 assembly on subsets of RNA-binding regions, which contain unusually long clusters of motifs of characteristic types and density. These "binding-region condensates" are promoted by homomeric CTD-driven interactions and required for efficient regulation of a subset of bound transcripts, including autoregulation of TDP-43 mRNA. We establish that RBP condensation can occur in a binding-region-specific manner to selectively modulate transcriptome-wide RNA regulation, which has implications for remodeling RNA networks in the context of signaling, disease, and evolution.
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Affiliation(s)
- Martina Hallegger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Genetics, Evolution and Environment, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Flora C Y Lee
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aram G Amalietti
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jack D Rubien
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klara Kuret
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Ina Huppertz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Frédérique Rau
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Genetics, Evolution and Environment, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK; Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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117
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Gil‐Garcia M, Iglesias V, Pallarès I, Ventura S. Prion-like proteins: from computational approaches to proteome-wide analysis. FEBS Open Bio 2021; 11:2400-2417. [PMID: 34057308 PMCID: PMC8409284 DOI: 10.1002/2211-5463.13213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Prions are self-perpetuating proteins able to switch between a soluble state and an aggregated-and-transmissible conformation. These proteinaceous entities have been widely studied in yeast, where they are involved in hereditable phenotypic adaptations. The notion that such proteins could play functional roles and be positively selected by evolution has triggered the development of computational tools to identify prion-like proteins in different kingdoms of life. These algorithms have succeeded in screening multiple proteomes, allowing the identification of prion-like proteins in a diversity of unrelated organisms, evidencing that the prion phenomenon is well conserved among species. Interestingly enough, prion-like proteins are not only connected with the formation of functional membraneless protein-nucleic acid coacervates, but are also linked to human diseases. This review addresses state-of-the-art computational approaches to identify prion-like proteins, describes proteome-wide analysis efforts, discusses these unique proteins' functional role, and illustrates recently validated examples in different domains of life.
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Affiliation(s)
- Marcos Gil‐Garcia
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Valentín Iglesias
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Irantzu Pallarès
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
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118
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Mann JR, Donnelly CJ. RNA modulates physiological and neuropathological protein phase transitions. Neuron 2021; 109:2663-2681. [PMID: 34297914 PMCID: PMC8434763 DOI: 10.1016/j.neuron.2021.06.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/21/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022]
Abstract
Aggregation of RNA-binding proteins (RBPs) is a pathological hallmark of neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In these diseases, TDP-43 and FUS RBPs are depleted from the nuclear compartment, where they are normally localized, and found within cytoplasmic inclusions in degenerating regions of affected individuals' postmortem tissue. The mechanisms responsible for aggregation of these proteins has remained elusive, but recent studies suggest liquid-liquid phase separation (LLPS) might serve as a critical nucleation step in formation of pathological inclusions. The process of phase separation also underlies the formation and maintenance of several functional membraneless organelles (MLOs) throughout the cell, some of which contain TDP-43, FUS, and other disease-linked RBPs. One common ligand of disease-linked RBPs, RNA, is a major component of MLOs containing RBPs and has been demonstrated to be a strong modulator of RBP phase transitions. Although early evidence suggested a largely synergistic effect of RNA on RBP phase separation and MLO assembly, recent work indicates that RNA can also antagonize RBP phase behavior under certain physiological and pathological conditions. In this review, we describe the mechanisms underlying RNA-mediated phase transitions of RBPs and examine the molecular properties of these interactions, such as RNA length, sequence, and secondary structure, that mediate physiological or pathological LLPS.
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Affiliation(s)
- Jacob R Mann
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA; LiveLikeLouCenter for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA 15213, USA; Center for Protein Conformational Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Christopher J Donnelly
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; LiveLikeLouCenter for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA 15213, USA; Center for Protein Conformational Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Institute for Neurodegeneration, University of Pittsburgh, Pittsburgh PA 15213.
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119
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The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis. Life (Basel) 2021; 11:life11090872. [PMID: 34575021 PMCID: PMC8467930 DOI: 10.3390/life11090872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/11/2021] [Accepted: 08/22/2021] [Indexed: 11/18/2022] Open
Abstract
In this paper the hypothesis that prions and prion-like molecules could have initiated the chemical evolutionary process which led to the eventual emergence of life is reappraised. The prions first hypothesis is a specific application of the protein-first hypothesis which asserts that protein-based chemical evolution preceded the evolution of genetic encoding processes. This genetics-first hypothesis asserts that an “RNA-world era” came before protein-based chemical evolution and rests on a singular premise that molecules such as RNA, acetyl-CoA, and NAD are relics of a long line of chemical evolutionary processes preceding the Last Universal Common Ancestor (LUCA). Nevertheless, we assert that prions and prion-like molecules may also be relics of chemical evolutionary processes preceding LUCA. To support this assertion is the observation that prions and prion-like molecules are involved in a plethora of activities in contemporary biology in both complex (eukaryotes) and primitive life forms. Furthermore, a literature survey reveals that small RNA virus genomes harbor information about prions (and amyloids). If, as has been presumed by proponents of the genetics-first hypotheses, small viruses were present during an RNA world era and were involved in some of the earliest evolutionary processes, this places prions and prion-like molecules potentially at the heart of the chemical evolutionary process whose eventual outcome was life. We deliberate on the case for prions and prion-like molecules as the frontier molecules at the dawn of evolution of living systems.
