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Rzepnikowska W, Kaminska J, Kochański A. The molecular mechanisms that underlie IGHMBP2-related diseases. Neuropathol Appl Neurobiol 2024; 50:e13005. [PMID: 39119929 DOI: 10.1111/nan.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 08/10/2024]
Abstract
Immunoglobulin Mu-binding protein 2 (IGHMBP2) pathogenic variants result in the fatal, neurodegenerative disease spinal muscular atrophy with respiratory distress type 1 (SMARD1) and the milder, Charcot-Marie-Tooth (CMT) type 2S (CMT2S) neuropathy. More than 20 years after the link between IGHMBP2 and SMARD1 was revealed, and 10 years after the discovery of the association between IGHMBP2 and CMT2S, the pathogenic mechanism of these diseases is still not well defined. The discovery that IGHMBP2 functions as an RNA/DNA helicase was an important step, but it did not reveal the pathogenic mechanism. Helicases are enzymes that use ATP hydrolysis to catalyse the separation of nucleic acid strands. They are involved in numerous cellular processes, including DNA repair and transcription; RNA splicing, transport, editing and degradation; ribosome biogenesis; translation; telomere maintenance; and homologous recombination. IGHMBP2 appears to be a multifunctional factor involved in several cellular processes that regulate gene expression. It is difficult to determine which processes, when dysregulated, lead to pathology. Here, we summarise our current knowledge of the clinical presentation of IGHMBP2-related diseases. We also overview the available models, including yeast, mice and cells, which are used to study the function of IGHMBP2 and the pathogenesis of the related diseases. Further, we discuss the structure of the IGHMBP2 protein and its postulated roles in cellular functioning. Finally, we present potential anomalies that may result in the neurodegeneration observed in IGHMBP2-related disease and highlight the most prominent ones.
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Affiliation(s)
- Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, 02-106, Poland
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2
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Chuang HY, He RY, Huang YA, Hsu WT, Cheng YJ, Guo ZR, Wali N, Hwang IS, Shie JJ, Huang JJT. Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein. Nat Commun 2024; 15:5686. [PMID: 38971830 PMCID: PMC11227587 DOI: 10.1038/s41467-024-50025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.
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Affiliation(s)
- Hao-Yu Chuang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ya-Jen Cheng
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Zheng-Rong Guo
- Institute of Physics, Academia Sinica, Taipei, 115, Taiwan
| | - Niaz Wali
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | | | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
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3
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Zuniga G, Katsumura S, De Mange J, Ramirez P, Atrian F, Morita M, Frost B. Pathogenic tau induces an adaptive elevation in mRNA translation rate at early stages of disease. Aging Cell 2024:e14245. [PMID: 38932463 DOI: 10.1111/acel.14245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Alterations in the rate and accuracy of messenger RNA (mRNA) translation are associated with aging and several neurodegenerative disorders, including Alzheimer's disease and related tauopathies. We previously reported that error-containing RNA that are normally cleared via nonsense-mediated mRNA decay (NMD), a key RNA surveillance mechanism, are translated in the adult brain of a Drosophila model of tauopathy. In the current study, we find that newly-synthesized peptides and translation machinery accumulate within nuclear envelope invaginations that occur as a consequence of tau pathology, and that the rate of mRNA translation is globally elevated in early stages of disease in adult brains of Drosophila models of tauopathy. Polysome profiling from adult heads of tau transgenic Drosophila reveals the preferential translation of specific mRNA that have been previously linked to neurodegeneration. Unexpectedly, we find that panneuronal elevation of NMD further elevates the global translation rate in tau transgenic Drosophila, as does treatment with rapamycin. As NMD activation and rapamycin both suppress tau-induced neurodegeneration, their shared effect on translation suggests that elevated rates of mRNA translation are an early adaptive mechanism to limit neurodegeneration. Our work provides compelling evidence that tau-induced deficits in NMD reshape the tau translatome by increasing translation of RNA that are normally repressed in healthy cells.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Sakie Katsumura
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan
| | - Jasmine De Mange
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Farzaneh Atrian
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Masahiro Morita
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, San Antonio, Texas, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
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Hu Y, Chen W, Wei C, Jiang S, Li S, Wang X, Xu R. Pathological mechanisms of amyotrophic lateral Sclerosis. Neural Regen Res 2024; 19:1036-1044. [PMID: 37862206 PMCID: PMC10749610 DOI: 10.4103/1673-5374.382985] [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: 02/11/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 10/22/2023] Open
Abstract
Amyotrophic lateral sclerosis refers to a neurodegenerative disease involving the motor system, the cause of which remains unexplained despite several years of research. Thus, the journey to understanding or treating amyotrophic lateral sclerosis is still a long one. According to current research, amyotrophic lateral sclerosis is likely not due to a single factor but rather to a combination of mechanisms mediated by complex interactions between molecular and genetic pathways. The progression of the disease involves multiple cellular processes and the interaction between different complex mechanisms makes it difficult to identify the causative factors of amyotrophic lateral sclerosis. Here, we review the most common amyotrophic lateral sclerosis-associated pathogenic genes and the pathways involved in amyotrophic lateral sclerosis, as well as summarize currently proposed potential mechanisms responsible for amyotrophic lateral sclerosis disease and their evidence for involvement in amyotrophic lateral sclerosis. In addition, we discuss current emerging strategies for the treatment of amyotrophic lateral sclerosis. Studying the emergence of these new therapies may help to further our understanding of the pathogenic mechanisms of the disease.
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Affiliation(s)
- Yushu Hu
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Wenzhi Chen
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Caihui Wei
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Shishi Jiang
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Shu Li
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Xinxin Wang
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
- Department of Neurology, The First Affiliated Hospital of Nanchang Medical College; The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
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5
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Ge J, Wang Z, Wu J. NAT10-mediated ac 4C modification promotes ectoderm differentiation of human embryonic stem cells via acetylating NR2F1 mRNA. Cell Prolif 2024; 57:e13577. [PMID: 38041497 PMCID: PMC10984107 DOI: 10.1111/cpr.13577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/11/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023] Open
Abstract
Cell fate determination in mammalian development is complex and precisely controlled and accumulating evidence indicates that epigenetic mechanisms are crucially involved. N4-acetylcytidine (ac4C) is a recently identified modification of messenger RNA (mRNA); however, its functions are still elusive in mammalian. Here, we show that N-acetyltransferase 10 (NAT10)-mediated ac4C modification promotes ectoderm differentiation of human embryonic stem cells (hESCs) by acetylating nuclear receptor subfamily 2 group F member 1 (NR2F1) mRNA to enhance translation efficiency (TE). Acetylated RNA immunoprecipitation sequencing (acRIP-seq) revealed that levels of ac4C modification were higher in ectodermal neuroepithelial progenitor (NEP) cells than in hESCs or mesoendoderm cells. In addition, integrated analysis of acRIP-seq and ribosome profiling sequencing revealed that NAT10 catalysed ac4C modification to improve TE in NEP cells. RIP-qRT-PCR analysis identified an interaction between NAT10 and NR2F1 mRNA in NEP cells and NR2F1 accelerated the nucleus-to-cytoplasm translocation of yes-associated protein 1, which contributed to ectodermal differentiation of hESCs. Collectively, these findings point out the novel regulatory role of ac4C modification in the early ectodermal differentiation of hESCs and will provide a new strategy for the treatment of neuroectodermal defects diseases.
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Affiliation(s)
- Junbang Ge
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoxia Wang
- Laboratory Animal Center of Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Ji Wu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical SciencesNingxia Medical UniversityYinchuanChina
- Shanghai Key Laboratory of Reproductive MedicineShanghaiChina
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6
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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7
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Wang PS, Liu Z, Sweef O, Xie J, Chen J, Zhu H, Zeidler-Erdely PC, Yang C, Wang Z. Long noncoding RNA ABHD11-AS1 interacts with SART3 and regulates CD44 RNA alternative splicing to promote lung carcinogenesis. ENVIRONMENT INTERNATIONAL 2024; 185:108494. [PMID: 38364571 PMCID: PMC11375692 DOI: 10.1016/j.envint.2024.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Hexavalent chromium [Cr(VI)] is a common environmental pollutant and chronic exposure to Cr(VI) causes lung cancer in humans, however, the mechanism of Cr(VI) carcinogenesis has not been well understood. Lung cancer is the leading cause of cancer-related death, although the mechanisms of how lung cancer develops and progresses have been poorly understood. While long non-coding RNAs (lncRNAs) are found abnormally expressed in cancer, how dysregulated lncRNAs contribute to carcinogenesis remains largely unknown. The goal of this study is to investigate the mechanism of Cr(VI)-induced lung carcinogenesis focusing on the role of the lncRNA ABHD11 antisense RNA 1 (tail to tail) (ABHD11-AS1). It was found that the lncRNA ABHD11-AS1 expression levels are up-regulated in chronic Cr(VI) exposure-transformed human bronchial epithelial cells, chronically Cr(VI)-exposed mouse lung tissues, and human lung cancer cells as well. Bioinformatics analysis revealed that ABHD11-AS1 levels are up-regulated in lung adenocarcinomas (LUADs) tissues and associated with worse overall survival of LUAD patients but not in lung squamous cell carcinomas. It was further determined that up-regulation of ABHD11-AS1 expression plays an important role in chronic Cr(VI) exposure-induced cell malignant transformation and tumorigenesis, and the stemness of human lung cancer cells. Mechanistically, it was found that ABHD11-AS1 directly binds SART3 (spliceosome associated factor 3, U4/U6 recycling protein). The interaction of ABHD11-AS1 with SART3 promotes USP15 (ubiquitin specific peptidase 15) nuclear localization. Nuclear localized USP15 interacts with pre-mRNA processing factor 19 (PRPF19) to increase CD44 RNA alternative splicing activating β-catenin and enhancing cancer stemness. Together, these findings indicate that lncRNA ABHD11-AS1 interacts with SART3 and regulates CD44 RNA alternative splicing to promote cell malignant transformation and lung carcinogenesis.
