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Qi Z, Xue S, Chen J, Zhao W, Johnson K, Wen X, Richard JLC, Zhong S. Genome-Wide Mapping of RNA-Protein Associations via Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611288. [PMID: 39282297 PMCID: PMC11398515 DOI: 10.1101/2024.09.04.611288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
RNA-protein interactions are crucial for regulating gene expression and cellular functions, with their dysregulation potentially impacting disease progression. Systematically mapping these interactions is resource-intensive due to the vast number of potential RNA and protein interactions. Here, we introduce PRIM-seq ( P rotein- R NA Interaction M apping by sequencing), a method for the concurrent de novo identification of RNA-binding proteins (RBPs) and the elucidation of their associated RNAs. PRIM-seq works by converting each RNA-protein pair into a unique chimeric DNA sequence, which is then decoded through DNA sequencing. Applied to two human cell types, PRIM-seq generated a comprehensive human RNA-protein association network (HuRPA), consisting of more than 350,000 RNA-proteins pairs involving approximately 7,000 RNAs and 11,000 proteins. The data revealed an enrichment of previously reported RBPs and RNA-protein interactions within HuRPA. We also identified LINC00339 as a protein-associating non-coding RNA and PHGDH as an RNA-associating protein. Notably, PHGDH interacts with BECN1 and ATF4 mRNAs, suppressing their protein expression and consequently inhibiting autophagy, apoptosis, and neurite outgrowth while promoting cell proliferation. PRIM-seq offers a powerful tool for discovering RBPs and RNA-protein associations, contributing to more comprehensive functional genome annotations.
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Kodavati M, Maloji Rao VH, Provasek VE, Hegde ML. Regulation of DNA damage response by RNA/DNA-binding proteins: Implications for neurological disorders and aging. Ageing Res Rev 2024; 100:102413. [PMID: 39032612 PMCID: PMC11463832 DOI: 10.1016/j.arr.2024.102413] [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: 06/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
RNA-binding proteins (RBPs) are evolutionarily conserved across most forms of life, with an estimated 1500 RBPs in humans. Traditionally associated with post-transcriptional gene regulation, RBPs contribute to nearly every known aspect of RNA biology, including RNA splicing, transport, and decay. In recent years, an increasing subset of RBPs have been recognized for their DNA binding properties and involvement in DNA transactions. We refer to these RBPs with well-characterized DNA binding activity as RNA/DNA binding proteins (RDBPs), many of which are linked to neurological diseases. RDBPs are associated with both nuclear and mitochondrial DNA repair. Furthermore, the presence of intrinsically disordered domains in RDBPs appears to be critical for regulating their diverse interactions and plays a key role in controlling protein aggregation, which is implicated in neurodegeneration. In this review, we discuss the emerging roles of common RDBPs from the heterogeneous nuclear ribonucleoprotein (hnRNP) family, such as TAR DNA binding protein-43 (TDP43) and fused in sarcoma (FUS) in controlling DNA damage response (DDR). We also explore the implications of RDBP pathology in aging and neurodegenerative diseases and provide a prospective on the therapeutic potential of targeting RDBP pathology mediated DDR defects for motor neuron diseases and aging.
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Affiliation(s)
- Manohar Kodavati
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA.
| | - Vikas H Maloji Rao
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA
| | - Vincent E Provasek
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Muralidhar L Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA; Department of Neurosurgery, Weill Medical College, New York, NY 10065, USA.
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Scott-Hewitt N, Mahoney M, Huang Y, Korte N, Yvanka de Soysa T, Wilton DK, Knorr E, Mastro K, Chang A, Zhang A, Melville D, Schenone M, Hartigan C, Stevens B. Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging brain. Cell 2024; 187:4193-4212.e24. [PMID: 38942014 DOI: 10.1016/j.cell.2024.05.058] [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: 05/31/2023] [Revised: 01/08/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Abstract
Neuroimmune interactions mediate intercellular communication and underlie critical brain functions. Microglia, CNS-resident macrophages, modulate the brain through direct physical interactions and the secretion of molecules. One such secreted factor, the complement protein C1q, contributes to complement-mediated synapse elimination in both developmental and disease models, yet brain C1q protein levels increase significantly throughout aging. Here, we report that C1q interacts with neuronal ribonucleoprotein (RNP) complexes in an age-dependent manner. Purified C1q protein undergoes RNA-dependent liquid-liquid phase separation (LLPS) in vitro, and the interaction of C1q with neuronal RNP complexes in vivo is dependent on RNA and endocytosis. Mice lacking C1q have age-specific alterations in neuronal protein synthesis in vivo and impaired fear memory extinction. Together, our findings reveal a biophysical property of C1q that underlies RNA- and age-dependent neuronal interactions and demonstrate a role of C1q in critical intracellular neuronal processes.
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Affiliation(s)
- Nicole Scott-Hewitt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Matthew Mahoney
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Youtong Huang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nils Korte
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - T Yvanka de Soysa
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel K Wilton
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emily Knorr
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Mastro
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Allison Chang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Allison Zhang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - David Melville
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Monica Schenone
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Hartigan
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beth Stevens
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Investigator, Boston Children's Hospital, Boston, MA 02115, USA.
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4
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Ding Y, Lin M, Wang J, Shang X. RBM3 enhances the stability of MEF2C mRNA and modulates blood-brain barrier permeability in AD microenvironment. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119738. [PMID: 38670534 DOI: 10.1016/j.bbamcr.2024.119738] [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: 11/12/2023] [Revised: 03/27/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Blood-brain barrier (BBB) changes are acknowledged as early indicators of Alzheimer's disease (AD). The permeability and integrity of the BBB rely significantly on the essential role played by the tight junction proteins (TJPs) connecting endothelial cells. This study found the reduced RNA binding motif protein 3 (RBM3) expression in brain microvascular endothelial cells (BMECs) incubated with Aβ1-42. This downregulation of RBM3 caused a decrease in the levels of ZO-1 and occludin and increased the permeability of BBB cell model in AD microenvironment. Myocyte enhancer factor 2C (MEF2C) expression was also inhibited in BMECs incubated with Aβ1-42. A decrease in MEF2C expression led to increased permeability of BBB cell model in AD microenvironment and reductions in the levels of ZO-1 and occludin. Further analysis of the underlying mechanism revealed that RBM3 binds to and stabilizes MEF2C mRNA. MEF2C binds to the promoters of ZO-1 and occludin, enhancing their transcriptional activities and modulating BBB permeability. RBM3 increases the stability of MEF2C mRNA and subsequently modulates BBB permeability through the paracellular pathway of TJPs. This may provide new insights for AD research.
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Affiliation(s)
- Ye Ding
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Meiqing Lin
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jirui Wang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiuli Shang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China.
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Lumpkin CJ, Patel H, Potts GK, Chaurasia S, Gibilisco L, Srivastava GP, Lee JY, Brown NJ, Amarante P, Williams JD, Karran E, Townsend M, Woods D, Ravikumar B. Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson's disease pathogenesis. Mol Brain 2024; 17:26. [PMID: 38778381 PMCID: PMC11110445 DOI: 10.1186/s13041-024-01099-1] [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: 07/03/2023] [Accepted: 05/11/2024] [Indexed: 05/25/2024] Open
Abstract
Aggregation of misfolded α-synuclein (α-syn) is a key characteristic feature of Parkinson's disease (PD) and related synucleinopathies. The nature of these aggregates and their contribution to cellular dysfunction is still not clearly elucidated. We employed mass spectrometry-based total and phospho-proteomics to characterize the underlying molecular and biological changes due to α-syn aggregation using the M83 mouse primary neuronal model of PD. We identified gross changes in the proteome that coincided with the formation of large Lewy body-like α-syn aggregates in these neurons. We used protein-protein interaction (PPI)-based network analysis to identify key protein clusters modulating specific biological pathways that may be dysregulated and identified several mechanisms that regulate protein homeostasis (proteostasis). The observed changes in the proteome may include both homeostatic compensation and dysregulation due to α-syn aggregation and a greater understanding of both processes and their role in α-syn-related proteostasis may lead to improved therapeutic options for patients with PD and related disorders.
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Affiliation(s)
- Casey J Lumpkin
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Hiral Patel
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Gregory K Potts
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Shilpi Chaurasia
- Excelra Knowledge Solutions Pvt Ltd, Uppal, Hyderabad, India, 500039
| | - Lauren Gibilisco
- Genomics Research Center, Computational Biology Neuroscience, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Gyan P Srivastava
- Data & Statistical Sciences, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Janice Y Lee
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Nathan J Brown
- Biotherapeutics, AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | - Patricia Amarante
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Jon D Williams
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Eric Karran
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Matthew Townsend
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Dori Woods
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA.
| | - Brinda Ravikumar
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA.
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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7
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Taha MS, Ahmadian MR. Fragile X Messenger Ribonucleoprotein Protein and Its Multifunctionality: From Cytosol to Nucleolus and Back. Biomolecules 2024; 14:399. [PMID: 38672417 PMCID: PMC11047961 DOI: 10.3390/biom14040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Silencing of the fragile X messenger ribonucleoprotein 1 (FMR1) gene and a consequent lack of FMR protein (FMRP) synthesis are associated with fragile X syndrome, one of the most common inherited intellectual disabilities. FMRP is a multifunctional protein that is involved in many cellular functions in almost all subcellular compartments under both normal and cellular stress conditions in neuronal and non-neuronal cell types. This is achieved through its trafficking signals, nuclear localization signal (NLS), nuclear export signal (NES), and nucleolar localization signal (NoLS), as well as its RNA and protein binding domains, and it is modulated by various post-translational modifications such as phosphorylation, ubiquitination, sumoylation, and methylation. This review summarizes the recent advances in understanding the interaction networks of FMRP with a special focus on FMRP stress-related functions, including stress granule formation, mitochondrion and endoplasmic reticulum plasticity, ribosome biogenesis, cell cycle control, and DNA damage response.