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120
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Aledo JC. The Role of Methionine Residues in the Regulation of Liquid-Liquid Phase Separation. Biomolecules 2021; 11:biom11081248. [PMID: 34439914 PMCID: PMC8394241 DOI: 10.3390/biom11081248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Membraneless organelles are non-stoichiometric supramolecular structures in the micron scale. These structures can be quickly assembled/disassembled in a regulated fashion in response to specific stimuli. Membraneless organelles contribute to the spatiotemporal compartmentalization of the cell, and they are involved in diverse cellular processes often, but not exclusively, related to RNA metabolism. Liquid-liquid phase separation, a reversible event involving demixing into two distinct liquid phases, provides a physical framework to gain insights concerning the molecular forces underlying the process and how they can be tuned according to the cellular needs. Proteins able to undergo phase separation usually present a modular architecture, which favors a multivalency-driven demixing. We discuss the role of low complexity regions in establishing networks of intra- and intermolecular interactions that collectively control the phase regime. Post-translational modifications of the residues present in these domains provide a convenient strategy to reshape the residue-residue interaction networks that determine the dynamics of phase separation. Focus will be placed on those proteins with low complexity domains exhibiting a biased composition towards the amino acid methionine and the prominent role that reversible methionine sulfoxidation plays in the assembly/disassembly of biomolecular condensates.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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121
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Chien HM, Lee CC, Huang JJT. The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22158213. [PMID: 34360978 PMCID: PMC8348237 DOI: 10.3390/ijms22158213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) is a nucleic acid-binding protein that is involved in transcription and translation regulation, non-coding RNA processing, and stress granule assembly. Aside from its multiple functions, it is also known as the signature protein in the hallmark inclusions of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) patients. TDP-43 is built of four domains, but its low-complexity domain (LCD) has become an intense research focus that brings to light its possible role in TDP-43 functions and involvement in the pathogenesis of these neurodegenerative diseases. Recent endeavors have further uncovered the distinct biophysical properties of TDP-43 under various circumstances. In this review, we summarize the multiple structural and biochemical properties of LCD in either promoting the liquid droplets or inducing fibrillar aggregates. We also revisit the roles of the LCD in paraspeckles, stress granules, and cytoplasmic inclusions to date.
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Affiliation(s)
- Hung-Ming Chien
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Chemistry, National Taiwan University, Taipei City 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei City 115, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Applied Chemistry, National Chiayi University, Chiayi City 600, Taiwan
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei City 115, Taiwan
- Correspondence: ; Tel.: +886-2-5572-8652
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122
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Beijer D, Kim HJ, Guo L, O'Donovan K, Mademan I, Deconinck T, Van Schil K, Fare CM, Drake LE, Ford AF, Kochański A, Kabzińska D, Dubuisson N, Van den Bergh P, Voermans NC, Lemmers RJ, van der Maarel SM, Bonner D, Sampson JB, Wheeler MT, Mehrabyan A, Palmer S, De Jonghe P, Shorter J, Taylor JP, Baets J. Characterization of HNRNPA1 mutations defines diversity in pathogenic mechanisms and clinical presentation. JCI Insight 2021; 6:e148363. [PMID: 34291734 PMCID: PMC8410042 DOI: 10.1172/jci.insight.148363] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in HNRNPA1 encoding heterogeneous nuclear ribonucleoprotein (hnRNP) A1 are a rare cause of amyotrophic lateral sclerosis (ALS) and multisystem proteinopathy (MSP). hnRNPA1 is part of the group of RNA-binding proteins (RBPs) that assemble with RNA to form RNPs. hnRNPs are concentrated in the nucleus and function in pre-mRNA splicing, mRNA stability, and the regulation of transcription and translation. During stress, hnRNPs, mRNA, and other RBPs condense in the cytoplasm to form stress granules (SGs). SGs are implicated in the pathogenesis of (neuro-)degenerative diseases, including ALS and inclusion body myopathy (IBM). Mutations in RBPs that affect SG biology, including FUS, TDP-43, hnRNPA1, hnRNPA2B1, and TIA1, underlie ALS, IBM, and other neurodegenerative diseases. Here, we characterize 4 potentially novel HNRNPA1 mutations (yielding 3 protein variants: *321Eext*6, *321Qext*6, and G304Nfs*3) and 2 known HNRNPA1 mutations (P288A and D262V), previously connected to ALS and MSP, in a broad spectrum of patients with hereditary motor neuropathy, ALS, and myopathy. We establish that the mutations can have different effects on hnRNPA1 fibrillization, liquid-liquid phase separation, and SG dynamics. P288A accelerated fibrillization and decelerated SG disassembly, whereas *321Eext*6 had no effect on fibrillization but decelerated SG disassembly. By contrast, G304Nfs*3 decelerated fibrillization and impaired liquid phase separation. Our findings suggest different underlying pathomechanisms for HNRNPA1 mutations with a possible link to clinical phenotypes.
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Affiliation(s)
- Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lin Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kevin O'Donovan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Inès Mademan
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium
| | - Tine Deconinck
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Kristof Van Schil
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren E Drake
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alice F Ford
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Nicolas Dubuisson
- Neuromuscular Reference Centre, University Hospitals St-Luc, University of Louvain, Brussels, Belgium
| | - Peter Van den Bergh
- Neuromuscular Reference Centre, University Hospitals St-Luc, University of Louvain, Brussels, Belgium
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Jacinda B Sampson
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Anahit Mehrabyan
- Department of Neurology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven Palmer
- Department of Neurology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peter De Jonghe
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Wilrijk, Belgium
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Wilrijk, Belgium
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123
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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124
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Portz B, Lee BL, Shorter J. FUS and TDP-43 Phases in Health and Disease. Trends Biochem Sci 2021; 46:550-563. [PMID: 33446423 PMCID: PMC8195841 DOI: 10.1016/j.tibs.2020.12.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/24/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
The distinct prion-like domains (PrLDs) of FUS and TDP-43, modulate phase transitions that result in condensates with a range of material states. These assemblies are implicated in both health and disease. In this review, we examine how sequence, structure, post-translational modifications, and RNA can affect the self-assembly of these RNA-binding proteins (RBPs). We discuss how our emerging understanding of FUS and TDP-43 liquid-liquid phase separation (LLPS) and aggregation, could be leveraged to design new therapies for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43 encephalopathy (LATE).