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Affiliation(s)
- Po-Shun Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zulong Liu
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Osama Sweef
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jie Xie
- Department of Toxicology and Cancer Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Haining Zhu
- Department of Biochemistry and Molecular Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Patti C Zeidler-Erdely
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Chengfeng Yang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Zhishan Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
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Gomez N, Hsieh C, Li X, Dykstra M, Waksmacki J, Altheim C, Bechar Y, Klim J, Zaepfel B, Rothstein J, Tank EE, Barmada SJ. Counter-regulation of RNA stability by UPF1 and TDP43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578310. [PMID: 38352350 PMCID: PMC10862862 DOI: 10.1101/2024.01.31.578310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
RNA quality control is crucial for proper regulation of gene expression. Disruption of nonsense mediated mRNA decay (NMD), the primary RNA decay pathway responsible for the degradation of transcripts containing premature termination codons (PTCs), can disrupt development and lead to multiple diseases in humans and other animals. Similarly, therapies targeting NMD may have applications in hematological, neoplastic and neurological disorders. As such, tools capable of accurately quantifying NMD status could be invaluable for investigations of disease pathogenesis and biomarker identification. Toward this end, we assemble, validate, and apply a next-generation sequencing approach (NMDq) for identifying and measuring the abundance of PTC-containing transcripts. After validating NMDq performance and confirming its utility for tracking RNA surveillance, we apply it to determine pathway activity in two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) characterized by RNA misprocessing and abnormal RNA stability. Despite the genetic and pathologic evidence implicating dysfunctional RNA metabolism, and NMD in particular, in these conditions, we detected no significant differences in PTC-encoding transcripts in ALS models or disease. Contrary to expectations, overexpression of the master NMD regulator UPF1 had little effect on the clearance of transcripts with PTCs, but rather restored RNA homeostasis through differential use and decay of alternatively poly-adenylated isoforms. Together, these data suggest that canonical NMD is not a significant contributor to ALS/FTD pathogenesis, and that UPF1 promotes neuronal survival by regulating transcripts with abnormally long 3'UTRs.
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Rezvykh A, Shteinberg D, Bronovitsky E, Ustyugov A, Funikov S. Animal Models of FUS-Proteinopathy: A Systematic Review. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S34-S56. [PMID: 38621743 DOI: 10.1134/s0006297924140037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 04/17/2024]
Abstract
Mutations that disrupt the function of the DNA/RNA-binding protein FUS could cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. One of the key features in ALS pathogenesis is the formation of insoluble protein aggregates containing aberrant isoforms of the FUS protein in the cytoplasm of upper and lower motor neurons. Reproduction of human pathology in animal models is the main tool for studying FUS-associated pathology and searching for potential therapeutic agents for ALS treatment. In this review, we provide a systematic analysis of the role of FUS protein in ALS pathogenesis and an overview of the results of modelling FUS-proteinopathy in animals.
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Affiliation(s)
- Alexander Rezvykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Daniil Shteinberg
- Institute of Physiologically Active Compounds, Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, 142432, Russia
| | | | - Aleksey Ustyugov
- Institute of Physiologically Active Compounds, Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, 142432, Russia
| | - Sergei Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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10
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Assoni AF, Guerrero EN, Wardenaar R, Oliveira D, Bakker PL, Alves LM, Carvalho VM, Okamoto OK, Zatz M, Foijer F. IFNγ protects motor neurons from oxidative stress via enhanced global protein synthesis in FUS-associated amyotrophic lateral sclerosis. Brain Pathol 2024; 34:e13206. [PMID: 37582053 PMCID: PMC10711262 DOI: 10.1111/bpa.13206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/12/2023] [Indexed: 08/17/2023] Open
Abstract
Amyotrophic lateral sclerosis type 6 (ALS6) is a familial subtype of ALS linked to Fused in Sarcoma (FUS) gene mutation. FUS mutations lead to decreased global protein synthesis, but the mechanism that drives this has not been established. Here, we used ALS6 patient-derived induced pluripotent stem cells (hIPSCs) to study the effect of the ALS6 FUSR521H mutation on the translation machinery in motor neurons (MNs). We find, in agreement with findings of others, that protein synthesis is decreased in FUSR521H MNs. Furthermore, FUSR521H MNs are more sensitive to oxidative stress and display reduced expression of TGF-β and mTORC gene pathways when stressed. Finally, we show that IFNγ treatment reduces apoptosis of FUSR521H MNs exposed to oxidative stress and partially restores the translation rates in FUSR521H MNs. Overall, these findings suggest that a functional IFNγ response is important for FUS-mediated protein synthesis, possibly by FUS nuclear translocation in ALS6.
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Affiliation(s)
- Amanda Faria Assoni
- European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Erika N. Guerrero
- European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Stem Cell ResearchGorgas Memorial Institute for Health StudiesPanama CityRepublic of Panama
| | - René Wardenaar
- European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Danyllo Oliveira
- Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Petra L. Bakker
- European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Luciana M. Alves
- Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | | | | | - Mayana Zatz
- Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
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Zhao B, Cowan CM, Coutts JA, Christy DD, Saraph A, Hsueh SCC, Plotkin SS, Mackenzie IR, Kaplan JM, Cashman NR. Targeting RACK1 to alleviate TDP-43 and FUS proteinopathy-mediated suppression of protein translation and neurodegeneration. Acta Neuropathol Commun 2023; 11:200. [PMID: 38111057 PMCID: PMC10726565 DOI: 10.1186/s40478-023-01705-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) and Fused in Sarcoma/Translocated in Sarcoma (FUS) are ribonucleoproteins associated with pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Under physiological conditions, TDP-43 and FUS are predominantly localized in the nucleus, where they participate in transcriptional regulation, RNA splicing and metabolism. In disease, however, they are typically mislocalized to the cytoplasm where they form aggregated inclusions. A number of shared cellular pathways have been identified that contribute to TDP-43 and FUS toxicity in neurodegeneration. In the present study, we report a novel pathogenic mechanism shared by these two proteins. We found that pathological FUS co-aggregates with a ribosomal protein, the Receptor for Activated C-Kinase 1 (RACK1), in the cytoplasm of spinal cord motor neurons of ALS, as previously reported for pathological TDP-43. In HEK293T cells transiently transfected with TDP-43 or FUS mutant lacking a functional nuclear localization signal (NLS; TDP-43ΔNLS and FUSΔNLS), cytoplasmic TDP-43 and FUS induced co-aggregation with endogenous RACK1. These co-aggregates sequestered the translational machinery through interaction with the polyribosome, accompanied by a significant reduction of global protein translation. RACK1 knockdown decreased cytoplasmic aggregation of TDP-43ΔNLS or FUSΔNLS and alleviated associated global translational suppression. Surprisingly, RACK1 knockdown also led to partial nuclear localization of TDP-43ΔNLS and FUSΔNLS in some transfected cells, despite the absence of NLS. In vivo, RACK1 knockdown alleviated retinal neuronal degeneration in transgenic Drosophila melanogaster expressing hTDP-43WT or hTDP-43Q331K and improved motor function of hTDP-43WT flies, with no observed adverse effects on neuronal health in control knockdown flies. In conclusion, our results revealed a novel shared mechanism of pathogenesis for misfolded aggregates of TDP-43 and FUS mediated by interference with protein translation in a RACK1-dependent manner. We provide proof-of-concept evidence for targeting RACK1 as a potential therapeutic approach for TDP-43 or FUS proteinopathy associated with ALS and FTLD.
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Affiliation(s)
- Beibei Zhao
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
- ProMIS Neurosciences, Cambridge, MA, 02142, USA
| | - Catherine M Cowan
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Juliane A Coutts
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Darren D Christy
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Ananya Saraph
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Stephen S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ian R Mackenzie
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | | | - Neil R Cashman
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada.
- ProMIS Neurosciences, Cambridge, MA, 02142, USA.
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12
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Tsui A, Kouznetsova VL, Kesari S, Fiala M, Tsigelny IF. Role of Senataxin in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2023; 73:996-1009. [PMID: 37982993 DOI: 10.1007/s12031-023-02169-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, uncurable neurodegenerative disorder characterized by the degradation of motor neurons leading to muscle impairment, failure, and death. Senataxin, encoded by the SETX gene, is a human helicase protein whose mutations have been linked with ALS onset, particularly in its juvenile ALS4 form. Using senataxin's yeast homolog Sen1 as a model for study, it is suggested that senataxin's N-terminus interacts with RNA polymerase II, whilst its C-terminus engages in helicase activity. Senataxin is heavily involved in transcription regulation, termination, and R-loop resolution, enabled by recruitment and interactions with enzymes such as ubiquitin protein ligase SAN1 and ribonuclease H (RNase H). Senataxin also engages in DNA damage response (DDR), primarily interacting with the exosome subunit Rrp45. The Sen1 mutation E1597K, alongside the L389S and R2136H gain-of-function mutations to senataxin, is shown to cause negative structural and thus functional effects to the protein, thus contributing to a disruption in WT functions, motor neuron (MN) degeneration, and the manifestation of ALS clinical symptoms. This review corroborates and summarizes published papers concerning the structure and function of senataxin as well as the effects of their mutations in ALS pathology in order to compile current knowledge and provide a reference for future research. The findings compiled in this review are indicative of the experimental and therapeutic potential of senataxin and its mutations as a target in future ALS treatment/cure discovery, with some potential therapeutic routes also being discussed in the review.
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Affiliation(s)
- Andrew Tsui
- REHS Program, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
- CureScience Institute, San Diego, CA, USA
- BiAna, San Diego, La Jolla, CA, USA
| | | | - Milan Fiala
- Department of Integrative Biology and Physiology, School of Medicine, UCLA, Los Angeles, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- CureScience Institute, San Diego, CA, USA.
- BiAna, San Diego, La Jolla, CA, USA.