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Affiliation(s)
- Mohamed S. Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
- Research on Children with Special Needs Department, Institute of Medical Research and Clinical Studies, National Research Centre, Cairo 12622, Egypt
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
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Ramos-Velasco B, Naranjo R, Izquierdo JM. Bibliometric Overview on T-Cell Intracellular Antigens and Their Pathological Implications. BIOLOGY 2024; 13:195. [PMID: 38534464 DOI: 10.3390/biology13030195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation regulation, linking them to a wide range of diseases including neuronal disorders, cancer and other pathologies. From their discovery to the present day, many studies have focused on the behavior of these proteins in order to understand their impact on molecular and cellular processes and to understand their relationship to human pathologies. The volume of research on these proteins in various fields, including molecular biology, biochemistry, cell biology, immunology and cancer, has steadily increased, indicating a growing interest in these gene expression regulators among researchers. This information can be used to know the most productive institutions working in the field, understand the focus of research, identify key areas of involvement, delve deeper into their relationship and impact on different diseases, and to establish the level of study associated with them.
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Affiliation(s)
- Beatriz Ramos-Velasco
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rocío Naranjo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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9
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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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10
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Bhagat R, Minaya MA, Renganathan A, Mehra M, Marsh J, Martinez R, Eteleeb AM, Nana AL, Spina S, Seeley WW, Grinberg LT, Karch CM. Long non-coding RNA SNHG8 drives stress granule formation in tauopathies. Mol Psychiatry 2023; 28:4889-4901. [PMID: 37730840 PMCID: PMC10914599 DOI: 10.1038/s41380-023-02237-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Tauopathies are a heterogenous group of neurodegenerative disorders characterized by tau aggregation in the brain. In a subset of tauopathies, rare mutations in the MAPT gene, which encodes the tau protein, are sufficient to cause disease; however, the events downstream of MAPT mutations are poorly understood. Here, we investigate the role of long non-coding RNAs (lncRNAs), transcripts >200 nucleotides with low/no coding potential that regulate transcription and translation, and their role in tauopathy. Using stem cell derived neurons from patients carrying a MAPT p.P301L, IVS10 + 16, or p.R406W mutation and CRISPR-corrected isogenic controls, we identified transcriptomic changes that occur as a function of the MAPT mutant allele. We identified 15 lncRNAs that were commonly differentially expressed across the three MAPT mutations. The commonly differentially expressed lncRNAs interact with RNA-binding proteins that regulate stress granule formation. Among these lncRNAs, SNHG8 was significantly reduced in a mouse model of tauopathy and in FTLD-tau, progressive supranuclear palsy, and Alzheimer's disease brains. We show that SNHG8 interacts with tau and stress granule-associated RNA-binding protein TIA1. Overexpression of mutant tau in vitro is sufficient to reduce SNHG8 expression and induce stress granule formation. Rescuing SNHG8 expression leads to reduced stress granule formation and reduced TIA1 levels in immortalized cells and in MAPT mutant neurons, suggesting that dysregulation of this non-coding RNA is a causal factor driving stress granule formation via TIA1 in tauopathies.
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Affiliation(s)
- Reshma Bhagat
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Miguel A Minaya
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Arun Renganathan
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Muneshwar Mehra
- Department of Neuroscience, Washington University in St Louis, St Louis, MO, USA
| | - Jacob Marsh
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Rita Martinez
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Abdallah M Eteleeb
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Alissa L Nana
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Salvatore Spina
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William W Seeley
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Lea T Grinberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of Sao Paulo, São Paulo, Brazil
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA.
- Knight Alzheimer Disease Research Center, Washington University in St Louis, St Louis, MO, USA.
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11
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Ma N, Xu H, Zhang W, Sun X, Guo R, Liu D, Zhang L, Liu Y, Zhang J, Qiao C, Chen D, Luo A, Bai J. Genome-wide analysis revealed the dysregulation of RNA binding protein-correlated alternative splicing events in myocardial ischemia reperfusion injury. BMC Med Genomics 2023; 16:251. [PMID: 37858115 PMCID: PMC10585833 DOI: 10.1186/s12920-023-01706-5] [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: 01/10/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Myocardial ischemia reperfusion injury (MIRI), the tissue damage which is caused by the returning of blood supply to tissue after a period of ischemia, greatly reduces the therapeutic effect of treatment of myocardial infarction. But the underlying functional mechanisms of MIRI are still unclear. METHODS We constructed mouse models of MIRI, extracted injured and healthy myocardial tissues, and performed transcriptome sequencing experiments (RNA-seq) to systematically investigate the dysregulated transcriptome of MIRI, especially the alternative splicing (AS) regulation and RNA binding proteins (RBPs). Selected RBPs and MIRI-associated AS events were then validated by RT-qPCR experiments. RESULTS The differentially expressed gene (DEG) analyses indicated that transcriptome profiles were changed by MIRI and that DEGs' enriched functions were consistent with MIRI's dysregulated pathways. Furthermore, the AS profile was synergistically regulated and showed clear differences between the mouse model and the healthy samples. The exon skipping events significantly increased in MIRI model samples, while the opposite cassette exon events significantly decreased. According to the functional analysis, regulated alternative splicing genes (RASGs) were enriched in protein transport, cell division /cell cycle, RNA splicing, and endocytosis pathways, which were associated with the development of MIRI. Meanwhile, 493 differentially expressed RBPs (DE RBPs) were detected, most of which were correlated with the changed ratios of AS events. In addition, nine DE RBP genes were validated, including Eif5, Pdia6, Tagln2, Vasp, Zfp36l2, Grsf1, Idh2, Ndrg2, and Uqcrc1. These nine DE RBPs were correlated with RASGs enriched in translation process, cell growth and division, and endocytosis pathways, highly consistent with the functions of all RASGs. Finally, we validated the AS ratio changes of five regulated alternative splicing events (RASEs) derived from important regulatory genes, including Mtmr3, Cdc42, Cd47, Fbln2, Vegfa, and Fhl2. CONCLUSION Our study emphasized the critical roles of the dysregulated AS profiles in MIRI development, investigated the potential functions of MIRI-associated RASGs, and identified regulatory RBPs involved in AS regulation. We propose that the identified RASEs and RBPs could serve as important regulators and potential therapeutic targets in MIRI treatment in the future.
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Affiliation(s)
- Ning Ma
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Hao Xu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Weihua Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Xiaoke Sun
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Ruiming Guo
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Donghai Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Liang Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Yang Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Jian Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Chenhui Qiao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Ailing Luo
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Jingyun Bai
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China.
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12
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Wang C, Terrigno M, Li J, Distler T, Pandya NJ, Ebeling M, Tyanova S, Hoozemans JJM, Dijkstra AA, Fuchs L, Xiang S, Bonni A, Grüninger F, Jagasia R. Increased G3BP2-Tau interaction in tauopathies is a natural defense against Tau aggregation. Neuron 2023; 111:2660-2674.e9. [PMID: 37385246 DOI: 10.1016/j.neuron.2023.05.033] [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: 08/16/2022] [Revised: 02/21/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Many RNA-binding proteins (RBPs), particularly those associated with RNA granules, promote pathological protein aggregation in neurodegenerative diseases. Here, we demonstrate that G3BP2, a core component of stress granules, directly interacts with Tau and inhibits Tau aggregation. In the human brain, the interaction of G3BP2 and Tau is dramatically increased in multiple tauopathies, and it is independent of neurofibrillary tangle (NFT) formation in Alzheimer's disease (AD). Surprisingly, Tau pathology is significantly elevated upon loss of G3BP2 in human neurons and brain organoids. Moreover, we found that G3BP2 masks the microtubule-binding region (MTBR) of Tau, thereby inhibiting Tau aggregation. Our study defines a novel role for RBPs as a line of defense against Tau aggregation in tauopathies.
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Affiliation(s)
- Congwei Wang
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland.
| | - Marco Terrigno
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Juan Li
- School of Life Sciences, University of Science and Technology of China, 230026 Anhui, China
| | - Tania Distler
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Nikhil J Pandya
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Stefka Tyanova
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, 1081 HV Amsterdam, the Netherlands
| | - Anke A Dijkstra
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, 1081 HV Amsterdam, the Netherlands
| | - Luisa Fuchs
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Shengqi Xiang
- School of Life Sciences, University of Science and Technology of China, 230026 Anhui, China
| | - Azad Bonni
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Fiona Grüninger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Ravi Jagasia
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland.