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Affiliation(s)
- Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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125
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Phenotypic diversity in ALS and the role of poly-conformational protein misfolding. Acta Neuropathol 2021; 142:41-55. [PMID: 32930869 DOI: 10.1007/s00401-020-02222-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 12/11/2022]
Abstract
In many types of familial amyotrophic lateral sclerosis (fALS), mutations cause proteins to gain toxic properties that mediate neurodegenerative processes. It is becoming increasingly clear that the proteins involved in ALS, and those responsible for a host of other neurodegenerative diseases, share many characteristics with a growing number of prion diseases. ALS is a heterogenous disease in which the majority of cases are sporadic in their etiology. Studies investigating the inherited forms of the disease are now beginning to provide evidence that some of this heterogeneity may be due to the existence of distinct conformations that ALS-linked proteins can adopt to produce the equivalent of prion strains. In this review, we discuss the in vitro and in vivo evidence that has been generated to better understand the characteristics of these proteins and how their tertiary structure may impact the disease phenotype.
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126
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Impacts of chromatin dynamics and compartmentalization on DNA repair. DNA Repair (Amst) 2021; 105:103162. [PMID: 34182258 DOI: 10.1016/j.dnarep.2021.103162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 11/22/2022]
Abstract
The proper spatial organization of DNA, RNA, and proteins is critical for a variety of cellular processes. The genome is organized into numerous functional units, such as topologically associating domains (TADs), the formation of which is regulated by both proteins and RNA. In addition, a group of chromatin-bound proteins with the ability to undergo liquid-liquid phase separation (LLPS) can affect the spatial organization and compartmentalization of chromatin, RNA, and proteins by forming condensates, conferring unique properties to specific chromosomal regions. Although the regulation of DNA repair by histone modifications and chromatin accessibility is well established, the impacts of higher-order chromatin and protein organization on the DNA damage response (DDR) have not been appreciated until recently. In this review, we will focus on the movement of chromatin during the DDR, the compartmentalization of DDR proteins via LLPS, and the roles of membraneless nuclear bodies and transcription in DNA repair. With this backdrop, we will discuss the importance of the spatial organization of chromatin and proteins for the maintenance of genome integrity.
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127
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Fare CM, Villani A, Drake LE, Shorter J. Higher-order organization of biomolecular condensates. Open Biol 2021; 11:210137. [PMID: 34129784 PMCID: PMC8205532 DOI: 10.1098/rsob.210137] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization is achieved is through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic and reactive, and often contain a complex mixture of proteins and nucleic acids. In this review, we discuss how underlying physical and chemical processes generate internal condensate architectures. We then outline the diverse condensate architectures that are observed in biological systems. Finally, we discuss how specific condensate organization is critical for specific biological functions.
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Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - James Shorter
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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128
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Yoshizawa T, Guo L. Karyopherin-βs play a key role as a phase separation regulator. J Biochem 2021; 170:15-23. [PMID: 34223614 DOI: 10.1093/jb/mvab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have revealed that cells utilize liquid-liquid phase separation (LLPS) as a mechanism in assembly of membrane-less organelles, such as RNP granules. The nucleus is a well-known membrane-bound organelle surrounded by the nuclear envelope; the nuclear pore complex on the nuclear envelope likely applies LLPS in the central channel to facilitate selective biological macromolecule exchange. Karyopherin-β family proteins exclusively pass through the central channel with cargos by dissolving the phase separated hydrogel formed by the phenylalanine-glycine (FG) repeats-containing nucleoporins. Karyopherin-βs also exhibit dissolution activity for the phase separation of cargo proteins. Many cargos, including RNA-binding proteins containing intrinsically disordered regions (IDRs), undergo phase separation; however, aberrant phase separation is linked to fatal neurodegenerative diseases. Multiple weak interactions between karyopherin-βs and phase separation-prone proteins, such as FG repeats-containing nucleoporins or IDR-containing karyopherin-β cargos, are likely to be important for passing through the nuclear pore complex and maintaining the soluble state of cargo, respectively. In this review, we discuss how karyopherin-βs regulate phase separation to function.
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Affiliation(s)
- Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu-shi, Shiga 525-8577, Japan
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
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129
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Portz B, Shorter J. Biochemical Timekeeping Via Reentrant Phase Transitions. J Mol Biol 2021; 433:166794. [PMID: 33387533 PMCID: PMC8154630 DOI: 10.1016/j.jmb.2020.166794] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023]
Abstract
Appreciation for the role of liquid-liquid phase separation in the functional organization of cellular matter has exploded in recent years. More recently there has been a growing effort to understand the principles of heterotypic phase separation, the demixing of multiple proteins and nucleic acids into a single functional condensate. A phase transition is termed reentrant if it involves the transformation of a system from one state into a macroscopically similar or identical state via at least two phase transitions elicited by variation of a single parameter. Reentrant liquid-liquid phase separation can occur when the condensation of one species is tuned by another. Reentrant phase transitions have been modeled in vitro using protein and RNA mixtures. These biochemical studies reveal two features of reentrant phase separation that are likely important to functional cellular condensates: (1) the ability to generate condensates with layered functional topologies, and (2) the ability to generate condensates whose composition and duration are self-limiting to enable a form of biochemical timekeeping. We relate these biochemical studies to potential cellular examples and discuss how layered topologies and self-regulation may impact key biological processes.
