1
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Xiang JS, Schafer DM, Rothamel KL, Yeo GW. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet 2024:10.1038/s41576-024-00749-3. [PMID: 38982239 DOI: 10.1038/s41576-024-00749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/11/2024]
Abstract
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding proteins and their binding sites on RNA - in particular, ultraviolet crosslinking followed by immunoprecipitation (CLIP) - have helped to map the RNA interactome, yielding transcriptome-wide protein-RNA atlases that have contributed to key mechanistic insights into gene expression and gene-regulatory networks. Here, we review these recent advances, explore the effects of cellular context on RNA binding, and discuss how these insights are shaping our understanding of cellular biology. We also review the potential therapeutic applications arising from new knowledge of protein-RNA interactions.
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Affiliation(s)
- Joy S Xiang
- Division of Biomedical Sciences, UC Riverside, Riverside, CA, USA
| | - Danielle M Schafer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Laboratories for Innovative Medicines, La Jolla, CA, USA.
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2
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Li QJ, Fang XL, Li YQ, Lin JY, Huang CL, He SW, Huang SY, Li JY, Gong S, Liu N, Ma J, Zhao Y, Tang LL. DCAF7 Acts as A Scaffold to Recruit USP10 for G3BP1 Deubiquitylation and Facilitates Chemoresistance and Metastasis in Nasopharyngeal Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403262. [PMID: 38973296 DOI: 10.1002/advs.202403262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/13/2024] [Indexed: 07/09/2024]
Abstract
Despite docetaxel combined with cisplatin and 5-fluorouracil (TPF) being the established treatment for advanced nasopharyngeal carcinoma (NPC), there are patients who do not respond positively to this form of therapy. However, the mechanisms underlying this lack of benefit remain unclear. DCAF7 is identified as a chemoresistance gene attenuating the response to TPF therapy in NPC patients. DCAF7 promotes the cisplatin resistance and metastasis of NPC cells in vitro and in vivo. Mechanistically, DCAF7 serves as a scaffold protein that facilitates the interaction between USP10 and G3BP1, leading to the elimination of K48-linked ubiquitin moieties from Lys76 of G3BP1. This process helps prevent the degradation of G3BP1 via the ubiquitin‒proteasome pathway and promotes the formation of stress granule (SG)-like structures. Moreover, knockdown of G3BP1 successfully reversed the formation of SG-like structures and the oncogenic effects of DCAF7. Significantly, NPC patients with increased levels of DCAF7 showed a high risk of metastasis, and elevated DCAF7 levels are linked to an unfavorable prognosis. The study reveals DCAF7 as a crucial gene for cisplatin resistance and offers further understanding of how chemoresistance develops in NPC. The DCAF7-USP10-G3BP1 axis contains potential targets and biomarkers for NPC treatment.
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Affiliation(s)
- Qing-Jie Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Xue-Liang Fang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jia-Yi Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Cheng-Long Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Shi-Wei He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Sheng-Yan Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jun-Yan Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Sha Gong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Yin Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Ling-Long Tang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
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3
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Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [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: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
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Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
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4
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Shelkovnikova TA, Hautbergue GM. RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:455-479. [PMID: 38802180 DOI: 10.1016/bs.irn.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.
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Affiliation(s)
- Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom; Healthy Lifespan Institute (HELSI), University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
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5
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Sato K, Takayama KI, Inoue S. Stress granule-mediated RNA regulatory mechanism in Alzheimer's disease. Geriatr Gerontol Int 2024; 24 Suppl 1:7-14. [PMID: 37726158 DOI: 10.1111/ggi.14663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/21/2023]
Abstract
Living organisms experience a range of stresses. To cope effectively with these stresses, eukaryotic cells have evolved a sophisticated mechanism involving the formation of stress granules (SGs), which play a crucial role in protecting various types of RNA species under stress, such as mRNAs and long non-coding RNAs (lncRNAs). SGs are non-membranous cytoplasmic ribonucleoprotein (RNP) granules, and the RNAs they contain are translationally stalled. Importantly, SGs have been thought to contribute to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD). SGs also contain multiple RNA-binding proteins (RBPs), several of which have been implicated in AD progression. SGs are transient structures that dissipate after stress relief. However, the chronic stresses associated with aging lead to the persistent formation of SGs and subsequently to solid-like pathological SGs, which could impair cellular RNA metabolism and also act as a nidus for the aberrant aggregation of AD-associated proteins. In this paper, we provide a comprehensive summary of the physical basis of SG-enriched RNAs and SG-resident RBPs. We then review the characteristics of AD-associated gene transcripts and their similarity to the SG-enriched RNAs. Furthermore, we summarize and discuss the functional implications of SGs in neuronal RNA metabolism and the aberrant aggregation of AD-associated proteins mediated by SG-resident RBPs in the context of AD pathogenesis. Geriatr Gerontol Int 2024; 24: 7-14.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
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6
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Zhan Y, Wang W, Wang H, Xu Y, Zhang Y, Ning Y, Zheng H, Luo J, Yang Y, Zang H, Zhou M, Fan S. G3BP1 Interact with JAK2 mRNA to Promote the Malignant Progression of Nasopharyngeal Carcinoma via Activating JAK2/STAT3 Signaling Pathway. Int J Biol Sci 2024; 20:94-112. [PMID: 38164170 PMCID: PMC10750281 DOI: 10.7150/ijbs.85341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/19/2023] [Indexed: 01/03/2024] Open
Abstract
Ras-GTPase-activating protein (GAP)-binding protein 1 (G3BP1) is an RNA-binding protein implicated in various malignancies. However, its role in nasopharyngeal carcinoma (NPC) remains elusive. This study elucidates the potential regulation mechanisms of G3BP1 and its significance in NPC advancement. Through knockdown and overexpression approaches, we validate G3BP1's oncogenic role by promoting proliferation, migration, and invasion in vitro and in vivo. Moreover, G3BP1 emerges as a key regulator of the JAK2/STAT3 signaling pathway, augmenting JAK2 expression via mRNA binding. Notably, epigallocatechin gallate (EGCG), a green tea-derived antioxidant, counteracts G3BP1-mediated pathway activation. Clinical analysis reveals heightened G3BP1, JAK2, and p-STAT3 as powerful prognostic markers, with G3BP1's expression standing as an independent indicator of poorer outcomes for NPC patients. In conclusion, the study unveils the oncogenic prowess of G3BP1, its orchestration of the JAK2/STAT3 signaling pathway, and its pivotal role in NPC progression.