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13
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Pelaez MC, Desmeules A, Gelon PA, Glasson B, Marcadet L, Rodgers A, Phaneuf D, Pozzi S, Dutchak PA, Julien JP, Sephton CF. Neuronal dysfunction caused by FUSR521G promotes ALS-associated phenotypes that are attenuated by NF-κB inhibition. Acta Neuropathol Commun 2023; 11:182. [PMID: 37974279 PMCID: PMC10652582 DOI: 10.1186/s40478-023-01671-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are related neurodegenerative diseases that belong to a common disease spectrum based on overlapping clinical, pathological and genetic evidence. Early pathological changes to the morphology and synapses of affected neuron populations in ALS/FTD suggest a common underlying mechanism of disease that requires further investigation. Fused in sarcoma (FUS) is a DNA/RNA-binding protein with known genetic and pathological links to ALS/FTD. Expression of ALS-linked FUS mutants in mice causes cognitive and motor defects, which correlate with loss of motor neuron dendritic branching and synapses, in addition to other pathological features of ALS/FTD. The role of ALS-linked FUS mutants in causing ALS/FTD-associated disease phenotypes is well established, but there are significant gaps in our understanding of the cell-autonomous role of FUS in promoting structural changes to motor neurons, and how these changes relate to disease progression. Here we generated a neuron-specific FUS-transgenic mouse model expressing the ALS-linked human FUSR521G variant, hFUSR521G/Syn1, to investigate the cell-autonomous role of FUSR521G in causing loss of dendritic branching and synapses of motor neurons, and to understand how these changes relate to ALS-associated phenotypes. Longitudinal analysis of mice revealed that cognitive impairments in juvenile hFUSR521G/Syn1 mice coincide with reduced dendritic branching of cortical motor neurons in the absence of motor impairments or changes in the neuromorphology of spinal motor neurons. Motor impairments and dendritic attrition of spinal motor neurons developed later in aged hFUSR521G/Syn1 mice, along with FUS cytoplasmic mislocalisation, mitochondrial abnormalities and glial activation. Neuroinflammation promotes neuronal dysfunction and drives disease progression in ALS/FTD. The therapeutic effects of inhibiting the pro-inflammatory nuclear factor kappa B (NF-κB) pathway with an analog of Withaferin A, IMS-088, were assessed in symptomatic hFUSR521G/Syn1 mice and were found to improve cognitive and motor function, increase dendritic branches and synapses of motor neurons, and attenuate other ALS/FTD-associated pathological features. Treatment of primary cortical neurons expressing FUSR521G with IMS-088 promoted the restoration of dendritic mitochondrial numbers and mitochondrial activity to wild-type levels, suggesting that inhibition of NF-κB permits the restoration of mitochondrial stasis in our models. Collectively, this work demonstrates that FUSR521G has a cell-autonomous role in causing early pathological changes to dendritic and synaptic structures of motor neurons, and that these changes precede motor defects and other well-known pathological features of ALS/FTD. Finally, these findings provide further support that modulation of the NF-κB pathway in ALS/FTD is an important therapeutic approach to attenuate disease.
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Affiliation(s)
- Mari Carmen Pelaez
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Antoine Desmeules
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Pauline A Gelon
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Bastien Glasson
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Laetitia Marcadet
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Alicia Rodgers
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Daniel Phaneuf
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Silvia Pozzi
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Paul A Dutchak
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Jean-Pierre Julien
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada.
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14
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Kour S, Fortuna T, Anderson EN, Mawrie D, Bilstein J, Sivasubramanian R, Ward C, Roy R, Rajasundaram D, Sterneckert J, Pandey UB. Drosha-dependent microRNAs modulate FUS-mediated neurodegeneration in vivo. Nucleic Acids Res 2023; 51:11258-11276. [PMID: 37791873 PMCID: PMC10639082 DOI: 10.1093/nar/gkad774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/03/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Mutations in the Fused in Sarcoma (FUS) gene cause the familial and progressive form of amyotrophic lateral sclerosis (ALS). FUS is a nuclear RNA-binding protein involved in RNA processing and the biogenesis of a specific set of microRNAs. Here we report that Drosha and two previously uncharacterized Drosha-dependent miRNAs are strong modulators of FUS expression and prevent the cytoplasmic segregation of insoluble mutant FUS in vivo. We demonstrate that depletion of Drosha mitigates FUS-mediated degeneration, survival and motor defects in Drosophila. Mutant FUS strongly interacts with Drosha and causes its cytoplasmic mis-localization into the insoluble FUS inclusions. Reduction in Drosha levels increases the solubility of mutant FUS. Interestingly, we found two Drosha dependent microRNAs, miR-378i and miR-6832-5p, which differentially regulate the expression, solubility and cytoplasmic aggregation of mutant FUS in iPSC neurons and mammalian cells. More importantly, we report different modes of action of these miRNAs against mutant FUS. Whereas miR-378i may regulate mutant FUS inclusions by preventing G3BP-mediated stress granule formation, miR-6832-5p may affect FUS expression via other proteins or pathways. Overall, our research reveals a possible association between ALS-linked FUS mutations and the Drosha-dependent miRNA regulatory circuit, as well as a useful perspective on potential ALS treatment via microRNAs.
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Affiliation(s)
- Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Tyler Fortuna
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Jessica Bilstein
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
| | - Ramakrishnan Sivasubramanian
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
| | - Caroline Ward
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Rishit Roy
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, 01307, Germany
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
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15
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Elmansy MF, Reidl CT, Rahaman M, Özdinler PH, Silverman RB. Small molecules targeting different cellular pathologies for the treatment of amyotrophic lateral sclerosis. Med Res Rev 2023; 43:2260-2302. [PMID: 37243319 PMCID: PMC10592673 DOI: 10.1002/med.21974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 02/28/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease in which the motor neuron circuitry displays progressive degeneration, affecting mostly the motor neurons in the brain and in the spinal cord. There are no effective cures, albeit three drugs, riluzole, edaravone, and AMX0035 (a combination of sodium phenylbutyrate and taurursodiol), have been approved by the Food and Drug Administration, with limited improvement in patients. There is an urgent need to build better and more effective treatment strategies for ALS. Since the disease is very heterogenous, numerous approaches have been explored, such as targeting genetic mutations, decreasing oxidative stress and excitotoxicity, enhancing mitochondrial function and protein degradation mechanisms, and inhibiting neuroinflammation. In addition, various chemical libraries or previously identified drugs have been screened for potential repurposing in the treatment of ALS. Here, we review previous drug discovery efforts targeting a variety of cellular pathologies that occur from genetic mutations that cause ALS, such as mutations in SOD1, C9orf72, FUS, and TARDP-43 genes. These mutations result in protein aggregation, which causes neuronal degeneration. Compounds used to target cellular pathologies that stem from these mutations are discussed and comparisons among different preclinical models are presented. Because the drug discovery landscape for ALS and other motor neuron diseases is changing rapidly, we also offer recommendations for a novel, more effective, direction in ALS drug discovery that could accelerate translation of effective compounds from animals to patients.
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Affiliation(s)
- Mohamed F. Elmansy
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
- Department of Organometallic and Organometalloid Chemistry, National Research Centre, Cairo, Egypt
| | - Cory T. Reidl
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
| | - Mizzanoor Rahaman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
| | - P. Hande Özdinler
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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16
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Petrić Howe M, Patani R. Nonsense-mediated mRNA decay in neuronal physiology and neurodegeneration. Trends Neurosci 2023; 46:879-892. [PMID: 37543480 DOI: 10.1016/j.tins.2023.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/19/2023] [Accepted: 07/09/2023] [Indexed: 08/07/2023]
Abstract
The processes of mRNA export from the nucleus and subsequent mRNA translation in the cytoplasm are of particular relevance in eukaryotic cells. In highly polarised cells such as neurons, finely-tuned molecular regulation of these processes serves to safeguard the spatiotemporal fidelity of gene expression. Nonsense-mediated mRNA decay (NMD) is a cytoplasmic translation-dependent quality control process that regulates gene expression in a wide range of scenarios in the nervous system, including neurodevelopment, learning, and memory formation. Moreover, NMD dysregulation has been implicated in a broad range of neurodevelopmental and neurodegenerative disorders. We discuss how NMD and related aspects of mRNA translation regulate key neuronal functions and, in particular, we focus on evidence implicating these processes in the molecular pathogenesis of neurodegeneration. Finally, we discuss the therapeutic potential and challenges of targeting mRNA translation and NMD across the spectrum of largely untreatable neurological diseases.
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Affiliation(s)
- Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
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17
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Mukherjee S, Schäfer LV. Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain. Nat Commun 2023; 14:5892. [PMID: 37735186 PMCID: PMC10514047 DOI: 10.1038/s41467-023-41586-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These results provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.
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Affiliation(s)
- Saumyak Mukherjee
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany.
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18
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Ghosh I, Kwon Y, Shabestari AB, Chikhale R, Chen J, Wiese C, Sung P, De Benedetti A. TLK1-mediated RAD54 phosphorylation spatio-temporally regulates Homologous Recombination Repair. Nucleic Acids Res 2023; 51:8643-8662. [PMID: 37439356 PMCID: PMC10484734 DOI: 10.1093/nar/gkad589] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Environmental agents like ionizing radiation (IR) and chemotherapeutic drugs can cause severe damage to the DNA, often in the form of double-strand breaks (DSBs). Remaining unrepaired, DSBs can lead to chromosomal rearrangements, and cell death. One major error-free pathway to repair DSBs is homologous recombination repair (HRR). Tousled-like kinase 1 (TLK1), a Ser/Thr kinase that regulates the DNA damage checkpoint, has been found to interact with RAD54, a central DNA translocase in HRR. To determine how TLK1 regulates RAD54, we inhibited or depleted TLK1 and tested how this impacts HRR in human cells using a ISce-I-GR-DsRed fused reporter endonuclease. Our results show that TLK1 phosphorylates RAD54 at three threonines (T41, T59 and T700), two of which are located within its N-terminal domain (NTD) and one is located within its C-terminal domain (CTD). Phosphorylation at both T41 and T59 supports HRR and protects cells from DNA DSB damage. In contrast, phosphorylation of T700 leads to impaired HRR and engenders no protection to cells from cytotoxicity and rather results in repair delay. Further, our work enlightens the effect of RAD54-T700 (RAD54-CTD) phosphorylation by TLK1 in mammalian system and reveals a new site of interaction with RAD51.