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Affiliation(s)
- Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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130
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Candelise N, Scaricamazza S, Salvatori I, Ferri A, Valle C, Manganelli V, Garofalo T, Sorice M, Misasi R. Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications. Int J Mol Sci 2021; 22:ijms22116016. [PMID: 34199513 PMCID: PMC8199687 DOI: 10.3390/ijms22116016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.
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Affiliation(s)
- Niccolò Candelise
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-338-891-2668
| | - Silvia Scaricamazza
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
| | - Illari Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Alberto Ferri
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Tina Garofalo
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Maurizio Sorice
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Roberta Misasi
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
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131
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Wiedner HJ, Giudice J. It's not just a phase: function and characteristics of RNA-binding proteins in phase separation. Nat Struct Mol Biol 2021; 28:465-473. [PMID: 34099940 PMCID: PMC8787349 DOI: 10.1038/s41594-021-00601-w] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/30/2021] [Indexed: 12/31/2022]
Abstract
Biomolecular condensates that form via phase separation are increasingly regarded as coordinators of cellular reactions that regulate a wide variety of biological phenomena. Mounting evidence suggests that multiple steps of the RNA life cycle are organized within RNA-binding protein-rich condensates. In this Review, we discuss recent insights into the influence of phase separation on RNA biology, which has implications for basic cell biology, the pathogenesis of human diseases and the development of novel therapies.
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Affiliation(s)
- Hannah J Wiedner
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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132
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Cascarina SM, King DC, Osborne Nishimura E, Ross ED. LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains. NAR Genom Bioinform 2021; 3:lqab048. [PMID: 34056598 PMCID: PMC8153834 DOI: 10.1093/nargab/lqab048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Low complexity domains (LCDs) in proteins are regions predominantly composed of a small subset of the possible amino acids. LCDs are involved in a variety of normal and pathological processes across all domains of life. Existing methods define LCDs using information-theoretical complexity thresholds, sequence alignment with repetitive regions, or statistical overrepresentation of amino acids relative to whole-proteome frequencies. While these methods have proven valuable, they are all indirectly quantifying amino acid composition, which is the fundamental and biologically-relevant feature related to protein sequence complexity. Here, we present a new computational tool, LCD-Composer, that directly identifies LCDs based on amino acid composition and linear amino acid dispersion. Using LCD-Composer's default parameters, we identified simple LCDs across all organisms available through UniProt and provide the resulting data in an accessible form as a resource. Furthermore, we describe large-scale differences between organisms from different domains of life and explore organisms with extreme LCD content for different LCD classes. Finally, we illustrate the versatility and specificity achievable with LCD-Composer by identifying diverse classes of LCDs using both simple and multifaceted composition criteria. We demonstrate that the ability to dissect LCDs based on these multifaceted criteria enhances the functional mapping and classification of LCDs.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - David C King
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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133
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Liu EA, Mori E, Hamasaki F, Lieberman AP. TDP-43 proteinopathy occurs independently of autophagic substrate accumulation and underlies nuclear defects in Niemann-Pick C disease. Neuropathol Appl Neurobiol 2021; 47:1019-1032. [PMID: 34048071 DOI: 10.1111/nan.12738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022]
Abstract
AIMS Neuronal cytoplasmic inclusions of TAR-DNA binding protein of 43 kDa (TDP-43) are a pathological hallmark of diverse neurodegenerative disorders, yet the processes that mediate their formation and their functional significance remain incompletely understood. Both dysfunction in autophagy and neuroinflammation have been linked to TDP-43 mislocalisation. Here, we investigate TDP-43 proteinopathy in Niemann-Pick type C disease (NPC), an autosomal recessive lysosomal storage disease (LSD) distinguished by the accumulation of unesterified cholesterol within late endosomes and lysosomes. NPC is characterised by neurodegeneration, neuroinflammation and multifocal disruption of the autophagy pathway. METHODS We utilised immunohistochemistry, confocal microscopy, electron microscopy and biochemical and gene expression studies to characterise TDP-43 pathology and autophagic substrate accumulation in Npc1-deficient mice. RESULTS In the NPC brain, cytoplasmic TDP-43 mislocalisation was independent of autophagic substrate accumulation. These pathologies occurred in distinct neuronal subtypes, as brainstem cholinergic neurons were more susceptible to TDP-43 mislocalisation, whereas glutamatergic neurons exhibited hallmarks of autophagic dysfunction. Furthermore, TDP-43 mislocalisation did not co-localise with markers of stress granules or progress to ubiquitinated aggregates over months in vivo, indicating a stable, early stage in the aggregation process. Neither microgliosis nor neuroinflammation were sufficient to drive TDP-43 proteinopathy in the NPC brain. Notably, cytoplasmic TDP-43 co-localised with the nuclear import factor importin α, and TDP-43 mislocalised neurons demonstrated nuclear membrane abnormalities and disruption of nucleocytoplasmic transport. CONCLUSION Our findings highlight the relationship between LSDs and TDP-43 proteinopathy, define its functional importance in NPC by triggering nuclear dysfunction, and expand the spectrum of TDP-43 pathology in the diseased brain.