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13
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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14
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Hnath B, Chen J, Reynolds J, Choi E, Wang J, Zhang D, Sha CM, Dokholyan NV. Big versus small: The impact of aggregate size in disease. Protein Sci 2023; 32:e4686. [PMID: 37243896 PMCID: PMC10273386 DOI: 10.1002/pro.4686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Protein aggregation results in an array of different size soluble oligomers and larger insoluble fibrils. Insoluble fibrils were originally thought to cause neuronal cell deaths in neurodegenerative diseases due to their prevalence in tissue samples and disease models. Despite recent studies demonstrating the toxicity associated with soluble oligomers, many therapeutic strategies still focus on fibrils or consider all types of aggregates as one group. Oligomers and fibrils require different modeling and therapeutic strategies, targeting the toxic species is crucial for successful study and therapeutic development. Here, we review the role of different-size aggregates in disease, and how factors contributing to aggregation (mutations, metals, post-translational modifications, and lipid interactions) may promote oligomers opposed to fibrils. We review two different computational modeling strategies (molecular dynamics and kinetic modeling) and how they are used to model both oligomers and fibrils. Finally, we outline the current therapeutic strategies targeting aggregating proteins and their strengths and weaknesses for targeting oligomers versus fibrils. Altogether, we aim to highlight the importance of distinguishing the difference between oligomers and fibrils and determining which species is toxic when modeling and creating therapeutics for protein aggregation in disease.
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Affiliation(s)
- Brianna Hnath
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jiaxing Chen
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Joshua Reynolds
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Esther Choi
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jian Wang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Dongyan Zhang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Congzhou M. Sha
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Nikolay V. Dokholyan
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biochemistry & Molecular BiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of ChemistryPenn State UniversityUniversity ParkPennsylvaniaUSA
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15
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Young-Pearse TL, Lee H, Hsieh YC, Chou V, Selkoe DJ. Moving beyond amyloid and tau to capture the biological heterogeneity of Alzheimer's disease. Trends Neurosci 2023; 46:426-444. [PMID: 37019812 PMCID: PMC10192069 DOI: 10.1016/j.tins.2023.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Alzheimer's disease (AD) manifests along a spectrum of cognitive deficits and levels of neuropathology. Genetic studies support a heterogeneous disease mechanism, with around 70 associated loci to date, implicating several biological processes that mediate risk for AD. Despite this heterogeneity, most experimental systems for testing new therapeutics are not designed to capture the genetically complex drivers of AD risk. In this review, we first provide an overview of those aspects of AD that are largely stereotyped and those that are heterogeneous, and we review the evidence supporting the concept that different subtypes of AD are important to consider in the design of agents for the prevention and treatment of the disease. We then dive into the multifaceted biological domains implicated to date in AD risk, highlighting studies of the diverse genetic drivers of disease. Finally, we explore recent efforts to identify biological subtypes of AD, with an emphasis on the experimental systems and data sets available to support progress in this area.
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Affiliation(s)
- Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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16
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Zhou Y, Wang Y, Wang Y, Chen L, Wang N, Su Y, Diwu Y, Zhang Q. LncRNA NKILA Exacerbates Alzheimer's Disease Progression by Regulating the FOXA1-Mediated Transcription of TNFAIP1. Neurochem Res 2023:10.1007/s11064-023-03944-6. [PMID: 37217807 DOI: 10.1007/s11064-023-03944-6] [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: 10/21/2022] [Revised: 04/03/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases in the world, which seriously affects AD patients' life quality. Recently, long non-coding RNAs (lncRNAs) have been reported to play a key role in AD pathogenesis, however, the specific mechanism remains unclear. Herein, we aimed to investigate the role of lncRNA NKILA in AD. The learning and memory performance of rats from streptozotocin (STZ)-treated or other treated groups were tested by Morris water maze test. Relative levels of genes and proteins were measured using RT-qPCR and Western blotting. Mitochondrial membrane potential was tested by JC-1 staining. Levels of ROS, SOD, MDA, GSH-Px, and LDH were measured using corresponding commercial kits. Apoptosis was evaluated by TUNEL staining or Flow cytometry assay. RNA Immunoprecipitation (RIP), RNA pulldown, Chromatin immunoprecipitation (ChIP), and dual-luciferase reporter assays were utilized to test the interaction between indicated molecules. STZ treatment caused learning and memory impairment in rats and oxidative stress damage in SH-SY5Y cells. LncRNA NKILA was found to be elevated in the hippocampal tissues of rats and SH-SY5Y cells after STZ exposure. Knockdown of lncRNA NKILA alleviated STZ-induced neuronal damage. Furthermore, lncRNA NKILA could bind to ELAVL1, which regulate the stability of FOXA1 mRNA. Moreover, TNFAIP1 transcription process was controlled by FOXA1, which targeted the promoter of TNFAIP1. In vivo results demonstrated that lncRNA NKILA accelerated STZ-induced neuronal damage and oxidative stress by FOXA1/TNFAIP1 axis. Our findings indicated that knockdown of lncRNA NKILA inhibited the neuronal damage and oxidative stress induced by STZ through the FOXA1/TNFAIP1 axis, thereby alleviating the development of AD, revealing a promising therapeutic axis for AD treatment.
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Affiliation(s)
- Yuan Zhou
- Department of Anatomy, Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
- Discipline Innovation Team of Shaanxi, University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
- Shaanxi Key Laboratory of Chinese Medicine Encephalopathy, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
- Shaanxi Key Laboratory of Research on TCM Physical Constitution and Diseases Prevention and Treatment, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
| | - Yujin Wang
- Department of TCM Diagnosis, Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
| | - Yalee Wang
- Discipline Innovation Team of Shaanxi, University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
- Affiliated Hospital of Shaanxi University of Chinese Medicine, No.2 Weiyang West Road, Xianyang, 712046, Shaanxi Province, People's Republic of China
| | - Lianji Chen
- Department of Anatomy, Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
| | - Nan Wang
- Department of Anatomy, Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China
| | - Yanjin Su
- Department of Endocrinology, Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China.
| | - Yongchang Diwu
- Discipline Innovation Team of Shaanxi, University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China.
- Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China.
| | - Qi Zhang
- Shaanxi Key Laboratory of Chinese Medicine Encephalopathy, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China.
- Shaanxi Key Laboratory of Research on TCM Physical Constitution and Diseases Prevention and Treatment, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi Province, People's Republic of China.
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17
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Xiong W, Li D, Feng Y, Jia C, Zhang X, Liu Z. CircLPAR1 Promotes Neuroinflammation and Oxidative Stress in APP/PS1 Mice by Inhibiting SIRT1/Nrf-2/HO-1 Axis Through Destabilizing GDF-15 mRNA. Mol Neurobiol 2023; 60:2236-2251. [PMID: 36646968 DOI: 10.1007/s12035-022-03177-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
Circular RNA LPAR1 (circLPAR1) was revealed to be elevated in Alzheimer's disease (AD); nevertheless, its role and mechanisms in AD remain unknown. Memory performance of APP/PS1 mice was assessed by Morris water maze test. Expression of circLPAR1 and indicated messenger RNA (mRNA) in mouse brain tissues or/and SH-SY5Y cells were tested by quantitative real-time PCR (qRT-PCR). Protein expression of indicated gene was examined by western blot. Production of proinflammatory cytokines (tumor necrosis factor-α, TNF-α; interleukin-6, IL-6; interleukin-1β, IL-1β; and interleukin-8, IL-8) and oxidative stress-related factors (reactive oxygen species, ROS; malondialdehyde, MDA; superoxide dismutase, SOD; and glutathione, GSH) were assessed by commercial kits. RNA pull down and RNA immunoprecipitation were performed to verify the interplay between up-frameshift protein 1 (UPF1) and circLPAR1 or growth differentiation factor 15 (GDF-15). CircLPAR1 was elevated, while GDF-15 was decreased in both APP/PS1 mice and Aβ-treated SH-SY5Y cells. Knockdown of circLPAR1 and overexpression of GDF-15 protected cells against Aβ-caused inflammation, oxidative stress, and neuronal apoptosis. CircLPAR1 knockdown was also proved to improve AD-related pathological traits and ameliorate cognitive dysfunctions in vivo. In mechanism, we found that circLPAR1 repressed GDF-15 expression by decreasing GDF-15 mRNA stability through UPF1 recruitment. Rescue assays suggested that sirtuin 1 (SIRT1) knockdown reversed GDF-15 overexpression-induced inhibition on Aβ-induced neuronal damage and nuclear factor E2-related factor (Nrf-2)/heme oxygenase-1 (HO-1) pathway inhibition. Moreover, the protective effect of circLPAR1 knockdown against Aβ-induced apoptosis was abolished by GDF-15 knockdown, and SIRT1 overexpression could counteract this effect of GDF-15 knockdown. CircLPAR1 knockdown improved AD-related pathological traits in vitro and in vivo by inhibiting SIRT1/Nrf-2/HO-1 axis through GDF-15.
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Affiliation(s)
- Wenping Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Dongming Li
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Yu Feng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Chenguang Jia
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Xiangyu Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Zheng Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China.