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Affiliation(s)
- Ishita Ghosh
- Department of Biochemistry and Molecular Biology, Louisiana Health Science Center-Shreveport, Shreveport, Louisiana 71130, US2. Texas 78229, USA
| | - Youngho Kwon
- Department of Biochemistry & Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Aida Badamchi Shabestari
- Department of Biochemistry & Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Rupesh Chikhale
- Division of Pharmacy & Optometry, University of Manchester, Manchester, UK
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry and Proteomics Core, Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Patrick Sung
- Department of Biochemistry & Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, Louisiana Health Science Center-Shreveport, Shreveport, Louisiana 71130, US2. Texas 78229, USA
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19
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Blazquez S, Sanchez‐Burgos I, Ramirez J, Higginbotham T, Conde MM, Collepardo‐Guevara R, Tejedor AR, Espinosa JR. Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207742. [PMID: 37386790 PMCID: PMC10477902 DOI: 10.1002/advs.202207742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/03/2023] [Indexed: 07/01/2023]
Abstract
Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein β-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, atomistic molecular dynamics simulations are combined with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed toward the center. Yet, at very long timescales, proteins with a single LARKS-independently of its location-can still relax and form high viscous liquid condensates. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated β-sheet networks that display gel-like behavior. Furthermore, as a work case example, they demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein toward its center effectively precludes the accumulation of β-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behavior without ageing.
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Affiliation(s)
- Samuel Blazquez
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Ignacio Sanchez‐Burgos
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Jorge Ramirez
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Tim Higginbotham
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Maria M. Conde
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Rosana Collepardo‐Guevara
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of GeneticsUniversity of CambridgeCambridgeCB2 3EH, UK
| | - Andres R. Tejedor
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Jorge R. Espinosa
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
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20
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Naskar A, Nayak A, Salaikumaran MR, Vishal SS, Gopal PP. Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders. Front Mol Neurosci 2023; 16:1242925. [PMID: 37720552 PMCID: PMC10502346 DOI: 10.3389/fnmol.2023.1242925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
Liquid-liquid phase separation results in the formation of dynamic biomolecular condensates, also known as membrane-less organelles, that allow for the assembly of functional compartments and higher order structures within cells. Multivalent, reversible interactions between RNA-binding proteins (RBPs), including FUS, TDP-43, and hnRNPA1, and/or RNA (e.g., RBP-RBP, RBP-RNA, RNA-RNA), result in the formation of ribonucleoprotein (RNP) condensates, which are critical for RNA processing, mRNA transport, stability, stress granule assembly, and translation. Stress granules, neuronal transport granules, and processing bodies are examples of cytoplasmic RNP condensates, while the nucleolus and Cajal bodies are representative nuclear RNP condensates. In neurons, RNP condensates promote long-range mRNA transport and local translation in the dendrites and axon, and are essential for spatiotemporal regulation of gene expression, axonal integrity and synaptic function. Mutations of RBPs and/or pathologic mislocalization and aggregation of RBPs are hallmarks of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. ALS/FTD-linked mutations of RBPs alter the strength and reversibility of multivalent interactions with other RBPs and RNAs, resulting in aberrant phase transitions. These aberrant RNP condensates have detrimental functional consequences on mRNA stability, localization, and translation, and ultimately lead to compromised axonal integrity and synaptic function in disease. Pathogenic protein aggregation is dependent on various factors, and aberrant dynamically arrested RNP condensates may serve as an initial nucleation step for pathologic aggregate formation. Recent studies have focused on identifying mechanisms by which neurons resolve phase transitioned condensates to prevent the formation of pathogenic inclusions/aggregates. The present review focuses on the phase separation of neurodegenerative disease-linked RBPs, physiological functions of RNP condensates, and the pathologic role of aberrant phase transitions in neurodegenerative disease, particularly ALS/FTD. We also examine cellular mechanisms that contribute to the resolution of aberrant condensates in neurons, and potential therapeutic approaches to resolve aberrantly phase transitioned condensates at a molecular level.
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Affiliation(s)
- Aditi Naskar
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Asima Nayak
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | | | - Sonali S. Vishal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Pallavi P. Gopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, CT, United States
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21
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Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener 2023; 18:58. [PMID: 37626421 PMCID: PMC10464328 DOI: 10.1186/s13024-023-00642-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
RNA translation is tightly controlled in eukaryotic cells to regulate gene expression and maintain proteome homeostasis. RNA binding proteins, translation factors, and cell signaling pathways all modulate the translation process. Defective translation is involved in multiple neurological diseases including amyotrophic lateral sclerosis (ALS). ALS is a progressive neurodegenerative disorder and poses a major public health challenge worldwide. Over the past few years, tremendous advances have been made in the understanding of the genetics and pathogenesis of ALS. Dysfunction of RNA metabolisms, including RNA translation, has been closely associated with ALS. Here, we first introduce the general mechanisms of translational regulation under physiological and stress conditions and review well-known examples of translation defects in neurodegenerative diseases. We then focus on ALS-linked genes and discuss the recent progress on how translation is affected by various mutant genes and the repeat expansion-mediated non-canonical translation in ALS.
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Affiliation(s)
- Shaopeng Wang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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22
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Bagyinszky E, Hulme J, An SSA. Studies of Genetic and Proteomic Risk Factors of Amyotrophic Lateral Sclerosis Inspire Biomarker Development and Gene Therapy. Cells 2023; 12:1948. [PMID: 37566027 PMCID: PMC10417729 DOI: 10.3390/cells12151948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5-10% of ALS cases are associated with positive family history (familial ALS or fALS), whilst the remainder are sporadic (sporadic ALS, sALS). At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 (SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially "at risk" individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.
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Affiliation(s)
- Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - John Hulme
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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23
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Rezvykh A, Ustyugov A, Chaprov K, Teterina E, Nebogatikov V, Spasskaya D, Evgen’ev M, Morozov A, Funikov S. Cytoplasmic aggregation of mutant FUS causes multistep RNA splicing perturbations in the course of motor neuron pathology. Nucleic Acids Res 2023; 51:5810-5830. [PMID: 37115004 PMCID: PMC10287951 DOI: 10.1093/nar/gkad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Dysfunction of the RNA-binding protein (RBP) FUS implicated in RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Mutations affecting FUS nuclear localization can drive RNA splicing defects and stimulate the formation of non-amyloid inclusions in affected neurons. However, the mechanism by which FUS mutations contribute to the development of ALS remains uncertain. Here we describe a pattern of RNA splicing changes in the dynamics of the continuous proteinopathy induced by mislocalized FUS. We show that the decrease in intron retention of FUS-associated transcripts represents the hallmark of the pathogenesis of ALS and is the earliest molecular event in the course of progression of the disease. As FUS aggregation increases, the pattern of RNA splicing changes, becoming more complex, including a decrease in the inclusion of neuron-specific microexons and induction of cryptic exon splicing due to the sequestration of additional RBPs into FUS aggregates. Crucially, the identified features of the pathological splicing pattern are also observed in ALS patients in both sporadic and familial cases. Our data provide evidence that both a loss of nuclear FUS function due to mislocalization and the subsequent cytoplasmic aggregation of mutant protein lead to the disruption of RNA splicing in a multistep fashion during FUS aggregation.
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Affiliation(s)
- Alexander P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Aleksey A Ustyugov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Kirill D Chaprov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Ekaterina V Teterina
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Vladimir O Nebogatikov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Daria S Spasskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Michael B Evgen’ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexey V Morozov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
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24
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Bertrand E, Demongin C, Dobra I, Rengifo-Gonzalez JC, Singatulina AS, Sukhanova MV, Lavrik OI, Pastré D, Hamon L. FUS fibrillation occurs through a nucleation-based process below the critical concentration required for liquid-liquid phase separation. Sci Rep 2023; 13:7772. [PMID: 37179431 PMCID: PMC10183042 DOI: 10.1038/s41598-023-34558-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid-liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.
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Affiliation(s)
- Emilie Bertrand
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Clément Demongin
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Ioana Dobra
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | | | - Anastasia S Singatulina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.
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25
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Mueller S, Decker L, Menge S, Ludolph AC, Freischmidt A. The Fragile X Protein Family in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2023; 60:3898-3910. [PMID: 36991279 DOI: 10.1007/s12035-023-03330-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
The fragile X protein (FXP) family comprises the multifunctional RNA-binding proteins FMR1, FXR1, and FXR2 that play an important role in RNA metabolism and regulation of translation, but also in DNA damage and cellular stress responses, mitochondrial organization, and more. FMR1 is well known for its implication in neurodevelopmental diseases. Recent evidence suggests substantial contribution of this protein family to amyotrophic lateral sclerosis (ALS) pathogenesis. ALS is a highly heterogeneous neurodegenerative disease with multiple genetic and unclear environmental causes and very limited treatment options. The loss of motoneurons in ALS is still poorly understood, especially because pathogenic mechanisms are often restricted to patients with mutations in specific causative genes. Identification of converging disease mechanisms evident in most patients and suitable for therapeutic intervention is therefore of high importance. Recently, deregulation of the FXPs has been linked to pathogenic processes in different types of ALS. Strikingly, in many cases, available data points towards loss of expression and/or function of the FXPs early in the disease, or even at the presymptomatic state. In this review, we briefly introduce the FXPs and summarize available data about these proteins in ALS. This includes their relation to TDP-43, FUS, and ALS-related miRNAs, as well as their possible contribution to pathogenic protein aggregation and defective RNA editing. Furthermore, open questions that need to be addressed before definitively judging suitability of these proteins as novel therapeutic targets are discussed.
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Affiliation(s)
- Sarah Mueller
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lorena Decker
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Sonja Menge
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- German Center For Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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26
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Gawade K, Plewka P, Häfner SJ, Lund AH, Marchand V, Motorin Y, Szczesniak MW, Raczynska KD. FUS regulates a subset of snoRNA expression and modulates the level of rRNA modifications. Sci Rep 2023; 13:2974. [PMID: 36806717 PMCID: PMC9941101 DOI: 10.1038/s41598-023-30068-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this work, we show that FUS depletion results in the differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2'-O methylation (2'-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2'-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2'-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and progression.
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Affiliation(s)
- Kishor Gawade
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Patrycja Plewka
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Sophia J Häfner
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Virginie Marchand
- Université de Lorraine, UAR2008/US40 IBSLor CNRS-INSERM and UMR7365 IMoPA CNRS, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, UAR2008/US40 IBSLor CNRS-INSERM and UMR7365 IMoPA CNRS, Nancy, France
| | - Michal W Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Katarzyna D Raczynska
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland.