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Affiliation(s)
- Yuting Zhan
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weiyuan Wang
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haihua Wang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Xu
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Zhang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Ning
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiadi Luo
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Yang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongjing Zang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Songqing Fan
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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7
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Mukhopadhyay A, Deshpande SN, Bhatia T, Thelma BK. Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case-control association study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1677-1691. [PMID: 37009928 DOI: 10.1007/s00406-023-01596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes-tardive dyskinesia (n = 176) and cognition (n = 565) using a case-control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Affiliation(s)
- Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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8
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Wang Z, Zhang C, Fan C, Liu Y. Post-translational modifications in stress granule and their implications in neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194989. [PMID: 37751804 DOI: 10.1016/j.bbagrm.2023.194989] [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: 05/29/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023]
Abstract
Stress granules (SGs) arise as formations of mRNAs and proteins in response to translation initiation inhibition during stress. These dynamic compartments adopt a fluidic nature through liquid-liquid phase separation (LLPS), exhibiting a composition subject to constant change within cellular contexts. Research has unveiled an array of post-translational modifications (PTMs) occurring on SG proteins, intricately orchestrating SG dynamics. In the realm of neurodegenerative diseases, pathological mutant proteins congregate into insoluble aggregates alongside numerous SG proteins, manifesting resilience against disassembly. Specific PTMs conspicuously label these aggregates, designating them for subsequent degradation. The strategic manipulation of aberrant SGs via PTMs emerges as a promising avenue for therapeutic intervention. This review discerns recent strides in comprehending the impact of PTMs on LLPS behavior and the assembly/disassembly kinetics of SGs. By delving into the roles of PTMs in governing SG dynamics, we augment our cognizance of the molecular underpinnings of neurodegeneration. Furthermore, we offer invaluable insights into potential targets for therapeutic intervention in neurodegenerative afflictions, encompassing conditions like amyotrophic lateral sclerosis and frontotemporal dementia.
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Affiliation(s)
- Zhangshun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chen'ang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chengyu Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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9
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Chathuranga WAG, Nikapitiya C, Kim JH, Chathuranga K, Weerawardhana A, Dodantenna N, Kim DJ, Poo H, Jung JU, Lee CH, Lee JS. Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation. Cell Rep 2023; 42:113358. [PMID: 37917584 DOI: 10.1016/j.celrep.2023.113358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/04/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Stress granules (SGs) constitute a signaling hub that plays a critical role in type I interferon responses. Here, we report that growth arrest and DNA damage-inducible beta (Gadd45β) act as a positive regulator of SG-mediated interferon signaling by targeting G3BP upon RNA virus infection. Gadd45β deficiency markedly impairs SG formation and SG-mediated activation of interferon signaling in vitro. Gadd45β knockout mice are highly susceptible to RNA virus infection, and their ability to produce interferon and cytokines is severely impaired. Specifically, Gadd45β interacts with the RNA-binding domain of G3BP, leading to conformational expansion of G3BP1 via dissolution of its autoinhibitory electrostatic intramolecular interaction. The acidic loop 1- and RNA-binding properties of Gadd45β markedly increase the conformational expansion and RNA-binding affinity of the G3BP1-Gadd45β complex, thereby promoting assembly of SGs. These findings suggest a role for Gadd45β as a component and critical regulator of G3BP1-mediated SG formation, which facilitates RLR-mediated interferon signaling.
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Affiliation(s)
- W A Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Jae-Hoon Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea; Livestock Products Analysis Division, Division of Animal Health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon 34146, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Doo-Jin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haryoung Poo
- Department of Biomedical Science and Engineering, Konkuk Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRRIB), Daejeon 34141, Republic of Korea.
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea.
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10
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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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11
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Kleiner RE. Chemical Approaches To Investigate Post-transcriptional RNA Regulation. ACS Chem Biol 2023; 18:1684-1697. [PMID: 37540831 PMCID: PMC11031734 DOI: 10.1021/acschembio.3c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
RNA plays a central role in biological processes, and its activity is regulated by a host of diverse chemical and biochemical mechanisms including post-transcriptional modification and interactions with RNA-binding proteins. Here, we describe our efforts to illuminate RNA biology through the application of chemical tools, focusing on post-transcriptional regulatory mechanisms. We describe the development of an activity-based protein profiling approach for discovery and characterization of RNA-modifying enzymes. Next, we highlight novel approaches for RNA imaging based upon metabolic labeling with modified nucleosides and engineering of the nucleotide salvage pathway. Finally, we discuss profiling RNA-protein interactions using small molecule-dependent RNA editing and synthetic photo-cross-linkable oligonucleotide probes. Our work provides enabling technologies for deciphering the complexity of RNA and its diverse functions in biology.