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18
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García-Ruiz S, Zhang D, Gustavsson EK, Rocamora-Perez G, Grant-Peters M, Fairbrother-Browne A, Reynolds RH, Brenton JW, Gil-Martínez AL, Chen Z, Rio DC, Botia JA, Guelfi S, Collado-Torres L, Ryten M. Splicing accuracy varies across human introns, tissues and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534370. [PMID: 37034741 PMCID: PMC10081249 DOI: 10.1101/2023.03.29.534370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
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Affiliation(s)
- S García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - D Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - E K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - G Rocamora-Perez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - M Grant-Peters
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - R H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - J W Brenton
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A L Gil-Martínez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Z Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - D C Rio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - J A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - S Guelfi
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Verge Genomics, South San Francisco, CA, 94080, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA , 21205
| | - M Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
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19
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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Bhagat R, Minaya MA, Renganathan A, Mehra M, Marsh J, Martinez R, Nana AL, Spina S, Seeley WW, Grinberg LT, Karch CM. Long non-coding RNA SNHG8 drives stress granule formation in tauopathies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23286548. [PMID: 36909621 PMCID: PMC10002771 DOI: 10.1101/2023.02.27.23286548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Tauopathies are a heterogenous group of neurodegenerative disorders characterized by tau aggregation in the brain. In a subset of tauopathies, rare mutations in the MAPT gene, which encodes the tau protein, are sufficient to cause disease; however, the events downstream of MAPT mutations are poorly understood. Here, we investigate the role of long non-coding RNAs (lncRNAs), transcripts >200 nucleotides with low/no coding potential that regulate transcription and translation, and their role in tauopathy. Using stem cell derived neurons from patients carrying a MAPT p.P301L, IVS10+16, or p.R406W mutation, and CRISPR-corrected isogenic controls, we identified transcriptomic changes that occur as a function of the MAPT mutant allele. We identified 15 lncRNAs that were commonly differentially expressed across the three MAPT mutations. The commonly differentially expressed lncRNAs interact with RNA-binding proteins that regulate stress granule formation. Among these lncRNAs, SNHG8 was significantly reduced in a mouse model of tauopathy and in FTLD-tau, progressive supranuclear palsy, and Alzheimer’s disease brains. We show that SNHG8 interacts with tau and stress granule-associated RNA-binding protein TIA1. Overexpression of mutant tau in vitro is sufficient to reduce SNHG8 expression and induce stress granule formation. Rescuing SNHG8 expression leads to reduced stress granule formation and reduced TIA1 levels, suggesting that dysregulation of this non-coding RNA is a causal factor driving stress granule formation via TIA1 in tauopathies.
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21
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Jahanbazi Jahan-Abad A, Salapa HE, Libner CD, Thibault PA, Levin MC. hnRNP A1 dysfunction in oligodendrocytes contributes to the pathogenesis of multiple sclerosis. Glia 2023; 71:633-647. [PMID: 36382566 DOI: 10.1002/glia.24300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022]
Abstract
Oligodendrocyte (OL) damage and death are prominent features of multiple sclerosis (MS) pathology, yet mechanisms contributing to OL loss are incompletely understood. Dysfunctional RNA binding proteins (RBPs), hallmarked by nucleocytoplasmic mislocalization and altered expression, have been shown to result in cell loss in neurologic diseases, including in MS. Since we previously observed that the RBP heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was dysfunctional in neurons in MS, we hypothesized that it might also contribute to OL pathology in MS and relevant models. We discovered that hnRNP A1 dysfunction is characteristic of OLs in MS brains. These findings were recapitulated in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS, where hnRNP A1 dysfunction was characteristic of OLs, including oligodendrocyte precursor cells and mature OLs in which hnRNP A1 dysfunction correlated with demyelination. We also found that hnRNP A1 dysfunction was induced by IFNγ, indicating that inflammation influences hnRNP A1 function. To fully understand the effects of hnRNP A1 dysfunction on OLs, we performed siRNA knockdown of hnRNP A1, followed by RNA sequencing. RNA sequencing detected over 4000 differentially expressed transcripts revealing alterations to RNA metabolism, cell morphology, and programmed cell death pathways. We confirmed that hnRNP A1 knockdown was detrimental to OLs and induced apoptosis and necroptosis. Together, these data demonstrate a critical role for hnRNP A1 in proper OL functioning and survival and suggest a potential mechanism of OL damage and death in MS that involves hnRNP A1 dysfunction.
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Affiliation(s)
- Ali Jahanbazi Jahan-Abad
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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22
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McCarthy KP, Go DB, Senapati S, Chang HC. An integrated ion-exchange membrane-based microfluidic device for irreversible dissociation and quantification of miRNA from ribonucleoproteins. LAB ON A CHIP 2023; 23:285-294. [PMID: 36524732 PMCID: PMC10697430 DOI: 10.1039/d2lc00517d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ribonucleoproteins (RNPs), particularly microRNA-induced silencing complex (miRISC), have been associated with cancer-related gene regulation. Specific RNA-protein associations in miRISC complexes or those found in let-7 lin28A complexes can downregulate tumor-suppressing genes and can be directly linked to cancer. The high protein-RNA electrostatic binding affinity is a particular challenge for the quantification of the associated microRNAs (miRNAs). We report here the first microfluidic point-of-care assay that allows direct quantification of RNP-associated RNAs, which has the potential to greatly advance RNP profiling for liquid biopsy. Key to the technology is an integrated cation-anion exchange membrane (CEM/AEM) platform for rapid and irreversible dissociation (k = 0.0025 s-1) of the RNP (Cas9-miR-21) complex and quantification of its associated miR-21 in 40 minutes. The CEM-induced depletion front is used to concentrate the RNP at the depletion front such that the high electric field (>100 V cm-1) within the concentration boundary layer induces irreversible dissociation of the low KD (∼0.5 nM) complex, with ∼100% dissociation even though the association rate (kon = 6.1 s-1) is 1000 times higher. The high field also electrophoretically drives the dissociated RNA out of the concentrated zone without reassociation. A detection limit of 1.1 nM is achieved for Cy3 labelled miR-21.
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Affiliation(s)
- Kyle P McCarthy
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | - David B Go
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
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23
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Minné D, Marnewick JL, Engel-Hills P. Early Chronic Stress Induced Changes within the Locus Coeruleus in Sporadic Alzheimer's Disease. Curr Alzheimer Res 2023; 20:301-317. [PMID: 37872793 DOI: 10.2174/1567205020666230811092956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 10/25/2023]
Abstract
Chronic exposure to stress throughout the lifespan has been the focus of many studies on Alzheimer's disease (AD) because of the similarities between the biological mechanisms involved in chronic stress and the pathophysiology of AD. In fact, the earliest abnormality associated with the disease is the presence of phosphorylated tau protein in locus coeruleus neurons, a brain structure highly responsive to stress and perceived threat. Here, we introduce allostatic load as a useful concept for understanding many of the complex, interacting neuropathological changes involved in the AD degenerative process. In response to chronic stress, aberrant tau proteins that begin to accumulate within the locus coeruleus decades prior to symptom onset appear to represent a primary pathological event in the AD cascade, triggering a wide range of interacting brain changes involving neuronal excitotoxicity, endocrine alterations, inflammation, oxidative stress, and amyloid plaque exacerbation. While it is acknowledged that stress will not necessarily be the major precipitating factor in all cases, early tau-induced changes within the locus coeruleus-norepinephrine pathway suggests that a therapeutic window might exist for preventative measures aimed at managing stress and restoring balance within the HPA axis.
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Affiliation(s)
- Donné Minné
- Applied Microbial & Health Biotechnology Institute, Cape Peninsula University of Technology, Cape Town, 7535, South Africa
- Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town, 7535, South Africa
| | - Jeanine L Marnewick
- Applied Microbial & Health Biotechnology Institute, Cape Peninsula University of Technology, Cape Town, 7535, South Africa
| | - Penelope Engel-Hills
- Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town, 7535, South Africa
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24
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Xiao J, Jin S, Wang X, Huang J, Zou H. CELF1 Selectively Regulates Alternative Splicing of DNA Repair Genes Associated With Cataract in Human Lens Cell Line. Biochem Genet 2022:10.1007/s10528-022-10324-2. [PMID: 36585568 DOI: 10.1007/s10528-022-10324-2] [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: 10/18/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022]
Abstract
Cataract is a global eye disease caused by the opacification of lens, while its underlying molecular pathogenesis is not clear, making it difficult for prevention. CELF1, an RNA binding protein, mediates Alternative Splicing (AS) of genes involved in diverse diseases and regulates development or defects of lens. Utilizing transcriptome-wide approaches, we analyzed and compared AS patterns between human lens epithelial cells (SRA01/04) with CELF1 overexpression (CELF1-OE) and control cells. Extensive changes in AS patterns upon CELF1-OE were identified in SRA01/04 cells. We finally identified 840 CELF1-regulated AS events (RASEs) and found that CELF1-OE preferred to repress exon skipping events in SRA01/04 cells. CELF1-regulated AS genes were enriched in the regulation of DNA repair, cellular response to DNA damage stimulus, and apoptosis pathways (including HMGA2, CSNK1E, and YAP1). These biological functions and pathways have been reported to be associated with lens development or other eye diseases. To further explore the mechanisms of CELF1 in regulating AS genes, we downloaded and re-analyzed a set of CELF1-RNA interactome data. We found that 194 genes were bound and regulated by CELF1 at the AS level. 10 genes involved in DNA repair-related pathways were also bound by CELF1. Motif analysis for CELF1-bound peaks and splicing sites of RASEs showed that CELF1 regulates AS by binding to the AGGU[AG]AG motif in SRA01/04 cells. CELF1 could mediate AS of DNA repair-related genes through directly binding to their transcripts with distinct motif bias. The functional mechanism of CELF1 may ultimately participate in cataract formation and lens development.
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Affiliation(s)
- Jun Xiao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Siyan Jin
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Xue Wang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Ju Huang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - He Zou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China.