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Affiliation(s)
- Elaine A Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.,Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Erika Mori
- Yamaguchi University School of Medicine, Ube, Japan
| | | | - Andrew P Lieberman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
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134
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Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PLoS One 2021; 16:e0247285. [PMID: 34019539 PMCID: PMC8139511 DOI: 10.1371/journal.pone.0247285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 11/23/2022] Open
Abstract
Across eukaryotes, homopolymeric repeats of amino acids are enriched in regulatory proteins such as transcription factors and chromatin remodelers. These domains play important roles in signaling, binding, prion formation, and functional phase separation. Azf1p is a prion-forming yeast transcription factor that contains two homorepeat domains, a polyglutamine and a polyasparagine domain. In this work, we report a new phenotype for Azf1p and identify a large set of genes that are regulated by Azf1p during growth in glucose. We show that the polyasparagine (polyN) domain plays a subtle role in transcription but is dispensable for Azf1p localization and prion formation. Genes upregulated upon deletion of the polyN domain are enriched in functions related to carbon metabolism and storage. This domain may therefore be a useful target for engineering yeast strains for fermentation applications and small molecule production. We also report that both the polyasparagine and polyglutamine domains vary in length across strains of S. cerevisiae and propose a model for how this variation may impact protein function.
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135
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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136
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Cicardi ME, Marrone L, Azzouz M, Trotti D. Proteostatic imbalance and protein spreading in amyotrophic lateral sclerosis. EMBO J 2021; 40:e106389. [PMID: 33792056 PMCID: PMC8126909 DOI: 10.15252/embj.2020106389] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/18/2020] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder whose exact causative mechanisms are still under intense investigation. Several lines of evidence suggest that the anatomical and temporal propagation of pathological protein species along the neural axis could be among the main driving mechanisms for the fast and irreversible progression of ALS pathology. Many ALS-associated proteins form intracellular aggregates as a result of their intrinsic prion-like properties and/or following impairment of the protein quality control systems. During the disease course, these mutated proteins and aberrant peptides are released in the extracellular milieu as soluble or aggregated forms through a variety of mechanisms. Internalization by recipient cells may seed further aggregation and amplify existing proteostatic imbalances, thus triggering a vicious cycle that propagates pathology in vulnerable cells, such as motor neurons and other susceptible neuronal subtypes. Here, we provide an in-depth review of ALS pathology with a particular focus on the disease mechanisms of seeding and transmission of the most common ALS-associated proteins, including SOD1, FUS, TDP-43, and C9orf72-linked dipeptide repeats. For each of these proteins, we report historical, biochemical, and pathological evidence of their behaviors in ALS. We further discuss the possibility to harness pathological proteins as biomarkers and reflect on the implications of these findings for future research.
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Affiliation(s)
- Maria Elena Cicardi
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Lara Marrone
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Mimoun Azzouz
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Davide Trotti
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
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137
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Li Y, Sun B, Wang Z, He Z, Yang F, Wang H, Cui F, Chen Z, Ling L, Wang C, Huang X. Mutation Screening of the GLE1 Gene in a Large Chinese Cohort of Amyotrophic Lateral Sclerosis Patients. Front Neurosci 2021; 15:595775. [PMID: 34025336 PMCID: PMC8131544 DOI: 10.3389/fnins.2021.595775] [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: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease involving the upper and lower motor neurons of the spinal cord, brainstem, and cerebral cortex. At least 30 genes have been implicated in familial ALS (fALS) and sporadic ALS (sALS). Kaneb et al. (2015) first carried out a large-scale sequencing study in ALS patients and identified two loss-of-function (LOF) variants in the GLE1 gene. The LOF mutation-induced disruption of RNA metabolism through the haploinsufficiency mechanism is implicated in ALS pathogenesis. A total of 628 ALS patients and 522 individuals without neurodegenerative disorders were enrolled in this study to explore the GLE1 gene contribution to ALS in the Chinese population. All 16 exons and the flanking intron of GLE1 were screened by Sanger sequencing. In total, we identified seven rare GLE1 coding variants, including one novel nonsense mutation and six rare missense mutations in 628 ALS patients. The frequency of GLE1 LOF mutations was 0.16% (1/628) among Chinese sALS patients, implying that it is an uncommon genetic determinant of ALS in Chinese patients. Additionally, the rare missense variants in the hCG1-binding domain of GLE1 impairing the distribution of the hGle1B isoform at the nuclear pore complex (NPC) region may be involved in the pathogenesis of ALS.
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Affiliation(s)
- Yanran Li
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bo Sun
- Geriatric Neurological Department of the Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhengqing He
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fei Yang
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongfen Wang
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fang Cui
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhaohui Chen
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Li Ling
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xusheng Huang
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, Beijing, China
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138
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Levone BR, Lenzken SC, Antonaci M, Maiser A, Rapp A, Conte F, Reber S, Mechtersheimer J, Ronchi AE, Mühlemann O, Leonhardt H, Cardoso MC, Ruepp MD, Barabino SM. FUS-dependent liquid-liquid phase separation is important for DNA repair initiation. J Cell Biol 2021; 220:e202008030. [PMID: 33704371 PMCID: PMC7953258 DOI: 10.1083/jcb.202008030] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/17/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important effectors of the cellular DNA damage response (DDR). The RBP FUS is implicated in RNA metabolism and DNA repair, and it undergoes reversible liquid-liquid phase separation (LLPS) in vitro. Here, we demonstrate that FUS-dependent LLPS is necessary for the initiation of the DDR. Using laser microirradiation in FUS-knockout cells, we show that FUS is required for the recruitment to DNA damage sites of the DDR factors KU80, NBS1, and 53BP1 and of SFPQ, another RBP implicated in the DDR. The relocation of KU80, NBS1, and SFPQ is similarly impaired by LLPS inhibitors, or LLPS-deficient FUS variants. We also show that LLPS is necessary for efficient γH2AX foci formation. Finally, using superresolution structured illumination microscopy, we demonstrate that the absence of FUS impairs the proper arrangement of γH2AX nanofoci into higher-order clusters. These findings demonstrate the early requirement for FUS-dependent LLPS in the activation of the DDR and the proper assembly of DSB repair complexes.