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Affiliation(s)
- Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA 08544
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12
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Zhao G, Zhang H, Zhang Y, Zhao N, Mao J, Shang P, Gao K, Meng Y, Tao Y, Wang A, Chen Z, Guo C. Oncoprotein SET dynamically regulates cellular stress response through nucleocytoplasmic transport in breast cancer. Cell Biol Toxicol 2023; 39:1795-1814. [PMID: 36534342 DOI: 10.1007/s10565-022-09784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
SETβ is the predominant isoform of oncoprotein SE translocation (SET) in various breast cancer cell lines. Interactome-transcriptome analysis has shown that SETβ is intimately associated with cellular stress response. Among various exogenous stimuli, formaldehyde (FA) causes distinct biological effects in a dose-dependent manner. In response to FA at different concentrations, SET dynamically shuttles between the nucleus and cytoplasm, performing diverse biofunctions to restore homeostasis. At a low concentration, FA acts as an epidermal growth factor (EGF) and activates the HER2 receptor and downstream signaling pathways in HER2+ breast cancer cells, resulting in enhanced cell proliferation. Nucleocytoplasmic transport of SETβ is controlled by the PI3K/PKCα/CK2α axis and depletion or blockade of the transport of SETβ suppresses EGF-induced activation of AKT and ERK. SETβ also inhibits not only stress-induced activation of p38 MAPK signaling pathway, but also assembly of stress granules by hindering formation of the G3BP1-RNA complex. Our findings suggest that SET functions as an important regulator which modulates cellular stress signaling pathways dynamically.
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Affiliation(s)
- Guomeng Zhao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Hongying Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yanchao Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Na Zhao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jinlei Mao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Pengzhao Shang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Kun Gao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yao Meng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yuhang Tao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Anlei Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Ziyi Chen
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| | - Changying Guo
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.
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13
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Dong R, Li X, Flores AD, Lai KO. The translation initiating factor eIF4E and arginine methylation underlie G3BP1 function in dendritic spine development of neurons. J Biol Chem 2023; 299:105029. [PMID: 37442236 PMCID: PMC10432808 DOI: 10.1016/j.jbc.2023.105029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Communication between neurons relies on neurotransmission that takes place at synapses. Excitatory synapses are located primarily on dendritic spines that possess diverse morphologies, ranging from elongated filopodia to mushroom-shaped spines. Failure in the proper development of dendritic spines has detrimental consequences on neuronal connectivity, but the molecular mechanism that controls the balance of filopodia and mushroom spines is not well understood. G3BP1 is the key RNA-binding protein that assembles the stress granules in non-neuronal cells to adjust protein synthesis upon exogenous stress. Emerging evidence suggests that the biological significance of G3BP1 extends beyond its role in stress response, especially in the nervous system. However, the mechanism underlying the regulation and function of G3BP1 in neurons remains elusive. Here we found that G3BP1 suppresses protein synthesis and binds to the translation initiation factor eIF4E via its NTF2-like domain. Notably, the over-production of filopodia caused by G3BP1 depletion can be alleviated by blocking the formation of the translation initiation complex. We further found that the interaction of G3BP1 with eIF4E is regulated by arginine methylation. Knockdown of the protein arginine methyltransferase PRMT8 leads to elevated protein synthesis and filopodia production, which is reversed by the expression of methylation-mimetic G3BP1. Our study, therefore, reveals arginine methylation as a key regulatory mechanism of G3BP1 during dendritic spine morphogenesis and identifies eIF4E as a novel downstream target of G3BP1 in neuronal development independent of stress response.
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Affiliation(s)
- Rui Dong
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Xuejun Li
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China; Hong Kong Institute for Advanced Study, City University of Hong Kong, Hong Kong, China
| | - Angelo D Flores
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Kwok-On Lai
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China; Hong Kong Institute for Advanced Study, City University of Hong Kong, Hong Kong, China.
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14
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Sato K, Takayama KI, Inoue S. Stress granules sequester Alzheimer's disease-associated gene transcripts and regulate disease-related neuronal proteostasis. Aging (Albany NY) 2023; 15:204737. [PMID: 37219408 DOI: 10.18632/aging.204737] [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: 03/24/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
Environmental and physiological stresses can accelerate Alzheimer's disease (AD) pathogenesis. Under stress, a cytoplasmic membraneless structure termed a stress granule (SG) is formed and is associated with various neurodegenerative disorders, including AD. SGs contain translationally arrested mRNAs, suggesting that impaired RNA metabolism in neurons causes AD progression; however, the underlying mechanism remains unclear. Here, we identified numerous mRNAs and long non-coding RNAs that are directly targeted by the SG core proteins G3BP1 and G3BP2. They redundantly target RNAs before and after stress conditions. We further identified RNAs within SGs, wherein AD-associated gene transcripts accumulated, suggesting that SGs can directly regulate AD development. Furthermore, gene-network analysis revealed a possible link between the sequestration of RNAs by SGs and the impairment of protein neurohomeostasis in AD brains. Together, our study provides a comprehensive RNA regulatory mechanism involving SGs, which could be targeted therapeutically to slow AD progression mediated by SGs.