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25
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Huai Y, Mao W, Wang X, Lin X, Li Y, Chen Z, Qian A. How do RNA binding proteins trigger liquid-liquid phase separation in human health and diseases? Biosci Trends 2022; 16:389-404. [PMID: 36464283 DOI: 10.5582/bst.2022.01449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
RNA-binding proteins (RBPs) lie at the center of post-transcriptional regulation and protein synthesis, adding complexity to RNA life cycle. RBPs also participate in the formation of membrane-less organelles (MLOs) via undergoing liquid-liquid phase separation (LLPS), which underlies the formation of MLOs in eukaryotic cells. RBPs-triggered LLPS mainly relies on the interaction between their RNA recognition motifs (RRMs) and capped mRNA transcripts and the heterotypic multivalent interactions between their intrinsically disordered regions (IDRs) or prion-like domains (PLDs). In turn, the aggregations of RBPs are also dependent on the process of LLPS. RBPs-driven LLPS is involved in many intracellular processes (regulation of translation, mRNA storage and stabilization and cell signaling) and serves as the heart of cellular physiology and pathology. Thus, it is essential to comprehend the potential roles and investigate the internal mechanism of RPBs-triggered LLPS. In this review, we primarily expound on our current understanding of RBPs and they-triggered LLPS and summarize their physiological and pathological functions. Furthermore, we also summarize the potential roles of RBPs-triggered LLPS as novel therapeutic mechanism for human diseases. This review will help understand the mechanisms underlying LLPS and downstream regulation of RBPs and provide insights into the pathogenesis and therapy of complex diseases.
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Affiliation(s)
- Ying Huai
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wenjing Mao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xuehao Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiao Lin
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yu Li
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhihao Chen
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
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26
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Nogami M, Sano O, Adachi-Tominari K, Hayakawa-Yano Y, Furukawa T, Iwata H, Ogi K, Okano H, Yano M. DNA damage stress-induced translocation of mutant FUS proteins into cytosolic granules and screening for translocation inhibitors. Front Mol Neurosci 2022; 15:953365. [PMID: 36606141 PMCID: PMC9808394 DOI: 10.3389/fnmol.2022.953365] [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: 05/27/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Fused in sarcoma/translated in liposarcoma (FUS) is an RNA-binding protein, and its mutations are associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), through the DNA damage stress response, aberrant stress granule (SG) formation, etc. We previously reported that translocation of endogenous FUS into SGs was achieved by cotreatment with a DNA double-strand break inducer and an inhibitor of DNA-PK activity. In the present study, we investigated cytoplasmic SG formation using various fluorescent protein-tagged mutant FUS proteins in a human astrocytoma cell (U251) model. While the synergistic enhancement of the migration of fluorescent protein-tagged wild-type FUS to cytoplasmic SGs upon DNA damage induction was observed when DNA-PK activity was suppressed, the fluorescent protein-tagged FUSP525L mutant showed cytoplasmic localization. It migrated to cytoplasmic SGs upon DNA damage induction alone, and DNA-PK inhibition also showed a synergistic effect. Furthermore, analysis of 12 sites of DNA-PK-regulated phosphorylation in the N-terminal LC region of FUS revealed that hyperphosphorylation of FUS mitigated the mislocalization of FUS into cytoplasmic SGs. By using this cell model, we performed screening of a compound library to identify compounds that inhibit the migration of FUS to cytoplasmic SGs but do not affect the localization of the SG marker molecule G3BP1 to cytoplasmic SGs. Finally, we successfully identified 23 compounds that inhibit FUS-containing SG formation without changing normal SG formation. Highlights Characterization of DNA-PK-dependent FUS stress granule localization.A compound library was screened to identify compounds that inhibit the formation of FUS-containing stress granules.
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Affiliation(s)
- Masahiro Nogami
- Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan,Shonan Incubation Laboratories, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan,*Correspondence: Masahiro Nogami,
| | - Osamu Sano
- Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Keiko Adachi-Tominari
- Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Yoshika Hayakawa-Yano
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan,Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Takako Furukawa
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hidehisa Iwata
- Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Kazuhiro Ogi
- Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan,Shonan Incubation Laboratories, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Hideyuki Okano
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan
| | - Masato Yano
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan,Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan,Masato Yano,
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27
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Cappelli S, Spalloni A, Feiguin F, Visani G, Šušnjar U, Brown AL, De Bardi M, Borsellino G, Secrier M, Phatnani H, Romano M, Fratta P, Longone P, Buratti E. NOS1AP is a novel molecular target and critical factor in TDP-43 pathology. Brain Commun 2022; 4:fcac242. [PMID: 36267332 PMCID: PMC9576154 DOI: 10.1093/braincomms/fcac242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/05/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Many lines of evidence have highlighted the role played by heterogeneous nuclear ribonucleoproteins in amyotrophic lateral sclerosis. In this study, we have aimed to identify transcripts co-regulated by TAR DNA-binding protein 43 kDa and highly conserved heterogeneous nuclear ribonucleoproteins which have been previously shown to regulate TAR DNA-binding protein 43 kDa toxicity (deleted in azoospermia-associated protein 1, heterogeneous nuclear ribonucleoprotein -Q, -D, -K and -U). Using the transcriptome analyses, we have uncovered that Nitric Oxide Synthase 1 Adaptor Protein mRNA is a direct TAR DNA-binding protein 43 kDa target, and in flies, its modulation alone can rescue TAR DNA-binding protein 43 kDa pathology. In primary mouse cortical neurons, we show that TAR DNA-binding protein 43 kDa mediated downregulation of Nitric Oxide Synthase 1 Adaptor Protein expression strongly affects the NMDA-receptor signalling pathway. In human patients, the downregulation of Nitric Oxide Synthase 1 Adaptor Protein mRNA strongly correlates with TAR DNA-binding protein 43 kDa proteinopathy as measured by cryptic Stathmin-2 and Unc-13 homolog A cryptic exon inclusion. Overall, our results demonstrate that Nitric Oxide Synthase 1 Adaptor Protein may represent a novel disease-relevant gene, potentially suitable for the development of new therapeutic strategies.
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Affiliation(s)
- Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Alida Spalloni
- Molecular Neurobiology, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Fabian Feiguin
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Giulia Visani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Urša Šušnjar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Marco De Bardi
- Neuroimmunology Unit, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy
| | - Giovanna Borsellino
- Neuroimmunology Unit, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Patrizia Longone
- Molecular Neurobiology, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
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28
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Nantacharoen W, Baek SJ, Plaingam W, Charoenkiatkul S, Tencomnao T, Sukprasansap M. Cleistocalyx nervosum var. paniala Berry Promotes Antioxidant Response and Suppresses Glutamate-Induced Cell Death via SIRT1/Nrf2 Survival Pathway in Hippocampal HT22 Neuronal Cells. Molecules 2022; 27:molecules27185813. [PMID: 36144547 PMCID: PMC9503107 DOI: 10.3390/molecules27185813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022] Open
Abstract
Excessive glutamate neurotransmitters result in oxidative neurotoxicity, similar to neurodegeneration. An indigenous berry of Thailand, Cleistocalyx nervosum var. paniala (CNP), has been recognized for its robust antioxidants. We investigated the effects and mechanisms of CNP fruit extracts on antioxidant-related survival pathways against glutamate-induced neurotoxicity. The extract showed strong antioxidant capability and had high total phenolic and flavonoid contents, particularly resveratrol. Next, the protective effects of the CNP extract or resveratrol on the glutamate-induced neurotoxicity were examined in HT22 hippocampal cells. Our investigation showed that the pretreatment of cells with the CNP extract or resveratrol attenuated glutamate-induced neuronal death via suppression of apoptosis cascade by inhibiting the levels of cleaved- and pro-caspase-3 proteins. The CNP extract and resveratrol suppressed the intracellular ROS by increasing the mRNA expression level of antioxidant enzymes (SODs, GPx1, and CAT). We found that this extract and resveratrol significantly increased SIRT1 expression as a survival-related protein. Moreover, they also promoted the activity of the Nrf2 protein translocation into the nucleus and could bind to the promoter containing the antioxidant response element, inducing the expression of the downstream GPx1-antioxidant protein. Our data illustrate that the CNP extract and resveratrol inhibit apoptotic neuronal death via glutamate-induced oxidative neurotoxicity in HT22 cells through the activation of the SIRT1/Nrf2 survival mechanism.
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Affiliation(s)
- Wanchanok Nantacharoen
- Master Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Seung Joon Baek
- Laboratory of Signal Transduction, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Waluga Plaingam
- College of Oriental Medicine, Rangsit University, Pathum Thani 12000, Thailand
| | - Somsri Charoenkiatkul
- Institute of Nutrition, Salaya Campus, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing (Neur-Age Natura) Research Unit, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.T.); (M.S.); Tel.: +66-22181533 (T.T.); +66-28002380 (M.S.)
| | - Monruedee Sukprasansap
- Food Toxicology Unit, Institute of Nutrition, Salaya Campus, Mahidol University, Nakhon Pathom 73170, Thailand
- Correspondence: (T.T.); (M.S.); Tel.: +66-22181533 (T.T.); +66-28002380 (M.S.)
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29
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Mishra P, Sankar SHH, Gosavi N, Bharathavikru RS. RNA nucleoprotein complexes in biological systems. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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30
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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31
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Houghton OH, Mizielinska S, Gomez-Suaga P. The Interplay Between Autophagy and RNA Homeostasis: Implications for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Front Cell Dev Biol 2022; 10:838402. [PMID: 35573690 PMCID: PMC9096704 DOI: 10.3389/fcell.2022.838402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/14/2022] [Indexed: 01/18/2023] Open
Abstract
Amyotrophic lateral sclerosis and frontotemporal dementia are neurodegenerative disorders that lie on a disease spectrum, sharing genetic causes and pathology, and both without effective therapeutics. Two pathways that have been shown to play major roles in disease pathogenesis are autophagy and RNA homeostasis. Intriguingly, there is an increasing body of evidence suggesting a critical interplay between these pathways. Autophagy is a multi-stage process for bulk and selective clearance of malfunctional cellular components, with many layers of regulation. Although the majority of autophagy research focuses on protein degradation, it can also mediate RNA catabolism. ALS/FTD-associated proteins are involved in many stages of autophagy and autophagy-mediated RNA degradation, particularly converging on the clearance of persistent pathological stress granules. In this review, we will summarise the progress in understanding the autophagy-RNA homeostasis interplay and how that knowledge contributes to our understanding of the pathobiology of ALS/FTD.