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland.
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27
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Lant JT, Hasan F, Briggs J, Heinemann IU, O’Donoghue P. Genetic Interaction of tRNA-Dependent Mistranslation with Fused in Sarcoma Protein Aggregates. Genes (Basel) 2023; 14:518. [PMID: 36833445 PMCID: PMC9956149 DOI: 10.3390/genes14020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
High-fidelity protein synthesis requires properly aminoacylated transfer RNAs (tRNAs), yet diverse cell types, from bacteria to humans, show a surprising ability to tolerate errors in translation resulting from mutations in tRNAs, aminoacyl-tRNA synthetases, and other components of protein synthesis. Recently, we characterized a tRNASerAGA G35A mutant (tRNASerAAA) that occurs in 2% of the human population. The mutant tRNA decodes phenylalanine codons with serine, inhibits protein synthesis, and is defective in protein and aggregate degradation. Here, we used cell culture models to test our hypothesis that tRNA-dependent mistranslation will exacerbate toxicity caused by amyotrophic lateral sclerosis (ALS)-associated protein aggregation. Relative to wild-type tRNA, we found cells expressing tRNASerAAA showed slower but effective aggregation of the fused in sarcoma (FUS) protein. Despite reduced levels in mistranslating cells, wild-type FUS aggregates showed similar toxicity in mistranslating cells and normal cells. The aggregation kinetics of the ALS-causative FUS R521C variant were distinct and more toxic in mistranslating cells, where rapid FUS aggregation caused cells to rupture. We observed synthetic toxicity in neuroblastoma cells co-expressing the mistranslating tRNA mutant and the ALS-causative FUS R521C variant. Our data demonstrate that a naturally occurring human tRNA variant enhances cellular toxicity associated with a known causative allele for neurodegenerative disease.
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Affiliation(s)
- Jeremy T. Lant
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Farah Hasan
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Julia Briggs
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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28
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Lyon A, Tripathi R, Meeks C, He D, Wu Y, Liu J, Wang C, Chen J, Zhu H, Mukherjee S, Ganguly S, Plattner R. ABL1/2 and DDR1 Drive MEKi Resistance in NRAS-Mutant Melanomas by Stabilizing RAF/MYC/ETS1 and Promoting RAF Homodimerization. Cancers (Basel) 2023; 15:954. [PMID: 36765910 PMCID: PMC9913232 DOI: 10.3390/cancers15030954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Melanomas harboring NRAS mutations are a particularly aggressive and deadly subtype. If patients cannot tolerate or the melanomas are insensitive to immune checkpoint blockade, there are no effective 2nd-line treatment options. Drugs targeting the RAF/MEK/ERK pathway, which are used for BRAF-mutant melanomas, do little to increase progression-free survival (PFS). Here, using both loss-of-function and gain-of-function approaches, we show that ABL1/2 and DDR1 are critical nodes during NRAS-mutant melanoma intrinsic and acquired MEK inhibitor (MEKi) resistance. In some acquired resistance cells, ABL1/2 and DDR1 cooperate to stabilize RAF proteins, activate ERK cytoplasmic and nuclear signaling, repress p27/KIP1 expression, and drive RAF homodimerization. In contrast, other acquired resistance cells depend solely on ABL1/2 for their survival, and are sensitive to highly specific allosteric ABL1/2 inhibitors, which prevent β-catenin nuclear localization and destabilize MYC and ETS1 in an ERK-independent manner. Significantly, targeting ABL1/2 and DDR1 with an FDA-approved anti-leukemic drug, reverses intrinsic MEKi resistance, delays acquisition of acquired resistance, and doubles the survival time in a NRAS-mutant mouse model. These data indicate that repurposing FDA-approved drugs targeting ABL1/2 and DDR1 may be a novel and effective strategy for treating patients with treatment-refractory NRAS-driven melanomas.
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Affiliation(s)
- Anastasia Lyon
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rakshamani Tripathi
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Christina Meeks
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Yuanyuan Wu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jinpeng Liu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Chi Wang
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Sujata Mukherjee
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Saptadwipa Ganguly
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rina Plattner
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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29
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Fare CM, Rhine K, Lam A, Myong S, Shorter J. A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity. J Biol Chem 2023; 299:102806. [PMID: 36529289 PMCID: PMC9860449 DOI: 10.1016/j.jbc.2022.102806] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Karyopherin-β2 (Kapβ2) is a nuclear-import receptor that recognizes proline-tyrosine nuclear localization signals of diverse cytoplasmic cargo for transport to the nucleus. Kapβ2 cargo includes several disease-linked RNA-binding proteins with prion-like domains, such as FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2. These RNA-binding proteins with prion-like domains are linked via pathology and genetics to debilitating degenerative disorders, including amyotrophic lateral sclerosis, frontotemporal dementia, and multisystem proteinopathy. Remarkably, Kapβ2 prevents and reverses aberrant phase transitions of these cargoes, which is cytoprotective. However, the molecular determinants of Kapβ2 that enable these activities remain poorly understood, particularly from the standpoint of nuclear-import receptor architecture. Kapβ2 is a super-helical protein comprised of 20 HEAT repeats. Here, we design truncated variants of Kapβ2 and assess their ability to antagonize FUS aggregation and toxicity in yeast and FUS condensation at the pure protein level and in human cells. We find that HEAT repeats 8 to 20 of Kapβ2 recapitulate all salient features of Kapβ2 activity. By contrast, Kapβ2 truncations lacking even a single cargo-binding HEAT repeat display reduced activity. Thus, we define a minimal Kapβ2 construct for delivery in adeno-associated viruses as a potential therapeutic for amyotrophic lateral sclerosis/frontotemporal dementia, multisystem proteinopathy, and related 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, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Lam
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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30
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Zuniga G, Levy S, Ramirez P, Mange JD, Gonzalez E, Gamez M, Frost B. Tau-induced deficits in nonsense-mediated mRNA decay contribute to neurodegeneration. Alzheimers Dement 2023; 19:405-420. [PMID: 35416419 PMCID: PMC9673995 DOI: 10.1002/alz.12653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/26/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION While brains of patients with Alzheimer's disease and related tauopathies have evidence of altered RNA processing, we lack a mechanistic understanding of how altered RNA processing arises in these disorders and if such changes are causally linked to neurodegeneration. METHODS Using Drosophila melanogaster models of tauopathy, we find that overall activity of nonsense-mediated mRNA decay (NMD), a key RNA quality-control mechanism, is reduced. Genetic manipulation of NMD machinery significantly modifies tau-induced neurotoxicity, suggesting that deficits in NMD are causally linked to neurodegeneration. Mechanistically, we find that deficits in NMD are a consequence of aberrant RNA export and RNA accumulation within nuclear envelope invaginations in tauopathy. We identify a pharmacological activator of NMD that suppresses neurodegeneration in tau transgenic Drosophila, indicating that tau-induced deficits in RNA quality control are druggable. DISCUSSION Our studies suggest that NMD activators should be explored for their potential therapeutic value to patients with tauopathies.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Simon Levy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Jasmine De Mange
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elias Gonzalez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Maria Gamez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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31
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McMillan M, Gomez N, Hsieh C, Bekier M, Li X, Miguez R, Tank EMH, Barmada SJ. RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia. Mol Cell 2023; 83:219-236.e7. [PMID: 36634675 PMCID: PMC9899051 DOI: 10.1016/j.molcel.2022.12.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/14/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023]
Abstract
RNA methylation at adenosine N6 (m6A) is one of the most common RNA modifications, impacting RNA stability, transport, and translation. Previous studies uncovered RNA destabilization in amyotrophic lateral sclerosis (ALS) models in association with accumulation of the RNA-binding protein TDP43. Here, we show that TDP43 recognizes m6A RNA and that RNA methylation is critical for both TDP43 binding and autoregulation. We also observed extensive RNA hypermethylation in ALS spinal cord, corresponding to methylated TDP43 substrates. Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via single-cell CRISPR-Cas9 in primary neurons. The most promising modifier-the canonical m6A reader YTHDF2-accumulated within ALS spinal neurons, and its knockdown prolonged the survival of human neurons carrying ALS-associated mutations. Collectively, these data show that m6A modifications modulate RNA binding by TDP43 and that m6A is pivotal for TDP43-related neurodegeneration in ALS.
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Affiliation(s)
- Michael McMillan
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicolas Gomez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caroline Hsieh
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roberto Miguez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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32
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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33
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Zhang Y, Kang JY, Liu M, Huang Y. Diverse roles of biomolecular condensation in eukaryotic translational regulation. RNA Biol 2023; 20:893-907. [PMID: 37906632 PMCID: PMC10730148 DOI: 10.1080/15476286.2023.2275108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/02/2023] Open
Abstract
Biomolecular condensates, forming membrane-less organelles, orchestrate the sub-cellular compartment to execute designated biological processes. An increasing body of evidence demonstrates the involvement of these biomolecular condensates in translational regulation. This review summarizes recent discoveries concerning biomolecular condensates associated with translational regulation, including their composition, assembly, and functions. Furthermore, we discussed the common features among these biomolecular condensates and the critical questions in the translational regulation areas. These emerging discoveries shed light on the enigmatic translational machinery, refine our understanding of translational regulation, and put forth potential therapeutic targets for diseases born out of translation dysregulation.