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Affiliation(s)
- Kaoru Sato
- Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Itabashi-ku, Tokyo 173-0015, Japan
- Integrated Research Initiative for Living Well with Dementia (IRIDE), TMIG, Itabashi-ku, Tokyo 173-0015, Japan
| | - Ken-Ichi Takayama
- Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Itabashi-ku, Tokyo 173-0015, Japan
| | - Satoshi Inoue
- Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Itabashi-ku, Tokyo 173-0015, Japan
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15
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Malvi P, Reddy DS, Kumar R, Chava S, Burela S, Parajuli K, Zhang X, Wajapeyee N. LIMK2 promotes melanoma tumor growth and metastasis through G3BP1-ESM1 pathway-mediated apoptosis inhibition. Oncogene 2023; 42:1478-1491. [PMID: 36922679 DOI: 10.1038/s41388-023-02658-x] [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: 10/07/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Melanoma is the leading cause of skin cancer-related deaths, and current melanoma therapies, including targeted therapies and immunotherapies, benefit only a subset of metastatic melanoma patients due to either intrinsic or acquired resistance. LIM domain kinase 2 (LIMK2) is a serine/threonine kinase that plays an important role in the regulation of actin filament dynamics. Here, we show that LIMK2 is overexpressed in melanoma, and its genetic or pharmacological inhibition impairs melanoma tumor growth and metastasis in both cell culture and mice. To determine the mechanism by which LIMK2 promotes melanoma tumor growth and metastatic progression, we performed a phosphoproteomics analysis and identified G3BP1 as a key LIMK2 target, which mirrored the effects of LIMK2 inhibition when inhibited. To further determine the role of G3BP1 downstream of LIMK2, we knocked down the expression of G3BP1, performed RNA-seq analysis, and identified ESM1 as a downstream target of G3BP1. G3BP1 was required for ESM1 mRNA stability, and ESM1 ectopic expression rescued LIMK2 or G3BP1 inhibition-induced suppression of melanoma growth and metastatic attributes. These results collectively identify the LIMK2→G3BP1→ESM1 pathway as a facilitator of melanoma tumor growth and metastasis and document that LIMK2 is a therapeutically tractable target for melanoma therapy.
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Affiliation(s)
- Parmanand Malvi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Dhana Sekhar Reddy
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Raj Kumar
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Suresh Chava
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Sneha Burela
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Keshab Parajuli
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Xuchen Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- UAB O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
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16
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Relton EL, Roth NJ, Yasa S, Kaleem A, Hermey G, Minnis CJ, Mole SE, Shelkovnikova T, Lefrancois S, McCormick PJ, Locker N. The Batten disease protein CLN3 is important for stress granules dynamics and translational activity. J Biol Chem 2023; 299:104649. [PMID: 36965618 PMCID: PMC10149212 DOI: 10.1016/j.jbc.2023.104649] [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: 01/24/2023] [Revised: 03/04/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
The assembly of membrane-less organelles such as stress granules (SGs) is emerging as central in helping cells rapidly respond and adapt to stress. Following stress sensing, the resulting global translational shutoff leads to the condensation of stalled mRNAs and proteins into SGs. By reorganizing cytoplasmic contents, SGs can modulate RNA translation, biochemical reactions, and signaling cascades to promote survival until the stress is resolved. While mechanisms for SG disassembly are not widely understood, the resolution of SGs is important for maintaining cell viability and protein homeostasis. Mutations that lead to persistent or aberrant SGs are increasingly associated with neuropathology and a hallmark of several neurodegenerative diseases. Mutations in CLN3 are causative of juvenile neuronal ceroid lipofuscinosis, a rare neurodegenerative disease affecting children also known as Batten disease. CLN3 encodes a transmembrane lysosomal protein implicated in autophagy, endosomal trafficking, metabolism, and response to oxidative stress. Using a HeLa cell model lacking CLN3, we now show that CLN3KO is associated with an altered metabolic profile, reduced global translation, and altered stress signaling. Furthermore, loss of CLN3 function results in perturbations in SG dynamics, resulting in assembly and disassembly defects, and altered expression of the key SG nucleating factor G3BP1. With a growing interest in SG-modulating drugs for the treatment of neurodegenerative diseases, novel insights into the molecular basis of CLN3 Batten disease may reveal avenues for disease-modifying treatments for this debilitating childhood disease.
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Affiliation(s)
- Emily L Relton
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Nicolas J Roth
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary, University of London, Charterhouse Square, London, United Kingdom
| | - Seda Yasa
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Canada
| | - Abuzar Kaleem
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Hermey
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christopher J Minnis
- Great Ormond Street, Institute of Child Health and MRC Laboratory for Molecular Cell Biology and Great Ormond Street, Institute of Child Health, University College London, London, United Kingdom
| | - Sara E Mole
- Great Ormond Street, Institute of Child Health and MRC Laboratory for Molecular Cell Biology and Great Ormond Street, Institute of Child Health, University College London, London, United Kingdom
| | - Tatyana Shelkovnikova
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Stephane Lefrancois
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada; Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, Canada
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary, University of London, Charterhouse Square, London, United Kingdom
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom.