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Affiliation(s)
- O H Houghton
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - S Mizielinska
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - P Gomez-Suaga
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Cáceres, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, Spain
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32
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TARBP2-stablized SNHG7 regulates blood-brain barrier permeability by acting as a competing endogenous RNA to miR-17-5p/NFATC3 in Aβ-microenvironment. Cell Death Dis 2022; 13:457. [PMID: 35562351 PMCID: PMC9106673 DOI: 10.1038/s41419-022-04920-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/14/2022]
Abstract
Breakdown of blood-brain barrier (BBB) is recognized as serious pathological marker of Alzheimer's disease development. Studies confirmed that β-amyloid (Aβ) deposition induced high BBB permeability by disrupting tight junction (TJ) proteins formed from endothelial cells (ECs). Here, we found TARBP2, SNHG7 and NFATC3 in expressions were increased and miR-17-5p expression was decreased in Aβ(1-42)-incubated ECs. Overexpression of TARBP2, SNHG7 and NFATC3 elevated BBB permeability and knockdown of them had converse results. Agomir-17-5p decreased BBB permeability and antagomir-17-5p increased BBB permeability. TARBP2 as a RNA-binding protein (RBP) bound to SNHG7 and resulted in longer half-life of SNHG7. The decreased expression of miR-17-5p had a negative post-transcriptional regulation to NFATC3, leading to the increased expression of NFATC3. In addition, SNHG7 regulated NFATC3 expression by acting as a molecule sponge targeting to miR-17-5p. NFATC3 inhibited TJ proteins expression by functioning as a transcription factor. TARBP2/SNHG7/miR-17-5p/NFATC3 pathway implied a potential mechanism in studies of BBB changes in AD pathological progression.
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33
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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Montalbano M, Jaworski E, Garcia S, Ellsworth A, McAllen S, Routh A, Kayed R. Tau Modulates mRNA Transcription, Alternative Polyadenylation Profiles of hnRNPs, Chromatin Remodeling and Spliceosome Complexes. Front Mol Neurosci 2021; 14:742790. [PMID: 34924950 PMCID: PMC8678415 DOI: 10.3389/fnmol.2021.742790] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tau protein is a known contributor in several neurodegenerative diseases, including Alzheimer’s disease (AD) and frontotemporal dementia (FTD). It is well-established that tau forms pathological aggregates and fibrils in these diseases. Tau has been observed within the nuclei of neurons, but there is a gap in understanding regarding the mechanism by which tau modulates transcription. We are interested in the P301L mutation of tau, which has been associated with FTD and increased tau aggregation. Our study utilized tau-inducible HEK (iHEK) cells to reveal that WT and P301L tau distinctively alter the transcription and alternative polyadenylation (APA) profiles of numerous nuclear precursors mRNAs, which then translate to form proteins involved in chromatin remodeling and splicing. We isolated total mRNA before and after over-expressing tau and then performed Poly(A)-ClickSeq (PAC-Seq) to characterize mRNA expression and APA profiles. We characterized changes in Gene Ontology (GO) pathways using EnrichR and Gene Set Enrichment Analysis (GSEA). We observed that P301L tau up-regulates genes associated with reactive oxygen species responsiveness as well as genes involved in dendrite, microtubule, and nuclear body/speckle formation. The number of genes regulated by WT tau is greater than the mutant form, which indicates that the P301L mutation causes loss-of-function at the transcriptional level. WT tau up-regulates genes contributing to cytoskeleton-dependent intracellular transport, microglial activation, microtubule and nuclear chromatin organization, formation of nuclear bodies and speckles. Interestingly, both WT and P301L tau commonly down-regulate genes responsible for ubiquitin-proteosome system. In addition, WT tau significantly down-regulates several genes implicated in chromatin remodeling and nucleosome organization. Although there are limitations inherent to the model systems used, this study will improve understanding regarding the nuclear impact of tau at the transcriptional and post-transcriptional level. This study also illustrates the potential impact of P301L tau on the human brain genome during early phases of pathogenesis.
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Affiliation(s)
- Mauro Montalbano
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Stephanie Garcia
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Anna Ellsworth
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Salome McAllen
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
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35
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Zaepfel BL, Rothstein JD. Polyadenylated RNA and RNA-Binding Proteins Exhibit Unique Response to Hyperosmotic Stress. Front Cell Dev Biol 2021; 9:809859. [PMID: 34970554 PMCID: PMC8712688 DOI: 10.3389/fcell.2021.809859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Stress granule formation is a complex and rapidly evolving process that significantly disrupts cellular metabolism in response to a variety of cellular stressors. Recently, it has become evident that different chemical stressors lead to the formation of compositionally distinct stress granules. However, it is unclear which proteins are required for the formation of stress granules under different conditions. In addition, the effect of various stressors on polyadenylated RNA metabolism remains enigmatic. Here, we demonstrate that G3BP1/2, which are common stress granule components, are not required for the formation of stress granules specifically during osmotic stress induced by sorbitol and related polyols. Furthermore, sorbitol-induced osmotic stress leads to significant depletion of nuclear polyadenylated RNA, a process that we demonstrate is dependent on active mRNA export, as well as cytoplasmic and subnuclear shifts in the presence of many nuclear RNA-binding proteins. We assessed the function of multiple shifted RBPs and found that hnRNP U, but not TDP-43 or hnRNP I, exhibit reduced function following this cytoplasmic shift. Finally, we observe that multiple stress pathways lead to a significant reduction in transcription, providing a possible explanation for our inability to observe loss of TDP-43 or hnRNP I function. Overall, we identify unique outcomes following osmotic stress that provide important insight into the regulation of RNA-binding protein localization and function.
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Affiliation(s)
- Benjamin L. Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Molecular Biology and Genetics Department, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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36
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Fenix AM, Miyaoka Y, Bertero A, Blue SM, Spindler MJ, Tan KKB, Perez-Bermejo JA, Chan AH, Mayerl SJ, Nguyen TD, Russell CR, Lizarraga PP, Truong A, So PL, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE, Conklin BR, Salomonis N. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nat Commun 2021; 12:6324. [PMID: 34732726 PMCID: PMC8566601 DOI: 10.1038/s41467-021-26623-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart tissues made from these cell lines recapitulate contractile dysfunction of RBM20-associated DCM and reveal greater dysfunction with missense mutations than KO. Analysis of RBM20 RNA binding by eCLIP reveals a gain-of-function preference of mutant RBM20 for 3' UTR sequences that are shared with amyotrophic lateral sclerosis (ALS) and processing-body associated RNA binding proteins (FUS, DDX6). Deep RNA sequencing reveals that the RBM20 R636S mutant has unique gene, splicing, polyadenylation and circular RNA defects that differ from RBM20 KO. Super-resolution microscopy verifies that mutant RBM20 maintains very limited nuclear localization potential; rather, the mutant protein associates with cytoplasmic processing bodies (DDX6) under basal conditions, and with stress granules (G3BP1) following acute stress. Taken together, our results highlight a pathogenic mechanism in cardiac disease through splicing-dependent and -independent pathways.
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Affiliation(s)
- Aidan M Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Kenneth K B Tan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | - Amanda H Chan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Steven J Mayerl
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Trieu D Nguyen
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | | | - Annie Truong
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Po-Lin So
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Aishwarya Kulkarni
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nathan J Sniadecki
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
- Department of Mechanical Engineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Charles E Murry
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA.
- Department of Medicine/Cardiology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Sana Biotechnology, 188 E Blaine Street, Seattle, WA, 98102, USA.
| | - Bruce R Conklin
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA.
- Department of Medicine, Cellular and Molecular Pharmacology, and Ophthalmology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA.
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37
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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38
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Mann JR, Donnelly CJ. RNA modulates physiological and neuropathological protein phase transitions. Neuron 2021; 109:2663-2681. [PMID: 34297914 PMCID: PMC8434763 DOI: 10.1016/j.neuron.2021.06.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/21/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022]
Abstract
Aggregation of RNA-binding proteins (RBPs) is a pathological hallmark of neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In these diseases, TDP-43 and FUS RBPs are depleted from the nuclear compartment, where they are normally localized, and found within cytoplasmic inclusions in degenerating regions of affected individuals' postmortem tissue. The mechanisms responsible for aggregation of these proteins has remained elusive, but recent studies suggest liquid-liquid phase separation (LLPS) might serve as a critical nucleation step in formation of pathological inclusions. The process of phase separation also underlies the formation and maintenance of several functional membraneless organelles (MLOs) throughout the cell, some of which contain TDP-43, FUS, and other disease-linked RBPs. One common ligand of disease-linked RBPs, RNA, is a major component of MLOs containing RBPs and has been demonstrated to be a strong modulator of RBP phase transitions. Although early evidence suggested a largely synergistic effect of RNA on RBP phase separation and MLO assembly, recent work indicates that RNA can also antagonize RBP phase behavior under certain physiological and pathological conditions. In this review, we describe the mechanisms underlying RNA-mediated phase transitions of RBPs and examine the molecular properties of these interactions, such as RNA length, sequence, and secondary structure, that mediate physiological or pathological LLPS.