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Affiliation(s)
- Brunno R. Levone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Silvia C. Lenzken
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marco Antonaci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Andreas Maiser
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Alexander Rapp
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Francesca Conte
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Stefan Reber
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Jonas Mechtersheimer
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Antonella E. Ronchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Marc-David Ruepp
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Silvia M.L. Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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139
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Abstract
Neurodegenerative diseases and other protein-misfolding disorders represent a longstanding biomedical challenge, and effective therapies remain largely elusive. This failure is due, in part, to the recalcitrant and diverse nature of misfolded protein conformers. Recent work has uncovered that many aggregation-prone proteins can also undergo liquid-liquid phase separation, a process by which macromolecules self-associate to form dense condensates with liquid properties that are compositionally distinct from the bulk cellular milieu. Efforts to combat diseases caused by toxic protein states focus on exploiting or enhancing the proteostasis machinery to prevent and reverse pathological protein conformations. Here, we discuss recent advances in elucidating and engineering therapeutic agents to combat the diverse aberrant protein states that underlie protein-misfolding disorders.
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Affiliation(s)
- Charlotte M. Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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140
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Fonda BD, Jami KM, Boulos NR, Murray DT. Identification of the Rigid Core for Aged Liquid Droplets of an RNA-Binding Protein Low Complexity Domain. J Am Chem Soc 2021; 143:6657-6668. [PMID: 33896178 DOI: 10.1021/jacs.1c02424] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biomolecular condensation of proteins with low complexity sequences plays a functional role in RNA metabolism and a pathogenic role in neurodegenerative diseases. The formation of dynamic liquid droplets brings biomolecules together to achieve complex cellular functions. The rigidification of liquid droplets into β-strand-rich hydrogel structures composed of protein fibrils is thought to be purely pathological in nature. However, low complexity sequences often harbor multiple fibril-prone regions with delicately balanced functional and pathological interactions. Here, we investigate the maturation of liquid droplets formed by the low complexity domain of the TAR DNA-binding protein 43 (TDP-43). Solid state nuclear magnetic resonance measurements on the aged liquid droplets identify residues 365-400 as the structured core, which are squarely outside the region between residues 311-360 thought to be most important for pathological fibril formation and aggregation. The results of this study suggest that multiple segments of this low complexity domain are prone to form fibrils and that stabilization of β-strand-rich structure in one segment precludes the other region from adopting a rigid fibril structure.
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Affiliation(s)
- Blake D Fonda
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Khaled M Jami
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Natalie R Boulos
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dylan T Murray
- Department of Chemistry, University of California, Davis, California 95616, United States
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141
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Zhang S, Qiu M, Gao S, Tian T. Circular RNA PCDH10 regulates the tumorigenesis of pancreatic cancer through the miR-338-3p/hTERT axis. Am J Transl Res 2021; 13:2181-2197. [PMID: 34017382 PMCID: PMC8129247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Protocadherin-10 (PCDH10) was previously identified as a pancreatic cancer (PC) suppressor by reducing telomerase activity through binding with human telomerase reverse transcriptase (hTERT). However, we did not observe any effects of PCDH10 on hTERT mRNA or protein expression. Our research found that the PCDH10 gene could be transcribed into linear mRNA or circular RNA, and FUS could bind to the introns flanking the circularized exons, inducing the PCDH10 linear mRNA to shift to circPCDH10 in PC cells. Knockdown of circPCDH10 significantly inhibited PC progression. Mechanistically, circPCDH10 acted as a sponge of miR-338-3p, which could negatively regulate hTERT expression in PC cells. The inhibitory effects of circPCDH10 knockdown on PC cells could be notably reversed by miR-338-3p inhibition and ectopic expression of hTERT. Overall, we propose that the increased FUS expression in PC cells made circPCDH10 the preferred product of the PCDH10 gene, and circPCDH10 might promote PC progression through upregulation of hTERT expression by targeting miR-338-3p.
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Affiliation(s)
- Shenfeng Zhang
- Department of Oncology, Zaozhuang Municipal Hospital Zaozhuang 277000, Shandong Province, China
| | - Meiqing Qiu
- Department of Oncology, Zaozhuang Municipal Hospital Zaozhuang 277000, Shandong Province, China
| | - Shan Gao
- Department of Oncology, Zaozhuang Municipal Hospital Zaozhuang 277000, Shandong Province, China
| | - Tao Tian
- Department of Oncology, Zaozhuang Municipal Hospital Zaozhuang 277000, Shandong Province, China
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142
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Peggion C, Massimino ML, Stella R, Bortolotto R, Agostini J, Maldi A, Sartori G, Tonello F, Bertoli A, Lopreiato R. Nucleolin Rescues TDP-43 Toxicity in Yeast and Human Cell Models. Front Cell Neurosci 2021; 15:625665. [PMID: 33912014 PMCID: PMC8072491 DOI: 10.3389/fncel.2021.625665] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
TDP-43 is a nuclear protein involved in pivotal processes, extensively studied for its implication in neurodegenerative disorders. TDP-43 cytosolic inclusions are a common neuropathologic hallmark in amyotrophic lateral sclerosis (ALS) and related diseases, and it is now established that TDP-43 misfolding and aggregation play a key role in their etiopathology. TDP-43 neurotoxic mechanisms are not yet clarified, but the identification of proteins able to modulate TDP-43-mediated damage may be promising therapeutic targets for TDP-43 proteinopathies. Here we show by the use of refined yeast models that the nucleolar protein nucleolin (NCL) acts as a potent suppressor of TDP-43 toxicity, restoring cell viability. We provide evidence that NCL co-expression is able to alleviate TDP-43-induced damage also in human cells, further supporting its beneficial effects in a more consistent pathophysiological context. Presented data suggest that NCL could promote TDP-43 nuclear retention, reducing the formation of toxic cytosolic TDP-43 inclusions.