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17
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Schulte T, Panas MD, Han X, Williams L, Kedersha N, Fleck JS, Tan TJC, Dopico XC, Olsson A, Morro AM, Hanke L, Nilvebrant J, Giang KA, Nygren PÅ, Anderson P, Achour A, McInerney GM. Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH. Open Biol 2023; 13:220369. [PMID: 37161291 PMCID: PMC10170197 DOI: 10.1098/rsob.220369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
G3BP is the central node within stress-induced protein-RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
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Affiliation(s)
- Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Lucy Williams
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Nancy Kedersha
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Simon Fleck
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Timothy J. C. Tan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Anders Olsson
- Protein Expression and Characterization, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Johan Nilvebrant
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Kim Anh Giang
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Paul Anderson
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
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18
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Feng Z, Mao Z, Yang Z, Liu X, Nakamura F. The force-dependent filamin A-G3BP1 interaction regulates phase-separated stress granule formation. J Cell Sci 2023; 136:297259. [PMID: 36806943 DOI: 10.1242/jcs.260684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Filamin A (FLNA) is an actin crosslinking protein that mediates mechanotransduction. External and internal mechanical forces, through the actin cytoskeleton, can induce conformational changes of the FLNA molecule to expose cryptic binding sites for its binding partners. Here, we identified Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) as a new FLNA mechanobinding partner. Unlike other FLNA binding partners to the mechanosensing domain repeat 21 (R21), G3BP1 requires an additional neighboring repeat R22 to interact. We demonstrated that their interaction occurs in the cytosol of living cells in an actin polymerization-dependent manner. We also mapped the FLNA-binding site on G3BP1 and found that a F360A point mutation in the RNA recognition motif disrupts the interaction. RNA interfered with the FLNA-G3BP1 interaction, and FLNA did not localize in RNA-rich stress granules (SGs). Disruption of the interaction was sufficient to promote phase-separated SG formation, and arsenite treatment further stimulated the formation of SGs. Taken together, these data identify G3BP1 as a new mechanobinding protein that interacts with the FLNA mechanosensing domain R21 and suggest that SG formation is partially regulated by mechanical force.
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Affiliation(s)
- Ziyi Feng
- School of Pharmaceutical Science and Technology, Life Science Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Zhenfeng Mao
- School of Pharmaceutical Science and Technology, Life Science Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Ziwei Yang
- School of Pharmaceutical Science and Technology, Life Science Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Xiaowei Liu
- School of Pharmaceutical Science and Technology, Life Science Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Life Science Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
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19
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Natera‐de Benito D, Olival J, Garcia‐Cabau C, Jou C, Roldan M, Codina A, Expósito‐Escudero J, Batlle C, Carrera‐García L, Ortez C, Salvatella X, Palau F, Nascimento A, Hoenicka J. Common pathophysiology for ANXA11 disorders caused by aspartate 40 variants. Ann Clin Transl Neurol 2023; 10:408-425. [PMID: 36651622 PMCID: PMC10014011 DOI: 10.1002/acn3.51731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and have recently been identified as a cause of multisystem proteinopathy and adult-onset muscular dystrophy. These conditions are adult-onset diseases and result from the substitution of Aspartate 40 (Asp40) for an apolar residue in the intrinsically disordered domain (IDD) of ANXA11. Some ALS-related variants are known to affect ANXA11 IDD; however, the mechanism by which the myopathy occurs is unknown. METHODS Genetic analysis was performed using WES-trio. For the study of variant pathogenicity, we used recombinant proteins, muscle biopsy, and fibroblasts. RESULTS Here we describe an individual with severe and rapidly progressive childhood-onset oculopharyngeal muscular dystrophy who carries a new ANXA11 variant at position Asp40 (p.Asp40Ile; c.118_119delGAinsAT). p.Asp40Ile is predicted to enhance the aggregation propensity of ANXA11 to a greater extent than other changes affecting this residue. In vitro studies using recombinant ANXA11p.Asp40Ile showed abnormal phase separation and confirmed this variant is more aggregation-prone than the ALS-associated variant ANXA11p.Asp40Gly . The study of the patient's fibroblasts revealed defects in stress granules dynamics and clearance, and muscle histopathology showed a myopathic pattern with ANXA11 protein aggregates. Super-resolution imaging showed aggregates expressed as pearl strips or large complex structures in the sarcoplasm, and as layered subsarcolemmal chains probably reflecting ANXA11 multifunctionality. INTERPRETATION We demonstrate common pathophysiology for disorders associated with ANXA11 Asp40 allelic variants. Clinical phenotypes may result from different deleterious impacts of variants upon ANXA11 stability against aggregation, and differential muscle or motor neuron dysfunction expressed as a temporal and tissue-specific continuum.