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Affiliation(s)
- Jacob R Mann
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA; LiveLikeLouCenter for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA 15213, USA; Center for Protein Conformational Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Christopher J Donnelly
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; LiveLikeLouCenter for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA 15213, USA; Center for Protein Conformational Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Institute for Neurodegeneration, University of Pittsburgh, Pittsburgh PA 15213.
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39
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Rybak-Wolf A, Plass M. RNA Dynamics in Alzheimer's Disease. Molecules 2021; 26:5113. [PMID: 34500547 PMCID: PMC8433936 DOI: 10.3390/molecules26175113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder that heavily burdens healthcare systems worldwide. There is a significant requirement to understand the still unknown molecular mechanisms underlying AD. Current evidence shows that two of the major features of AD are transcriptome dysregulation and altered function of RNA binding proteins (RBPs), both of which lead to changes in the expression of different RNA species, including microRNAs (miRNAs), circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs). In this review, we will conduct a comprehensive overview of how RNA dynamics are altered in AD and how this leads to the differential expression of both short and long RNA species. We will describe how RBP expression and function are altered in AD and how this impacts the expression of different RNA species. Furthermore, we will also show how changes in the abundance of specific RNA species are linked to the pathology of AD.
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Affiliation(s)
- Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Mireya Plass
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
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40
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Zhou Y, Lu H, Liu Y, Zhao Z, Zhang Q, Xue C, Zou Y, Cao Z, Luo W. Cirbp-PSD95 axis protects against hypobaric hypoxia-induced aberrant morphology of hippocampal dendritic spines and cognitive deficits. Mol Brain 2021; 14:129. [PMID: 34419133 PMCID: PMC8379783 DOI: 10.1186/s13041-021-00827-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Hypobaric hypoxia (HH) is a typical characteristic of high altitude environment and causes a spectrum of pathophysiological effects, including headaches, gliovascular dysfunction and cognitive retardation. Here, we sought to understand the mechanisms underlying cognitive deficits under HH exposure. Our results showed that hypobaric hypoxia exposure impaired cognitive function and suppressed dendritic spine density accompanied with increased neck length in both basal and apical hippocampal CA1 region neurons in mice. The expression of PSD95, a vital synaptic scaffolding molecule, is down-regulated by hypobaric hypoxia exposure and post-transcriptionally regulated by cold-inducible RNA-binding protein (Cirbp) through 3′-UTR region binding. PSD95 expressing alleviates hypoxia-induced dendritic spine morphology changes of hippocampal neurons and memory deterioration. Moreover, overexpressed Cirbp in hippocampus rescues HH-induced abnormal expression of PSD95 and attenuates hypoxia-induced dendritic spine injury and cognitive retardation. Thus, our findings reveal a novel mechanism that Cirbp-PSD-95 axis appears to play an essential role in HH-induced cognitive dysfunction in mice.
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Affiliation(s)
- Yang Zhou
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Huanyu Lu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Ying Liu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Zaihua Zhao
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Qian Zhang
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Chong Xue
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Yuankang Zou
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Zipeng Cao
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China.
| | - Wenjing Luo
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China.
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41
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Corbet GA, Wheeler JR, Parker R, Weskamp K. TDP43 ribonucleoprotein granules: physiologic function to pathologic aggregates. RNA Biol 2021; 18:128-138. [PMID: 34412568 DOI: 10.1080/15476286.2021.1963099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Ribonucleoprotein (RNP) assemblies are ubiquitous in eukaryotic cells and have functions throughout RNA transcription, splicing, and stability. Of the RNA-binding proteins that form RNPs, TAR DNA-binding protein of 43 kD (TDP43) is of particular interest due to its essential nature and its association with disease. TDP43 plays critical roles in RNA metabolism, many of which require its recruitment to RNP granules such as stress granules, myo-granules, and neuronal transport granules. Moreover, the presence of cytoplasmic TDP43-positive inclusions is a pathological hallmark of several neurodegenerative diseases. Despite the pervasiveness of TDP43 aggregates, TDP43 mutations are exceedingly rare, suggesting that aggregation may be linked to dysregulation of TDP43 function. Oligomerization is a part of normal TDP43 function; thus, it is of interest to understand what triggers the irreversible aggregation that is seen in disease. Herein, we examine TDP43 functions, particularly in RNP granules, and the mechanisms which may explain pathological TDP43 aggregation.
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Affiliation(s)
- Giulia Ada Corbet
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | | | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Department of Chemistry, Howard Hughes Medical Institute, Chevy Chase, MD, USA
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Larrasa-Alonso J, Villalba-Orero M, Martí-Gómez C, Ortiz-Sánchez P, López-Olañeta MM, Rey-Martín MA, Sánchez-Cabo F, McNicoll F, Müller-McNicoll M, García-Pavía P, Lara-Pezzi E. The SRSF4-GAS5-Glucocorticoid Receptor Axis Regulates Ventricular Hypertrophy. Circ Res 2021; 129:669-683. [PMID: 34333993 PMCID: PMC8409900 DOI: 10.1161/circresaha.120.318577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supplemental Digital Content is available in the text. RBPs (RNA-binding proteins) play critical roles in human biology and disease. Aberrant RBP expression affects various steps in RNA processing, altering the function of the target RNAs. The RBP SRSF4 (serine/arginine-rich splicing factor 4) has been linked to neuropathies and cancer. However, its role in the heart is completely unknown.
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Affiliation(s)
- Javier Larrasa-Alonso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - María Villalba-Orero
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
| | - Carlos Martí-Gómez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Paula Ortiz-Sánchez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Marina M López-Olañeta
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - M Ascensión Rey-Martín
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Fátima Sánchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - François McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Pablo García-Pavía
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.).,Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, Madrid, Spain (P.G.-P.).,Facultad de Ciencias de la Salud, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, Spain (P.G.-P.)
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
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Cicardi ME, Marrone L, Azzouz M, Trotti D. Proteostatic imbalance and protein spreading in amyotrophic lateral sclerosis. EMBO J 2021; 40:e106389. [PMID: 33792056 PMCID: PMC8126909 DOI: 10.15252/embj.2020106389] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/18/2020] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder whose exact causative mechanisms are still under intense investigation. Several lines of evidence suggest that the anatomical and temporal propagation of pathological protein species along the neural axis could be among the main driving mechanisms for the fast and irreversible progression of ALS pathology. Many ALS-associated proteins form intracellular aggregates as a result of their intrinsic prion-like properties and/or following impairment of the protein quality control systems. During the disease course, these mutated proteins and aberrant peptides are released in the extracellular milieu as soluble or aggregated forms through a variety of mechanisms. Internalization by recipient cells may seed further aggregation and amplify existing proteostatic imbalances, thus triggering a vicious cycle that propagates pathology in vulnerable cells, such as motor neurons and other susceptible neuronal subtypes. Here, we provide an in-depth review of ALS pathology with a particular focus on the disease mechanisms of seeding and transmission of the most common ALS-associated proteins, including SOD1, FUS, TDP-43, and C9orf72-linked dipeptide repeats. For each of these proteins, we report historical, biochemical, and pathological evidence of their behaviors in ALS. We further discuss the possibility to harness pathological proteins as biomarkers and reflect on the implications of these findings for future research.
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Affiliation(s)
- Maria Elena Cicardi
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Lara Marrone
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Mimoun Azzouz
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Davide Trotti
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
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44
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Petyuk VA, Yu L, Olson HM, Yu F, Clair G, Qian WJ, Shulman JM, Bennett DA. Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss. J Proteome Res 2021; 20:2266-2282. [PMID: 33900085 PMCID: PMC9190253 DOI: 10.1021/acs.jproteome.0c00747] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteinaceous aggregates containing α-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson's disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights into proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss, and controls with no neuronal loss. Using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach, we characterized the proteome both in terms of protein abundances and peptide modifications. Statistical testing for differential abundance of the most abundant 2963 proteins, followed by pathway enrichment and Bayesian learning of the causal network structure, was performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g., TDP-43 and FUS), have a strong inverse correlation with Lewy bodies and may reflect an alternative mechanism of nigral neurodegeneration.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Heather M Olson
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Joshua M Shulman
- Departments of Neurology, Molecular & Human Genetics, and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
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45
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Tau oligomers accumulation sensitizes prostate cancer cells to docetaxel treatment. J Cancer Res Clin Oncol 2021; 147:1957-1971. [PMID: 33811272 PMCID: PMC8164592 DOI: 10.1007/s00432-021-03598-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/11/2021] [Indexed: 02/05/2023]
Abstract
PURPOSE Human tau is a highly dynamic, multifunctional protein expressed in different isoforms and conformers, known to modulate microtubule turnover. Tau oligomers are considered pathologic forms of the protein able to initiate specific protein accumulation diseases, called tauopathies. In our study, we investigated the potential association between autophagy and tau oligomers accumulation and its role in the response of prostate cancer cells to docetaxel. METHODS We evaluated in vitro the expression of tau oligomers in prostate cancer cell lines, PC3 and DU145, in presence of autophagy inhibitors and investigated the role of tau oligomers accumulation in resistance to docetaxel treatment. RESULTS Tau protein was basally expressed in prostate cancer lines as several monomeric and oligomeric forms. The pharmacologic inhibition of autophagy induced in cancer cells the accumulation of tau protein, with a prevalent expression of oligomeric forms. Immunofluorescence analysis of untreated cells revealed that tau was visible mainly in dividing cells where it was localized on the mitotic spindle. Inhibition of autophagy determined an evident upregulation of tau signal in dividing cells and the presence of aberrant monoastral mitotic spindles. The accumulation of tau oligomers was associated with DNA DSB and increased cytotoxic effect by docetaxel. CONCLUSIONS Our data indicate that autophagy could exert a promoting role in cancer growth and during chemotherapy facilitating degradation of tau protein and thus blocking the antimitotic effect of accumulated tau oligomers. Thus, therapeutic strategies aimed at stimulating tau oligomers formation, such as autophagy inhibition, could be an effective adjuvant in cancer therapy.