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Affiliation(s)
- Caterina Peggion
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Roberto Stella
- Food Safety Division, Department of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Raissa Bortolotto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Jessica Agostini
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Arianna Maldi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR - Neuroscience Institute, Padova, Italy.,Padova Neuroscience Center, University of Padova, Padova, Italy
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143
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Darling AL, Shorter J. Combating deleterious phase transitions in neurodegenerative disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118984. [PMID: 33549703 PMCID: PMC7965345 DOI: 10.1016/j.bbamcr.2021.118984] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022]
Abstract
Protein aggregation is a hallmark of neurodegenerative diseases. However, the mechanism that induces pathogenic aggregation is not well understood. Recently, it has emerged that several of the pathological proteins found in an aggregated or mislocalized state in neurodegenerative diseases are also able to undergo liquid-liquid phase separation (LLPS) under physiological conditions. Although these phase transitions are likely important for various physiological functions, neurodegenerative disease-related mutations and conditions can alter the LLPS behavior of these proteins, which can elicit toxicity. Therefore, therapeutics that antagonize aberrant LLPS may be able to mitigate toxicity and aggregation that is ubiquitous in neurodegenerative disease. Here, we discuss the mechanisms by which aberrant protein phase transitions may contribute to neurodegenerative disease. We also outline potential therapeutic strategies to counter deleterious phases. State without borders: Membrane-less organelles and liquid-liquid phase transitions edited by Vladimir N Uversky.
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Affiliation(s)
- April L Darling
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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144
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MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation. Commun Biol 2021; 4:414. [PMID: 33772081 PMCID: PMC7997880 DOI: 10.1038/s42003-021-01930-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
A disordered to β-sheet transition was thought to drive the functional switch of Q/N-rich prions, similar to pathogenic amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) regions within yeast prion domains in amyloid formation. We show that many human prion-like domains (PrLDs) contain CC regions that overlap with polyQ tracts. Most of the proteins bearing these domains are transcriptional coactivators, including the Mediator complex subunit 15 (MED15) involved in bridging enhancers and promoters. We demonstrate that the human MED15-PrLD forms homodimers in solution sustained by CC interactions and that it is this CC fold that mediates the transition towards a β-sheet amyloid state, its chemical or genetic disruption abolishing aggregation. As in functional yeast prions, a GFP globular domain adjacent to MED15-PrLD retains its structural integrity in the amyloid state. Expression of MED15-PrLD in human cells promotes the formation of cytoplasmic and perinuclear inclusions, kidnapping endogenous full-length MED15 to these aggregates in a prion-like manner. The prion-like properties of MED15 are conserved, suggesting novel mechanisms for the function and malfunction of this transcription coactivator.
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145
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Loughlin FE, West DL, Gunzburg MJ, Waris S, Crawford SA, Wilce MCJ, Wilce JA. Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1. Nucleic Acids Res 2021; 49:2403-2417. [PMID: 33621982 PMCID: PMC7969032 DOI: 10.1093/nar/gkab080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022] Open
Abstract
TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.
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Affiliation(s)
- Fionna E Loughlin
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Danella L West
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Menachem J Gunzburg
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria 3052, Australia
| | - Saboora Waris
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simon A Crawford
- Ramaciotti Centre For Cryo Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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146
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Yang X, Han B, Zhang R, Su Y, Hosseini DK, Wu H, Yang M, Sun H. Development and validation of a RNA binding protein-associated prognostic model for head and neck squamous cell carcinoma. Aging (Albany NY) 2021; 13:7975-7997. [PMID: 33758106 PMCID: PMC8034976 DOI: 10.18632/aging.202848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 03/13/2021] [Indexed: 12/13/2022]
Abstract
Evidence shows that defects in RNA-binding proteins (RBPs) are closely related to the occurrence and development of HNSCC. We obtained 502 tumors and 44 normal samples from the TCGA database, among which 190 differentially expressed RBPs were screened. Finally, a prognostic model containing nine RBPs (CELF2, CPEB1, DDX39B, EIF3L, EZH2, KHDRBS3, RNASE10, RNASE3 and SIDT1) was produced. Further analysis showed that the overall survival rate in the high-risk group was lower than that in the low-risk group. The area under the ROC curve (AUC) in the training and testing groups was significant (3-year AUC, 0.735 vs 0.796; 5-year AUC, 0.821 vs 0.804). In addition, a comprehensive analysis of nine identified RBPs showed that most of them were related to the OS of HNSCC patients, and three of them (CELF2, EZH2, and SIDT1) were differentially expressed in HNSCC and control tissues at the protein level. In addition, our data revealed that the identified RBPs are highly interconnected, with high frequency copy number changes in HNSCC samples. GSEA indicated that the abnormal biological processes related to RNA and the activation of some classical tumor signaling pathways were important driving forces for the development of HNSCC. Our results provide novel insights into the pathogenesis of HNSCC, among which nine RBP markers have potential application value in clinical decision-making and individualized treatment of HNSCC.