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Affiliation(s)
- Daniel Natera‐de Benito
- Neuromuscular Unit, Department of NeurologyHospital Sant Joan de DéuBarcelona08950Spain
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
| | - Jonathan Olival
- Laboratory of Neurogenetics and Molecular Medicine – IPERInstitut de Recerca Sant Joan de Déu08950BarcelonaSpain
| | - Carla Garcia‐Cabau
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and TechnologyBarcelona08029Spain
| | - Cristina Jou
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
- Department of PathologyHospital Sant Joan de DéuBarcelona08950Spain
| | - Mònica Roldan
- Confocal Microscopy and Cellular Imaging UnitInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
- Department of Genetics and Developmental Medicine – IPERHospital Sant Joan de DéuBarcelona08950Spain
| | - Anna Codina
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
| | - Jessica Expósito‐Escudero
- Neuromuscular Unit, Department of NeurologyHospital Sant Joan de DéuBarcelona08950Spain
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
| | - Cristina Batlle
- Laboratory of Neurogenetics and Molecular Medicine – IPERInstitut de Recerca Sant Joan de Déu08950BarcelonaSpain
| | - Laura Carrera‐García
- Neuromuscular Unit, Department of NeurologyHospital Sant Joan de DéuBarcelona08950Spain
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of NeurologyHospital Sant Joan de DéuBarcelona08950Spain
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER)ISCIIIBarcelonaSpain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and TechnologyBarcelona08029Spain
- ICREABarcelona08010Spain
| | - Francesc Palau
- Laboratory of Neurogenetics and Molecular Medicine – IPERInstitut de Recerca Sant Joan de Déu08950BarcelonaSpain
- Department of Genetics and Developmental Medicine – IPERHospital Sant Joan de DéuBarcelona08950Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER)ISCIIIBarcelonaSpain
- Division of Pediatrics, Faculty of Medicine and Health SciencesUniversity of BarcelonaBarcelona08007Spain
- ERN ITHACABarcelona08950Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Department of NeurologyHospital Sant Joan de DéuBarcelona08950Spain
- Applied Research in Neuromuscular DiseasesInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER)ISCIIIBarcelonaSpain
| | - Janet Hoenicka
- Laboratory of Neurogenetics and Molecular Medicine – IPERInstitut de Recerca Sant Joan de Déu08950BarcelonaSpain
- Center for Biomedical Research Network on Rare Diseases (CIBERER)ISCIIIBarcelonaSpain
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20
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McGoldrick P, Lau A, You Z, Durcan TM, Robertson J. Loss of C9orf72 perturbs the Ran-GTPase gradient and nucleocytoplasmic transport, generating compositionally diverse Importin β-1 granules. Cell Rep 2023; 42:112134. [PMID: 36821445 DOI: 10.1016/j.celrep.2023.112134] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
A hexanucleotide (GGGGCC)n repeat expansion in C9orf72 causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), eliciting toxic effects through generation of RNA foci, dipeptide repeat proteins, and/or loss of C9orf72 protein. Defects in nucleocytoplasmic transport (NCT) have been implicated as a pathogenic mechanism underlying repeat expansion toxicity. Here, we show that loss of C9orf72 disrupts the Ran-GTPase gradient and NCT in vitro and in vivo. NCT disruption in vivo is enhanced by the presence of compositionally different types of cytoplasmic Importin β-1 granule that exhibit neuronal subtype-specific properties. We show that the abundance of Importin β-1 granules is increased in the context of C9orf72 deficiency, disrupting interactions with nuclear pore complex proteins. These granules appear to associate with the nuclear envelope and are co-immunoreactive for G3BP1 and K63-ubiquitin. These findings link loss of C9orf72 protein to gain-of-function mechanisms and defects in NCT.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.
| | - Agnes Lau
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Zhipeng You
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada; Department of Laboratory Medicine and Pathobiology, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
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Maloney MT, Wang W, Bhowmick S, Millan I, Kapur M, Herrera N, Frost E, Zhang EY, Song S, Wang M, Park AB, Yao AY, Yang Y. Failure to Thrive: Impaired BDNF Transport along the Cortical-Striatal Axis in Mouse Q140 Neurons of Huntington's Disease. BIOLOGY 2023; 12:biology12020157. [PMID: 36829435 PMCID: PMC9952218 DOI: 10.3390/biology12020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Boosting trophic support to striatal neurons by increasing levels of brain-derived neurotrophic factor (BDNF) has been considered as a target for therapeutic intervention for several neurodegenerative diseases, including Huntington's disease (HD). To aid in the implementation of such a strategy, a thorough understanding of BDNF cortical-striatal transport is critical to help guide its strategic delivery. In this manuscript, we investigate the dynamic behavior of BDNF transport along the cortical-striatal axis in Q140 primary neurons, a mouse model for HD. We examine this by using single-molecule labeling of BDNF conjugated with quantum dots (QD-BDNF) to follow the transport along the cortical-striatal axis in a microfluidic chamber system specifically designed for the co-culture of cortical and striatal primary neurons. Using this approach, we observe a defect of QD-BDNF transport in Q140 neurons. Our study demonstrates that QD-BDNF transport along the cortical-striatal axis involves the impairment of anterograde transport within axons of cortical neurons, and of retrograde transport within dendrites of striatal neurons. One prominent feature we observe is the extended pause time of QD-BDNF retrograde transport within Q140 striatal dendrites. Taken together, these finding support the hypothesis that delinquent spatiotemporal trophic support of BDNF to striatal neurons, driven by impaired transport, may contribute to the pathogenesis of HD, providing us with insight into how a BDNF supplementation therapeutic strategy may best be applied for HD.
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22
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Abstract
Stress granules (SGs) are cytoplasmic biomolecular condensates containing proteins and RNAs in response to stress. Ras-GTPase–activating protein binding protein 1 (G3BP1) is a core SG protein. Caprin-1 and ubiquitin specific peptidase 10 (USP10) interact with G3BP1, facilitating and suppressing SG formation, respectively. The crystal structures of the nuclear transport factor 2-like (NTF2L) domain of G3BP1 in complex with the G3BP1-interacting motif (GIM) of Caprin-1 and USP10 show that both GIMs bind to the same hydrophobic pocket of G3BP1. Moreover, both GIMs suppressed the liquid–liquid phase separation (LLPS) of G3BP1, suggesting that Caprin-1 likely facilitates SG formation via other mechanisms. Thus, we dissected various domains of Caprin-1 and investigated their role in LLPS in vitro and SG formation in cells. The C-terminal domain of Caprin-1 underwent spontaneous LLPS, whereas the N-terminal domain and GIM of Caprin-1 suppressed LLPS of G3BP1. The opposing effect of the N- and C-terminal domains of Caprin-1 on SG formation were demonstrated in cells with or without the endogenous Caprin-1. We propose that the N- and C-terminal domains of Caprin-1 regulate SG formation in a “yin and yang” fashion, mediating the dynamic and reversible assembly of SGs.