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46
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Guo Q, Dammer EB, Zhou M, Kundinger SR, Gearing M, Lah JJ, Levey AI, Shulman JM, Seyfried NT. Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease. Front Mol Neurosci 2021; 14:623659. [PMID: 33815056 PMCID: PMC8014091 DOI: 10.3389/fnmol.2021.623659] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023] Open
Abstract
Core spliceosome and related RNA-binding proteins aggregate in Alzheimer’s disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including tau and amyloid beta (Aβ) in detergent insoluble fractions from control, AsymAD, AD and Parkinson’s disease (PD) brain. Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles showed stage-specific enrichment of insoluble RBPs from AsymAD and AD brains, whereas the RNA splicing module was reduced specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across the specific neurodegenerative diseases we examined.
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Affiliation(s)
- Qi Guo
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States
| | - Maotian Zhou
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Sean R Kundinger
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Joshua M Shulman
- Departments of Neurology, Neuroscience and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
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47
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Eshraghi M, Karunadharma PP, Blin J, Shahani N, Ricci EP, Michel A, Urban NT, Galli N, Sharma M, Ramírez-Jarquín UN, Florescu K, Hernandez J, Subramaniam S. Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease. Nat Commun 2021; 12:1461. [PMID: 33674575 PMCID: PMC7935949 DOI: 10.1038/s41467-021-21637-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
The polyglutamine expansion of huntingtin (mHTT) causes Huntington disease (HD) and neurodegeneration, but the mechanisms remain unclear. Here, we found that mHtt promotes ribosome stalling and suppresses protein synthesis in mouse HD striatal neuronal cells. Depletion of mHtt enhances protein synthesis and increases the speed of ribosomal translocation, while mHtt directly inhibits protein synthesis in vitro. Fmrp, a known regulator of ribosome stalling, is upregulated in HD, but its depletion has no discernible effect on protein synthesis or ribosome stalling in HD cells. We found interactions of ribosomal proteins and translating ribosomes with mHtt. High-resolution global ribosome footprint profiling (Ribo-Seq) and mRNA-Seq indicates a widespread shift in ribosome occupancy toward the 5' and 3' end and unique single-codon pauses on selected mRNA targets in HD cells, compared to controls. Thus, mHtt impedes ribosomal translocation during translation elongation, a mechanistic defect that can be exploited for HD therapeutics.
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Affiliation(s)
- Mehdi Eshraghi
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Pabalu P. Karunadharma
- grid.214007.00000000122199231The Scripps Research Institute, Genomic Core, Jupiter, FL USA
| | - Juliana Blin
- grid.462957.b0000 0004 0598 0706Laboratory of Biology and Cellular Modelling at Ecole Normale Supérieure of Lyon, RNA Metabolism in Immunity and Infection Lab, LBMC, Lyon, France
| | - Neelam Shahani
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Emiliano P. Ricci
- grid.462957.b0000 0004 0598 0706Laboratory of Biology and Cellular Modelling at Ecole Normale Supérieure of Lyon, RNA Metabolism in Immunity and Infection Lab, LBMC, Lyon, France
| | | | | | - Nicole Galli
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Manish Sharma
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Uri Nimrod Ramírez-Jarquín
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Katie Florescu
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Jennifer Hernandez
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Srinivasa Subramaniam
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
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Drepper F, Biernat J, Kaniyappan S, Meyer HE, Mandelkow EM, Warscheid B, Mandelkow E. A combinatorial native MS and LC-MS/MS approach reveals high intrinsic phosphorylation of human Tau but minimal levels of other key modifications. J Biol Chem 2020; 295:18213-18225. [PMID: 33106314 PMCID: PMC7939451 DOI: 10.1074/jbc.ra120.015882] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Abnormal changes of neuronal Tau protein, such as phosphorylation and aggregation, are considered hallmarks of cognitive deficits in Alzheimer's disease. Abnormal phosphorylation is thought to precede aggregation and therefore to promote aggregation, but the nature and extent of phosphorylation remain ill-defined. Tau contains ∼85 potential phosphorylation sites, which can be phosphorylated by various kinases because the unfolded structure of Tau makes them accessible. However, methodological limitations (e.g. in MS of phosphopeptides, or antibodies against phosphoepitopes) led to conflicting results regarding the extent of Tau phosphorylation in cells. Here we present results from a new approach based on native MS of intact Tau expressed in eukaryotic cells (Sf9). The extent of phosphorylation is heterogeneous, up to ∼20 phosphates per molecule distributed over 51 sites. The medium phosphorylated fraction Pm showed overall occupancies of ∼8 Pi (± 5) with a bell-shaped distribution; the highly phosphorylated fraction Ph had 14 Pi (± 6). The distribution of sites was highly asymmetric (with 71% of all P-sites in the C-terminal half of Tau). All sites were on Ser or Thr residues, but none were on Tyr. Other known posttranslational modifications were near or below our detection limit (e.g. acetylation, ubiquitination). These findings suggest that normal cellular Tau shows a remarkably high extent of phosphorylation, whereas other modifications are nearly absent. This implies that abnormal phosphorylations at certain sites may not affect the extent of phosphorylation significantly and do not represent hyperphosphorylation. By implication, the pathological aggregation of Tau is not likely a consequence of high phosphorylation.
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Affiliation(s)
- Friedel Drepper
- Group of Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Jacek Biernat
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany
| | - Senthilvelrajan Kaniyappan
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Helmut E Meyer
- Medical Proteome Center, Ruhr-University Bochum, Bochum, Germany; Department of Biomedical Research, Leibniz-Institute for Analytical Sciences (ISAS), Dortmund, Germany
| | - Eva Maria Mandelkow
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; CAESAR Research Center, Bonn, Germany
| | - Bettina Warscheid
- Group of Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| | - Eckhard Mandelkow
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; CAESAR Research Center, Bonn, Germany.
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Schwartz JL, Jones KL, Yeo GW. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies. Crit Rev Biochem Mol Biol 2020; 56:31-53. [PMID: 33172304 PMCID: PMC8192115 DOI: 10.1080/10409238.2020.1841726] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG50–3,500 in DMPK; DM2, CCTG75–11,000 in ZNF9), fragile X tremor ataxia syndrome (FXTAS, CGG50–200 in FMR1), spinal bulbar muscular atrophy (SBMA, CAG40–55 in AR), Huntington’s disease (HD, CAG36–121 in HTT), C9ORF72-amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD and C9-ALS/FTD, GGGGCC in C9ORF72), and many others, like ataxias. Recent research has highlighted several mechanisms that may contribute to pathology in this heterogeneous class of neurological MRE disorders – bidirectional transcription, intranuclear RNA foci, and repeat associated non-AUG (RAN) translation – which are the subject of this review. Additionally, many MRE disorders share similar underlying molecular pathologies that have been recently targeted in experimental and preclinical contexts. We discuss the therapeutic potential of versatile therapeutic strategies that may selectively target disrupted RNA-based processes and may be readily adaptable for the treatment of multiple MRE disorders. Collectively, the strategies under consideration for treatment of multiple MRE disorders include reducing levels of toxic RNA, preventing RNA foci formation, and eliminating the downstream cellular toxicity associated with peptide repeats produced by RAN translation. While treatments are still lacking for the majority of MRE disorders, several promising therapeutic strategies have emerged and will be evaluated within this review.
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Affiliation(s)
- Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten Leigh Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
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50
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Abstract
Abstract
Purpose of Review
Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum disorder is a rare fatal disease with strong genetic influences. The implementation of short-read sequencing methodologies in increasingly large patient cohorts has rapidly expanded our knowledge of the complex genetic architecture of the disease. We aim to convey the broad history of ALS gene discovery as context for a focused review of 11 ALS gene associations reported over the last 5 years. We also summarize the current level of genetic evidence for all previously reported genes.
Recent Findings
The history of ALS gene discovery has occurred in at least four identifiable phases, each powered by different technologies and scale of investigation. The most recent epoch, benefitting from population-scale genome data, large international consortia, and low-cost sequencing, has yielded 11 new gene associations. We summarize the current level of genetic evidence supporting these ALS genes, highlighting any genotype-phenotype or genotype-pathology correlations, and discussing preliminary understanding of molecular pathogenesis. This era has also raised uncertainty around prior ALS-associated genes and clarified the role of others.
Summary
Our understanding of the genetic underpinning of ALS has expanded rapidly over the last 25 years and has led directly to the clinical application of molecularly driven therapies. Ongoing sequencing efforts in ALS will identify new causative and risk factor genes while clarifying the status of genes reported in prior eras of research.
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