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Grants
- 32171186 AND 91940302 National Natural Science Foundation of China
- 91940305, 31830109, 31821004, 31961133022, 91640201, 32170815, AND 32101037 TO M.L., AND 32201058 National Natural Science Foundation of China
- 2022YFC2702600 National Key R&D Program of China
- 17JC1420100, 2017SHZDZX01, 19JC1410200, 21ZR1470200, 21PJ1413800, 21YF1452700, AND 21ZR1470500 Science and Technology Commission of Shanghai Municipality
- 2022YFC2702600 National Key R&D Program of China
- 2022T150425 China Postdoctoral Science Foundation
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Affiliation(s)
- Yuhan Zhang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Yan Kang
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mofang Liu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
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34
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Assoni AF, Foijer F, Zatz M. Amyotrophic Lateral Sclerosis, FUS and Protein Synthesis Defects. Stem Cell Rev Rep 2022; 19:625-638. [PMID: 36515764 DOI: 10.1007/s12015-022-10489-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that mainly affects the motor system. It is a very heterogeneous disorder, so far more than 40 genes have been described as responsible for ALS. The cause of motor neuron degeneration is not yet fully understood, but there is consensus in the literature that it is the result of a complex interplay of several pathogenic processes, which include alterations in nucleocytoplasmic transport, defects in transcription and splicing, altered formation and/or disassembly of stress granules and impaired proteostasis. These defects result in protein aggregation, impaired DNA repair, mitochondrial dysfunction and oxidative stress, neuroinflammation, impaired axonal transport, impaired vesicular transport, excitotoxicity, as well as impaired calcium influx. We argue here that all the above functions ultimately lead to defects in protein synthesis. Fused in Sarcoma (FUS) is one of the genes associated with ALS. It causes ALS type 6 when mutated and is found mislocalized to the cytoplasm in the motor neurons of sporadic ALS patients (without FUS mutations). In addition, FUS plays a role in all cellular functions that are impaired in degenerating motor neurons. Moreover, ALS patients with FUS mutations present the first symptoms significantly earlier than in other forms of the disease. Therefore, the aim of this review is to further discuss ALS6, detail the cellular functions of FUS, and suggest that the localization of FUS, as well as protein synthesis rates, could be hallmarks of the ALS phenotype and thus good therapeutic targets.
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Affiliation(s)
- Amanda Faria Assoni
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, 055080-090, CidadeUniversitária, São Paulo, Brazil.,European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, 055080-090, CidadeUniversitária, São Paulo, Brazil.
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35
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Cabral AJ, Costello DC, Farny NG. The enigma of ultraviolet radiation stress granules: Research challenges and new perspectives. Front Mol Biosci 2022; 9:1066650. [DOI: 10.3389/fmolb.2022.1066650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
Stress granules (SGs) are non-membrane bound cytoplasmic condensates that form in response to a variety of different stressors. Canonical SGs are thought to have a cytoprotective role, reallocating cellular resources during stress by activation of the integrated stress response (ISR) to inhibit translation and avoid apoptosis. However, different stresses result in compositionally distinct, non-canonical SG formation that is likely pro-apoptotic, though the exact function(s) of both SGs subtypes remain unclear. A unique non-canonical SG subtype is triggered upon exposure to ultraviolet (UV) radiation. While it is generally agreed that UV SGs are bona fide SGs due to their dependence upon the core SG nucleating protein Ras GTPase-activating protein-binding protein 1 (G3BP1), the localization of other key components of UV SGs are unknown or under debate. Further, the dynamics of UV SGs are not known, though unique properties such as cell cycle dependence have been observed. This Perspective compiles the available information on SG subtypes and on UV SGs in particular in an attempt to understand the formation, dynamics, and function of these mysterious stress-specific complexes. We identify key gaps in knowledge related to UV SGs, and examine the unique aspects of their formation. We propose that more thorough knowledge of the distinct properties of UV SGs will lead to new avenues of understanding of the function of SGs, as well as their roles in disease.
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36
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Yokoi S, Ito T, Sahashi K, Nakatochi M, Nakamura R, Tohnai G, Fujioka Y, Ishigaki S, Udagawa T, Izumi Y, Morita M, Kano O, Oda M, Sone T, Okano H, Atsuta N, Katsuno M, Okada Y, Sobue G. The SYNGAP1 3'UTR Variant in ALS Patients Causes Aberrant SYNGAP1 Splicing and Dendritic Spine Loss by Recruiting HNRNPK. J Neurosci 2022; 42:8881-8896. [PMID: 36261283 PMCID: PMC9698725 DOI: 10.1523/jneurosci.0455-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/28/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022] Open
Abstract
Fused in sarcoma (FUS) is a pathogenic RNA-binding protein in amyotrophic lateral sclerosis (ALS). We previously reported that FUS stabilizes Synaptic Ras-GTPase activating protein 1 (Syngap1) mRNA at its 3' untranslated region (UTR) and maintains spine maturation. To elucidate the pathologic roles of this mechanism in ALS patients, we identified the SYNGAP1 3'UTR variant rs149438267 in seven (four males and three females) out of 807 ALS patients at the FUS binding site from a multicenter cohort in Japan. Human-induced pluripotent stem cell (hiPSC)-derived motor neurons with the SYNGAP1 variant showed aberrant splicing, increased isoform α1 levels, and decreased isoform γ levels, which caused dendritic spine loss. Moreover, the SYNGAP1 variant excessively recruited FUS and heterogeneous nuclear ribonucleoprotein K (HNRNPK), and antisense oligonucleotides (ASOs) blocking HNRNPK altered aberrant splicing and ameliorated dendritic spine loss. These data suggest that excessive recruitment of RNA-binding proteins, especially HNRNPK, as well as changes in SYNGAP1 isoforms, are crucial for spine formation in motor neurons.SIGNIFICANCE STATEMENT It is not yet known which RNAs cause the pathogenesis of amyotrophic lateral sclerosis (ALS). We previously reported that Fused in sarcoma (FUS), a pathogenic RNA-binding protein in ALS, stabilizes synaptic Ras-GTPase activating protein 1 (Syngap1) mRNA at its 3' untranslated region (UTR) and maintains dendritic spine maturation. To elucidate whether this mechanism is crucial for ALS, we identified the SYNGAP1 3'UTR variant rs149438267 at the FUS binding site. Human-induced pluripotent stem cell (hiPSC)-derived motor neurons with the SYNGAP1 variant showed aberrant splicing, which caused dendritic spine loss along with excessive recruitment of FUS and heterogeneous nuclear ribonucleoprotein K (HNRNPK). Our findings that dendritic spine loss is because of excess recruitment of RNA-binding proteins provide a basis for the future exploration of ALS-related RNA-binding proteins.
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Affiliation(s)
- Satoshi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Takuji Ito
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
- Department of Neural iPSC Research, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Kentaro Sahashi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya 461-8673, Japan
| | - Ryoichi Nakamura
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
| | - Genki Tohnai
- Division of ALS Research, Aichi Medical University, Aichi 480-1195, Japan
| | - Yusuke Fujioka
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shinsuke Ishigaki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuishin Izumi
- Department of Neurology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Mitsuya Morita
- Division of Neurology, Department of Internal Medicine, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Osamu Kano
- Department of Neurology, Toho University Faculty of Medicine, Tokyo 143-8540, Japan
| | - Masaya Oda
- Department of Neurology, Vihara Hananosato Hospital, Miyoshi 728-0001, Japan
| | - Takefumi Sone
- Department of Physiology, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Naoki Atsuta
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yohei Okada
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
- Department of Neural iPSC Research, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Gen Sobue
- Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Aichi Medical University, Aichi 480-1195, Japan
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37
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Pokorná P, Krepl M, Campagne S, Šponer J. Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. J Phys Chem B 2022; 126:9207-9221. [PMID: 36348631 DOI: 10.1021/acs.jpcb.2c06168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RNA-protein complexes use diverse binding strategies, ranging from structurally well-defined interfaces to completely disordered regions. Experimental characterization of flexible segments is challenging and can be aided by atomistic molecular dynamics (MD) simulations. Here, we used an extended set of microsecond-scale MD trajectories (400 μs in total) to study two FUS-RNA constructs previously characterized by nuclear magnetic resonance (NMR) spectroscopy. The FUS protein contains a well-structured RNA recognition motif domain followed by a presumably disordered RGG tail that binds RNA stem-loop hairpins. Our simulations not only provide several suggestions complementing the experiments but also reveal major methodological difficulties in studies of such complex RNA-protein interfaces. Despite efforts to stabilize the binding via system-specific force-field adjustments, we have observed progressive distortions of the RNA-protein interface inconsistent with experimental data. We propose that the dynamics is so rich that its converged description is not achievable even upon stabilizing the system. Still, after careful analysis of the trajectories, we have made several suggestions regarding the binding. We identify substates in the RNA loops, which can explain the NMR data. The RGG tail localized in the minor groove remains disordered, sampling countless transient interactions with the RNA. There are long-range couplings among the different elements contributing to the recognition, which can lead to allosteric communication throughout the system. Overall, the RNA-FUS systems form dynamical ensembles that cannot be fully represented by single static structures. Thus, albeit imperfect, MD simulations represent a viable tool to investigate dynamic RNA-protein complexes.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Sébastien Campagne
- INSERM U1212, CNRS UMR 5320, ARNA Laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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Abstract
Stress granules (SGs) are cytoplasmic biomolecular condensates containing proteins and RNAs in response to stress. Ras-GTPase–activating protein binding protein 1 (G3BP1) is a core SG protein. Caprin-1 and ubiquitin specific peptidase 10 (USP10) interact with G3BP1, facilitating and suppressing SG formation, respectively. The crystal structures of the nuclear transport factor 2-like (NTF2L) domain of G3BP1 in complex with the G3BP1-interacting motif (GIM) of Caprin-1 and USP10 show that both GIMs bind to the same hydrophobic pocket of G3BP1. Moreover, both GIMs suppressed the liquid–liquid phase separation (LLPS) of G3BP1, suggesting that Caprin-1 likely facilitates SG formation via other mechanisms. Thus, we dissected various domains of Caprin-1 and investigated their role in LLPS in vitro and SG formation in cells. The C-terminal domain of Caprin-1 underwent spontaneous LLPS, whereas the N-terminal domain and GIM of Caprin-1 suppressed LLPS of G3BP1. The opposing effect of the N- and C-terminal domains of Caprin-1 on SG formation were demonstrated in cells with or without the endogenous Caprin-1. We propose that the N- and C-terminal domains of Caprin-1 regulate SG formation in a “yin and yang” fashion, mediating the dynamic and reversible assembly of SGs.