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23
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Jin G, Zhang Z, Wan J, Wu X, Liu X, Zhang W. G3BP2: Structure and Function. Pharmacol Res 2022; 186:106548. [DOI: 10.1016/j.phrs.2022.106548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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24
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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25
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Yusufujiang A, Zeng S, Yang C, Jing S, Yang L, Li H. PCBP-1 Regulates the Transcription and Alternative Splicing of Inflammation and Ubiquitination-Related Genes in PC12 Cell. Front Aging Neurosci 2022; 14:884837. [PMID: 35795237 PMCID: PMC9251440 DOI: 10.3389/fnagi.2022.884837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
PCBP-1, a multifunctional RNA binding protein, is expressed in various human cell/tissue types and involved in post-transcriptional gene regulation. PCBP-1 has important roles in cellular Iron homeostasis, mitochondrial stability, and other cellular activities involved in the pathophysiological process of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD). However, it remains enigmatic whether PCPB-1 is associated with the pathogenesis of PD. In this study, we cloned and constitutively overexpressed PCBP-1 in rat PC12 cells (PC12 cell is the common cell line studying neurodegenerative disease include PD). RNA-seq was performed to analyze PCBP-1-regulated differentially expressed genes (DEGs) and alternative splicing events (ASEs) between control and PCBP1-overexpressed cells. GO and KEGG pathway analyses were performed to identify functional DEGs and alternatively spliced genes. Consequently, we validated PCBP-1-regulated genes using RT-qPCR. Finally, we downloaded CLIP-seq data from GEO (GSE84700) to analyze the mechanisms of PCBP-1’s regulation of gene expression and ASEs by revealing the binding profile of PCBP-1 on its target pre-mRNAs. Overexpression of PCBP-1 partially regulated the ASE and expression of genes enriched in neuroinflammation and protein ubiquitination, which were also associated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expression of neuroinflammatory genes, like LCN-2, and alternative splicing (AS) of ubiquitination-related gene WWP-2. Finally, CLIP-seq data analysis indicated that the first UC motif was the critical site for PCBP-1 binding to its targets. In this study, we provided evidence that PCBP-1 could regulate the expression of LCN-2 gene expression associated with neuroinflammation and AS of WWP-2 in relation to protein ubiquitination. These findings thus provided novel insights into the potential application of PCBP-1 as the disease pathophysiological or therapeutic target for neurodegenerative disease.
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Affiliation(s)
- Aishanjiang Yusufujiang
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
| | - Shan Zeng
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
| | - Chen Yang
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
| | - Sha Jing
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
| | - Lijuan Yang
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
| | - Hongyan Li
- Department of Neurology, People’s Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Stroke and Neurological Rare Disease, Ürümqi, China
- *Correspondence: Hongyan Li,
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26
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Krause LJ, Herrera MG, Winklhofer KF. The Role of Ubiquitin in Regulating Stress Granule Dynamics. Front Physiol 2022; 13:910759. [PMID: 35694405 PMCID: PMC9174786 DOI: 10.3389/fphys.2022.910759] [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: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Stress granules (SGs) are dynamic, reversible biomolecular condensates, which assemble in the cytoplasm of eukaryotic cells under various stress conditions. Formation of SGs typically occurs upon stress-induced translational arrest and polysome disassembly. The increase in cytoplasmic mRNAs triggers the formation of a protein-RNA network that undergoes liquid-liquid phase separation when a critical interaction threshold has been reached. This adaptive stress response allows a transient shutdown of several cellular processes until the stress is removed. During the recovery from stress, SGs disassemble to re-establish cellular activities. Persistent stress and disease-related mutations in SG components favor the formation of aberrant SGs that are impaired in disassembly and prone to aggregation. Recently, posttranslational modifications of SG components have been identified as major regulators of SG dynamics. Here, we summarize new insights into the role of ubiquitination in affecting SG dynamics and clearance and discuss implications for neurodegenerative diseases linked to aberrant SG formation.
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Affiliation(s)
- Laura J. Krause
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Maria G. Herrera
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F. Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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27
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Jahan S, Ansari UA, Siddiqui AJ, Iqbal D, Khan J, Banawas S, Alshehri B, Alshahrani MM, Alsagaby SA, Redhu NS, Pant AB. Nobiletin Ameliorates Cellular Damage and Stress Response and Restores Neuronal Identity Altered by Sodium Arsenate Exposure in Human iPSCs-Derived hNPCs. Pharmaceuticals (Basel) 2022; 15:ph15050593. [PMID: 35631419 PMCID: PMC9147161 DOI: 10.3390/ph15050593] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 02/01/2023] Open
Abstract
Environmental exposure to arsenic has been profoundly associated with chronic systemic disorders, such as neurodegeneration, in both experimental models and clinical studies. The neuronal cells of the brain and the nervous system have a limited regeneration capacity, thus making them more vulnerable to exposure to xenobiotics, leading to long-lasting disabilities. The functional and anatomical complexity of these cells hinders the complete understanding of the mechanisms of neurodegeneration and neuroprotection. The present investigations aimed to evaluate the neuroprotective efficacy of a herbal formulation of Nobiletin (NOB) against the toxic insult induced by sodium arsenate (NA) in human neural progenitor cells (hNPCs) derived from human induced pluripotent stem cells (hiPSCs). Prior to the neuroprotective experiments, biologically safe doses of both NOB and NA were ascertained using standard endpoints of cytotoxicity. Thereafter, the hNPCs were exposed to either NOB (50 μM) or NA (50 μM) and co-exposed to biologically safe concentrations of NA (50 μM) with NOB (50 μM) for a period of up to 48 h. NOB treatment restored the morphological damage (neurite damage), the levels of stress granule G3BP1 (Ras-GTPase-activating protein (SH3 domain)-binding protein) and TIA1 (T cell-restricted intracellular antigen), and the expression of neuronal markers (Tuj1, Nestin, MAP2, and PAX6) when compared to NA-exposed cells. A substantial restoration of reactive oxygen species and mitochondrial membrane potential was also witnessed in the co-exposure group (NA + NOB) in comparison to the NA-exposed group. The findings suggest that NOB possesses a significant restorative/protective potential against the NA challenge in hNPCs under experimental conditions and imply that nobiletin may impart a potential therapeutic impact if studied adequately using in vivo studies.