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Affiliation(s)
- Xiuping Yang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Baoai Han
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Runshi Zhang
- Department of Clinical Laboratory, Xi'an No. 1 Hospital, Xi'an 710000, China
| | - Yuan Su
- Department of Clinical Laboratory, Xi'an Labor Union Hospital, Xi'an 710000, China
| | - Davood K Hosseini
- Department of Internal Medicine, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Han Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Minlan Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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147
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Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degenerations: Similarities in Genetic Background. Diagnostics (Basel) 2021; 11:diagnostics11030509. [PMID: 33805659 PMCID: PMC7998502 DOI: 10.3390/diagnostics11030509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/27/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating, uniformly lethal progressive degenerative disorder of motor neurons that overlaps with frontotemporal lobar degeneration (FTLD) clinically, morphologically, and genetically. Although many distinct mutations in various genes are known to cause amyotrophic lateral sclerosis, it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neuronal degeneration. Many of the gene mutations are in proteins that share similar functions. They can be grouped into those associated with cell axon dynamics and those associated with cellular phagocytic machinery, namely protein aggregation and metabolism, apoptosis, and intracellular nucleic acid transport. Analysis of pathways implicated by mutant ALS genes has provided new insights into the pathogenesis of both familial forms of ALS (fALS) and sporadic forms (sALS), although, regrettably, this has not yet yielded definitive treatments. Many genes play an important role, with TARDBP, SQSTM1, VCP, FUS, TBK1, CHCHD10, and most importantly, C9orf72 being critical genetic players in these neurological disorders. In this mini-review, we will focus on the molecular mechanisms of these two diseases.
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148
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Multiple Sclerosis-Associated hnRNPA1 Mutations Alter hnRNPA1 Dynamics and Influence Stress Granule Formation. Int J Mol Sci 2021; 22:ijms22062909. [PMID: 33809384 PMCID: PMC7998649 DOI: 10.3390/ijms22062909] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
Evidence indicates that dysfunctional heterogeneous ribonucleoprotein A1 (hnRNPA1; A1) contributes to the pathogenesis of neurodegeneration in multiple sclerosis. Understanding molecular mechanisms of neurodegeneration in multiple sclerosis may result in novel therapies that attenuate neurodegeneration, thereby improving the lives of MS patients with multiple sclerosis. Using an in vitro, blue light induced, optogenetic protein expression system containing the optogene Cryptochrome 2 and a fluorescent mCherry reporter, we examined the effects of multiple sclerosis-associated somatic A1 mutations (P275S and F281L) in A1 localization, cluster kinetics and stress granule formation in real-time. We show that A1 mutations caused cytoplasmic mislocalization, and significantly altered the kinetics of A1 cluster formation/dissociation, and the quantity and size of clusters. A1 mutations also caused stress granule formation to occur more quickly and frequently in response to blue light stimulation. This study establishes a live cell optogenetics imaging system to probe localization and association characteristics of A1. It also demonstrates that somatic mutations in A1 alter its function and promote stress granule formation, which supports the hypothesis that A1 dysfunction may exacerbate neurodegeneration in multiple sclerosis.
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149
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Rawat P, Boehning M, Hummel B, Aprile-Garcia F, Pandit AS, Eisenhardt N, Khavaran A, Niskanen E, Vos SM, Palvimo JJ, Pichler A, Cramer P, Sawarkar R. Stress-induced nuclear condensation of NELF drives transcriptional downregulation. Mol Cell 2021; 81:1013-1026.e11. [PMID: 33548202 PMCID: PMC7939545 DOI: 10.1016/j.molcel.2021.01.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 10/20/2020] [Accepted: 01/11/2021] [Indexed: 12/21/2022]
Abstract
In response to stress, human cells coordinately downregulate transcription and translation of housekeeping genes. To downregulate transcription, the negative elongation factor (NELF) is recruited to gene promoters impairing RNA polymerase II elongation. Here we report that NELF rapidly forms nuclear condensates upon stress in human cells. Condensate formation requires NELF dephosphorylation and SUMOylation induced by stress. The intrinsically disordered region (IDR) in NELFA is necessary for nuclear NELF condensation and can be functionally replaced by the IDR of FUS or EWSR1 protein. We find that biomolecular condensation facilitates enhanced recruitment of NELF to promoters upon stress to drive transcriptional downregulation. Importantly, NELF condensation is required for cellular viability under stressful conditions. We propose that stress-induced NELF condensates reported here are nuclear counterparts of cytosolic stress granules. These two stress-inducible condensates may drive the coordinated downregulation of transcription and translation, likely forming a critical node of the stress survival strategy.
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Affiliation(s)
- Prashant Rawat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany.
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Anwit S Pandit
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; CIBSS, Centre for Integrative Biological Signaling Studies, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ashkan Khavaran
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Einari Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; CIBSS, Centre for Integrative Biological Signaling Studies, Freiburg, Germany; MRC, University of Cambridge, Cambridge, UK.
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150
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Shen B, Chen Z, Yu C, Chen T, Shi M, Li T. Computational Screening of Phase-separating Proteins. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:13-24. [PMID: 33610793 PMCID: PMC8498823 DOI: 10.1016/j.gpb.2020.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/17/2020] [Accepted: 12/10/2020] [Indexed: 11/27/2022]
Abstract
Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells. Proteins that can undergo phase separation in cells share certain typical sequence features, like intrinsically disordered regions (IDRs) and multiple modular domains. Sequence-based analysis tools are commonly used in the screening of these proteins. However, current phase separation predictors are mostly designed for IDR-containing proteins, thus inevitably overlook the phase-separating proteins with relatively low IDR content. Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins: protein–protein interaction (PPI) networks show multivalent interactions that underlie phase separation process; post-translational modifications (PTMs) are crucial in the regulation of phase separation behavior; spherical structures revealed in immunofluorescence (IF)images indicate condensed droplets formed by phase-separating proteins, distinguishing these proteins from non-phase-separating proteins. Here, we summarize the sequence-based tools for predicting phase-separating proteins and highlight the importance of incorporating PPIs, PTMs, and IF images into phase separation prediction in future studies.
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Affiliation(s)
- Boyan Shen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhaoming Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chunyu Yu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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