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Wang Y, Li S, Chen J, Zhu H, Harsh BN, Boler DD, Dilger AC, Shike DW, Suman SP. Supranutritional Supplementation of Vitamin E Influences Myoglobin Post-Translational Modifications in Postmortem Beef Longissimus Lumborum Muscle. MEAT AND MUSCLE BIOLOGY 2022. [DOI: 10.22175/mmb.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modifications (PTM) in myoglobin (Mb) can influence fresh meat color stability. Dietary supplementation of vitamin E improves beef color stability by delaying lipid oxidation–induced Mb oxidation and influences proteome profile of postmortem beef skeletal muscles. Nonetheless, the influence of vitamin E on Mb PTM in postmortem beef skeletal muscles has yet to be investigated. Therefore, the objective of the current study was to examine the effect of dietary vitamin E on Mb PTM in postmortem beef longissimus lumborum muscle. Beef longissimus lumborum muscle samples (24 h postmortem) were obtained from the carcasses of 9 vitamin E–supplemented (VITE; 1,000 IU vitamin E diet/heifer·d−1for 89 d) and 9 control (CONT; no supplemental vitamin E) heifers. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used to separate Mb from other sarcoplasmic proteins of beef longissimus lumborum muscle. Tandem mass spectrometry identified multiple PTM (phosphorylation, acetylation, 4-hydroxynonenalalkylation, methylation, dimethylation, trimethylation, and carboxymethylation) in the protein bands (17 kDa) representing Mb. The amino acids susceptible to phosphorylation were threonine (T) and tyrosine (Y), whereas lysine (K) residues were prone to other PTM. The same sites of phosphorylation (T34, T67, Y103), carboxymethylation (K77, K78), and 4-hydroxynonenal alkylation (K77, K78, K79) were identified in Mb from CONT and VITE samples, indicating that these PTM were not influenced by the vitamin E supplementation in cattle. Nonetheless, differential occurrence of acetylation, methylation, dimethylation, and trimethylation were identified in Mb from CONT and VITE samples. Overall, a greater number of amino acids were modified in CONT than VITE, suggesting that the supplementation of vitamin E decreased thenumbers of post-translationally modified residues in Mb. Additionally, PTM at K87, K96, K98, and K102 were unique to CONT, whereas PTM at K118 were unique to VITE. These findings suggested that dietary supplementation of vitamin E in beef cattle might protect amino acid residues in Mb—especially those located spatially close to proximal histidine—from undergoing PTM, thereby improving Mb redox stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
| | - Bailey N. Harsh
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Dustin D. Boler
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Anna C. Dilger
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Daniel W. Shike
- University of Illinois Urbana-Champaign Department of Animal Sciences
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40
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Gelon PA, Dutchak PA, Sephton CF. Synaptic dysfunction in ALS and FTD: anatomical and molecular changes provide insights into mechanisms of disease. Front Mol Neurosci 2022; 15:1000183. [PMID: 36263379 PMCID: PMC9575515 DOI: 10.3389/fnmol.2022.1000183] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
Synaptic loss is a pathological feature of all neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS is a disease of the cortical and spinal motor neurons resulting in fatal paralysis due to denervation of muscles. FTD is a form of dementia that primarily affects brain regions controlling cognition, language and behavior. Once classified as two distinct diseases, ALS and FTD are now considered as part of a common disease spectrum based on overlapping clinical, pathological and genetic evidence. At the cellular level, aggregation of common proteins and overlapping gene susceptibilities are shared in both ALS and FTD. Despite the convergence of these two fields of research, the underlying disease mechanisms remain elusive. However, recent discovers from ALS and FTD patient studies and models of ALS/FTD strongly suggests that synaptic dysfunction is an early event in the disease process and a unifying hallmark of these diseases. This review provides a summary of the reported anatomical and cellular changes that occur in cortical and spinal motor neurons in ALS and FTD tissues and models of disease. We also highlight studies that identify changes in the proteome and transcriptome of ALS and FTD models and provide a conceptual overview of the processes that contribute to synaptic dysfunction in these diseases. Due to space limitations and the vast number of publications in the ALS and FTD fields, many articles have not been discussed in this review. As such, this review focuses on the three most common shared mutations in ALS and FTD, the hexanucleuotide repeat expansion within intron 1 of chromosome 9 open reading frame 72 (C9ORF72), transactive response DNA binding protein 43 (TARDBP or TDP-43) and fused in sarcoma (FUS), with the intention of highlighting common pathways that promote synaptic dysfunction in the ALS-FTD disease spectrum.
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41
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Tejedor AR, Sanchez-Burgos I, Estevez-Espinosa M, Garaizar A, Collepardo-Guevara R, Ramirez J, Espinosa JR. Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it. Nat Commun 2022; 13:5717. [PMID: 36175408 PMCID: PMC9522849 DOI: 10.1038/s41467-022-32874-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/18/2022] [Indexed: 12/03/2022] Open
Abstract
Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the progressive formation of inter-protein β-sheets. To bridge microscopic understanding between accumulation of inter-protein β-sheets over time and the modulation of FUS and hnRNPA1 condensate viscoelasticity, we develop a multiscale simulation approach. Our method integrates atomistic simulations with sequence-dependent coarse-grained modelling of condensates that exhibit accumulation of inter-protein β-sheets over time. We reveal that inter-protein β-sheets notably increase condensate viscosity but does not transform the phase diagrams. Strikingly, the network of molecular connections within condensates is drastically altered, culminating in gelation when the network of strong β-sheets fully percolates. However, high concentrations of RNA decelerate the emergence of inter-protein β-sheets. Our study uncovers molecular and kinetic factors explaining how the accumulation of inter-protein β-sheets can trigger liquid-to-solid transitions in condensates, and suggests a potential mechanism to slow such transitions down. In this work the authors propose a multiscale computational approach, integrating atomistic and coarse-grained models simulations, to study the thermodynamic and kinetic factors playing a major role in the liquid-to-solid transition of biomolecular condensates. It is revealed how the gradual accumulation of inter-protein β-sheets increases the viscosity of functional liquid-like condensates, transforming them into gel-like pathological aggregates, and it is also shown how high concentrations of RNA can decelerate such transition.
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Affiliation(s)
- Andres R Tejedor
- Department of Chemical Engineering, Universidad Politécnica de Madrid, José Gutiérrez Abascal 2, 28006, Madrid, Spain.,Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Maria Estevez-Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.,Department of Biochemistry, University College London, Gower Street, London, WC1E 6BT, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Jorge Ramirez
- Department of Chemical Engineering, Universidad Politécnica de Madrid, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
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42
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Hikiami R, Morimura T, Ayaki T, Tsukiyama T, Morimura N, Kusui M, Wada H, Minamiyama S, Shodai A, Asada-Utsugi M, Muramatsu SI, Ueki T, Takahashi R, Urushitani M. Conformational change of RNA-helicase DHX30 by ALS/FTD-linked FUS induces mitochondrial dysfunction and cytosolic aggregates. Sci Rep 2022; 12:16030. [PMID: 36163369 PMCID: PMC9512926 DOI: 10.1038/s41598-022-20405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic mutations in fused in sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS). Although mitochondrial dysfunction and stress granule have been crucially implicated in FUS proteinopathy, the molecular basis remains unclear. Here, we show that DHX30, a component of mitochondrial RNA granules required for mitochondrial ribosome assembly, interacts with FUS, and plays a crucial role in ALS-FUS. WT FUS did not affect mitochondrial localization of DHX30, but the mutant FUS lowered the signal of mitochondrial DHX30 and promoted the colocalization of cytosolic FUS aggregates and stress granule markers. The immunohistochemistry of the spinal cord from an ALS-FUS patient also confirmed the colocalization, and the immunoelectron microscope demonstrated decreased mitochondrial DHX30 signal in the spinal motor neurons. Subcellular fractionation by the detergent-solubility and density-gradient ultracentrifugation revealed that mutant FUS also promoted cytosolic mislocalization of DHX30 and aggregate formation. Interestingly, the mutant FUS disrupted the DHX30 conformation with aberrant disulfide formation, leading to impaired mitochondrial translation. Moreover, blue-native gel electrophoresis revealed an OXPHOS assembly defect caused by the FUS mutant, which was similar to that caused by DHX30 knockdown. Collectively, our study proposes DHX30 as a pivotal molecule in which disulfide-mediated conformational change mediates mitochondrial dysfunction and cytosolic aggregate formation in ALS-FUS.
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Affiliation(s)
- Ryota Hikiami
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan.,Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan.,Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Toshifumi Morimura
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan
| | - Takashi Ayaki
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Tomoyuki Tsukiyama
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Naoko Morimura
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan
| | - Makiko Kusui
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Hideki Wada
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Sumio Minamiyama
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan.,Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan.,Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Akemi Shodai
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Megumi Asada-Utsugi
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Shin-Ichi Muramatsu
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, 320-0498, Japan.,Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-0071, Japan
| | - Takatoshi Ueki
- Department of Integrative Anatomy, Graduate School of Medical Sciences, Nagoya City University, Nagoya, 467-8601, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Makoto Urushitani
- Department of Neurology, Shiga University of Medical Science, Seta-Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan. .,Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan.
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43
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Martin H, Rupkey J, Asthana S, Yoon J, Patel S, Mott J, Pei Z, Mao Y. Diverse Roles of the Exon Junction Complex Factors in the Cell Cycle, Cancer, and Neurodevelopmental Disorders-Potential for Therapeutic Targeting. Int J Mol Sci 2022; 23:ijms231810375. [PMID: 36142288 PMCID: PMC9499366 DOI: 10.3390/ijms231810375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/04/2022] Open
Abstract
The exon junction complex (EJC) plays a crucial role in regulating gene expression at the levels of alternative splicing, translation, mRNA localization, and nonsense-mediated decay (NMD). The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (eIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), in addition to other peripheral factors whose structural integration is activity-dependent. The physiological and mechanistic roles of the EJC in contribution to molecular, cellular, and organismal level function continue to be explored for potential insights into genetic or pathological dysfunction. The EJC’s specific role in the cell cycle and its implications in cancer and neurodevelopmental disorders prompt enhanced investigation of the EJC as a potential target for these diseases. In this review, we highlight the current understanding of the EJC’s position in the cell cycle, its relation to cancer and developmental diseases, and potential avenues for therapeutic targeting.
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Affiliation(s)
- Hannah Martin
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Julian Rupkey
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Shravan Asthana
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
- Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Joy Yoon
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Shray Patel
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jennifer Mott
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Zifei Pei
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
- Correspondence:
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44
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Krokowski D, Jobava R, Szkop KJ, Chen CW, Fu X, Venus S, Guan BJ, Wu J, Gao Z, Banaszuk W, Tchorzewski M, Mu T, Ropelewski P, Merrick WC, Mao Y, Sevval AI, Miranda H, Qian SB, Manifava M, Ktistakis NT, Vourekas A, Jankowsky E, Topisirovic I, Larsson O, Hatzoglou M. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep 2022; 40:111092. [PMID: 35858571 PMCID: PMC9491157 DOI: 10.1016/j.celrep.2022.111092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 12/23/2022] Open
Abstract
The integrated stress response (ISR) plays a pivotal role in adaptation of translation machinery to cellular stress. Here, we demonstrate an ISR-independent osmoadaptation mechanism involving reprogramming of translation via coordinated but independent actions of mTOR and plasma membrane amino acid transporter SNAT2. This biphasic response entails reduced global protein synthesis and mTOR signaling followed by translation of SNAT2. Induction of SNAT2 leads to accumulation of amino acids and reactivation of mTOR and global protein synthesis, paralleled by partial reversal of the early-phase, stress-induced translatome. We propose SNAT2 functions as a molecular switch between inhibition of protein synthesis and establishment of an osmoadaptive translation program involving the formation of cytoplasmic condensates of SNAT2-regulated RNA-binding proteins DDX3X and FUS. In summary, we define key roles of SNAT2 in osmotolerance.
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Affiliation(s)
- Dawid Krokowski
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Raul Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xu Fu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wioleta Banaszuk
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland; EcoTech-Complex Centre, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tingwei Mu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Phil Ropelewski
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Aksoylu Inci Sevval
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Helen Miranda
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ivan Topisirovic
- The Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Department of Biochemistry and Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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Johnson MA, Nuckols TA, Merino P, Bagchi P, Nandy S, Root J, Taylor G, Seyfried NT, Kukar T. Proximity-based labeling reveals DNA damage-induced phosphorylation of fused in sarcoma (FUS) causes distinct changes in the FUS protein interactome. J Biol Chem 2022; 298:102135. [PMID: 35709984 PMCID: PMC9372748 DOI: 10.1016/j.jbc.2022.102135] [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: 10/05/2021] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 01/18/2023] Open
Abstract
Accumulation of cytoplasmic inclusions containing fused in sarcoma (FUS), an RNA/DNA-binding protein, is a common hallmark of frontotemporal lobar degeneration and amyotrophic lateral sclerosis neuropathology. We have previously shown that DNA damage can trigger the cytoplasmic accumulation of N-terminally phosphorylated FUS. However, the functional consequences of N-terminal FUS phosphorylation are unknown. To gain insight into this question, we utilized proximity-dependent biotin labeling via ascorbate peroxidase 2 aired with mass spectrometry to investigate whether N-terminal phosphorylation alters the FUS protein-protein interaction network (interactome), and subsequently, FUS function. We report the first analysis comparing the interactomes of three FUS variants: homeostatic wildtype FUS (FUS WT), phosphomimetic FUS (FUS PM; a proxy for N-terminally phosphorylated FUS), and the toxic FUS proline 525 to leucine mutant (FUS P525L) that causes juvenile amyotrophic lateral sclerosis. We found that the phosphomimetic FUS interactome is uniquely enriched for a group of cytoplasmic proteins that mediate mRNA metabolism and translation, as well as nuclear proteins involved in the spliceosome and DNA repair functions. Furthermore, we identified and validated the RNA-induced silencing complex RNA helicase MOV10 as a novel interacting partner of FUS. Finally, we provide functional evidence that N-terminally phosphorylated FUS may disrupt homeostatic translation and steady-state levels of specific mRNA transcripts. Taken together, these results highlight phosphorylation as a unique modulator of the interactome and function of FUS.
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Affiliation(s)
- Michelle A. Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Thomas A. Nuckols
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Paola Merino
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Srijita Nandy
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Georgia Taylor
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Nicholas T. Seyfried
- Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA,Emory Integrated Proteomics Core, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Neurology, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Biochemistry, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Neurology, Emory University, School of Medicine, Atlanta, Georgia, USA,For correspondence: Thomas Kukar
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46
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The Physiological Roles of the Exon Junction Complex in Development and Diseases. Cells 2022; 11:cells11071192. [PMID: 35406756 PMCID: PMC8997533 DOI: 10.3390/cells11071192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 01/12/2023] Open
Abstract
The exon junction complex (EJC) becomes an increasingly important regulator of early gene expression in the central nervous system (CNS) and other tissues. The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (EIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), together with various auxiliary factors. The EJC is assembled specifically at exon-exon junctions on mRNAs, hence the name of the complex. The EJC regulates multiple levels of gene expression, from splicing to translation and mRNA degradation. The functional roles of the EJC have been established as crucial to the normal progress of embryonic and neurological development, with wide ranging implications on molecular, cellular, and organism level function. Dysfunction of the EJC has been implicated in multiple developmental and neurological diseases. In this review, we discuss recent progress on the EJC’s physiological roles.
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47
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Antonelo DS, Gómez JF, Silva SL, Beline M, Zhang X, Wang Y, Pavan B, Koulicoff LA, Rosa AF, Goulart RS, Li S, Gerrard DE, Suman SP, Wes Schilling M, Balieiro JC. Proteome basis for the biological variations in color and tenderness of longissimus thoracis muscle from beef cattle differing in growth rate and feeding regime. Food Res Int 2022; 153:110947. [DOI: 10.1016/j.foodres.2022.110947] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/31/2022]
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Biomarkers in Human Peripheral Blood Mononuclear Cells: The State of the Art in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2022; 23:ijms23052580. [PMID: 35269723 PMCID: PMC8910056 DOI: 10.3390/ijms23052580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease, characterized by the progressive loss of lower motor neurons, weakness and muscle atrophy. ALS lacks an effective cure and diagnosis is often made by exclusion. Thus, it is imperative to search for biomarkers. Biomarkers can help in understanding ALS pathomechanisms, identification of targets for treatment and development of effective therapies. Peripheral blood mononuclear cells (PBMCs) represent a valid source for biomarkers compared to cerebrospinal fluid, as they are simple to collect, and to plasma, because of the possibility of detecting lower expressed proteins. They are a reliable model for patients’ stratification. This review provides an overview on PBMCs as a potential source of biomarkers in ALS. We focused on altered RNA metabolism (coding/non-coding RNA), including RNA processing, mRNA stabilization, transport and translation regulation. We addressed protein abnormalities (aggregation, misfolding and modifications); specifically, we highlighted that SOD1 appears to be the most characterizing protein in ALS. Finally, we emphasized the correlation between biological parameters and disease phenotypes, as regards prognosis, severity and clinical features. In conclusion, even though further studies are needed to standardize the use of PBMCs as a tool for biomarker investigation, they represent a promising approach in ALS research.
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49
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Nicolas G, Sévigny M, Lecoquierre F, Marguet F, Deschênes A, del Pelaez MC, Feuillette S, Audebrand A, Lecourtois M, Rousseau S, Richard AC, Cassinari K, Deramecourt V, Duyckaerts C, Boland A, Deleuze JF, Meyer V, Clarimon Echavarria J, Gelpi E, Akiyama H, Hasegawa M, Kawakami I, Wong TH, Van Rooij JGJ, Van Swieten JC, Campion D, Dutchak PA, Wallon D, Lavoie-Cardinal F, Laquerrière A, Rovelet-Lecrux A, Sephton CF. A postzygotic de novo NCDN mutation identified in a sporadic FTLD patient results in neurochondrin haploinsufficiency and altered FUS granule dynamics. Acta Neuropathol Commun 2022; 10:20. [PMID: 35151370 PMCID: PMC8841087 DOI: 10.1186/s40478-022-01314-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022] Open
Abstract
Frontotemporal dementia (FTD) is a heterogeneous clinical disorder characterized by progressive abnormalities in behavior, executive functions, personality, language and/or motricity. A neuropathological subtype of FTD, frontotemporal lobar degeneration (FTLD)-FET, is characterized by protein aggregates consisting of the RNA-binding protein fused in sarcoma (FUS). The cause of FTLD-FET is not well understood and there is a lack of genetic evidence to aid in the investigation of mechanisms of the disease. The goal of this study was to identify genetic variants contributing to FTLD-FET and to investigate their effects on FUS pathology. We performed whole-exome sequencing on a 50-year-old FTLD patient with ubiquitin and FUS-positive neuronal inclusions and unaffected parents, and identified a de novo postzygotic nonsense variant in the NCDN gene encoding Neurochondrin (NCDN), NM_014284.3:c.1206G > A, p.(Trp402*). The variant was associated with a ~ 31% reduction in full-length protein levels in the patient’s brain, suggesting that this mutation leads to NCDN haploinsufficiency. We examined the effects of NCDN haploinsufficiency on FUS and found that depleting primary cortical neurons of NCDN causes a reduction in the total number of FUS-positive cytoplasmic granules. Moreover, we found that these granules were significantly larger and more highly enriched with FUS. We then examined the effects of a loss of FUS function on NCDN in neurons and found that depleting cells of FUS leads to a decrease in NCDN protein and mRNA levels. Our study identifies the NCDN protein as a likely contributor of FTLD-FET pathophysiology. Moreover, we provide evidence for a negative feedback loop of toxicity between NCDN and FUS, where loss of NCDN alters FUS cytoplasmic dynamics, which in turn has an impact on NCDN expression.
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50
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English AM, Moon SL. Measuring Bulk Translation Activity in Single Mammalian Cells During the Integrated Stress Response. Methods Mol Biol 2022; 2428:63-73. [PMID: 35171473 DOI: 10.1007/978-1-0716-1975-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The attenuation of global translation is a critical outcome of the integrated stress response (ISR). Consequently, it is important to effectively detect and measure protein synthesis in studies seeking to evaluate the ISR. This chapter details two methods, surface sensing of translation (SUnSET) and fluorescent noncanonical amino acid tagging (FUNCAT), to measure global translation activity in individual cells using fluorescence microscopy as a read-out. Detecting bulk translation activity in single cells is advantageous for the concurrent observation of newly synthesized proteins and other cellular structures and to identify differences in translation activity among individuals within a population of cells.
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Affiliation(s)
- Alyssa M English
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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