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Affiliation(s)
- Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
- Correspondence: ; Tel.: +966-500590133
| | - Uzair Ahmad Ansari
- Developmental Toxicology Laboratory, Systems Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow 226001, Uttar Pradesh, India; (U.A.A.); (A.B.P.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Hail 55476, Saudi Arabia;
| | - Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran 61441, Saudi Arabia;
| | - Suliman A. Alsagaby
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia; (D.I.); (J.K.); (S.B.); (B.A.); (S.A.A.)
| | - Neeru Singh Redhu
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, Haryana, India;
| | - Aditya Bhushan Pant
- Developmental Toxicology Laboratory, Systems Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow 226001, Uttar Pradesh, India; (U.A.A.); (A.B.P.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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28
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Ge Y, Jin J, Li J, Ye M, Jin X. The roles of G3BP1 in human diseases (review). Gene X 2022; 821:146294. [PMID: 35176431 DOI: 10.1016/j.gene.2022.146294] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
Ras-GTPase-activating protein binding protein 1 (G3BP1) is a multifunctional binding protein involved in a variety of biological functions, including cell proliferation, metastasis, apoptosis, differentiation and RNA metabolism. It has been revealed that G3BP1, as an antiviral factor, can interact with viral proteins and regulate the assembly of stress granules (SGs), which can inhibit viral replication. Furthermore, several viruses have the ability to hijack G3BP1 as a cofactor, recruiting translation initiation factors to promote viral proliferation. However, many functions of G3BP1 are associated with other diseases. In various cancers, G3BP1 is a cancer-promoting factor, which can promote the proliferation, invasion and metastasis of cancer cells. Moreover, compared with normal tissues, G3BP1 expression is higher in tumor tissues, indicating that it can be used as an indicator for cancer diagnosis. In this review, the structure of G3BP1 and the regulation of G3BP1 in multiple dimensions are described. In addition, the effects and potential mechanisms of G3BP1 on various carcinomas, viral infections, nervous system diseases and cardiovascular diseases are elucidated, which may provide a direction for clinical applications of G3BP1 in the future.
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Affiliation(s)
- Yidong Ge
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jiabei Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jinyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
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29
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Wang J, Gan Y, Cao J, Dong X, Ouyang W. Pathophysiology of stress granules: An emerging link to diseases (Review). Int J Mol Med 2022; 49:44. [PMID: 35137915 PMCID: PMC8846937 DOI: 10.3892/ijmm.2022.5099] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/21/2022] [Indexed: 11/19/2022] Open
Abstract
Under unfavorable environmental conditions, eukaryotic cells may form stress granules (SGs) in the cytosol to protect against injury and promote cell survival. The initiation, mRNA and protein composition, distribution and degradation of SGs are subject to multiple intracellular post-translational modifications and signaling pathways to cope with stress damage. Despite accumulated comprehensive knowledge of their composition and dynamics, the function of SGs remains poorly understood. When the stress persists, aberrant and/or persistent intracellular SGs and aggregation of SGs-related proteins may lead to various diseases. In the present article, the research progress regarding the generation, modification and function of SGs was reviewed. The regulatory effects and influencing factors of SGs in the development of tumors, cardiovascular diseases, viral infections and neurodegenerative diseases were also summarized, which may provide novel insight for preventing and treating SG-related diseases.
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Affiliation(s)
- Jihui Wang
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Yixia Gan
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jian Cao
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Xuefen Dong
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Wei Ouyang
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
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30
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Ma Y, Wang X, Luo W, Xiao J, Song X, Wang Y, Shuai H, Ren Z, Wang Y. Roles of Emerging RNA-Binding Activity of cGAS in Innate Antiviral Response. Front Immunol 2021; 12:741599. [PMID: 34899698 PMCID: PMC8660693 DOI: 10.3389/fimmu.2021.741599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
cGAS, a DNA sensor in mammalian cells, catalyzes the generation of 2'-3'-cyclic AMP-GMP (cGAMP) once activated by the binding of free DNA. cGAMP can bind to STING, activating downstream TBK1-IRF-3 signaling to initiate the expression of type I interferons. Although cGAS has been considered a traditional DNA-binding protein, several lines of evidence suggest that cGAS is a potential RNA-binding protein (RBP), which is mainly supported by its interactions with RNAs, RBP partners, RNA/cGAS-phase-separations as well as its structural similarity with the dsRNA recognition receptor 2'-5' oligoadenylate synthase. Moreover, two influential studies reported that the cGAS-like receptors (cGLRs) of fly Drosophila melanogaster sense RNA and control 3'-2'-cGAMP signaling. In this review, we summarize and discuss in depth recent studies that identified or implied cGAS as an RBP. We also comprehensively summarized current experimental methods and computational tools that can identify or predict RNAs that bind to cGAS. Based on these discussions, we appeal that the RNA-binding activity of cGAS cannot be ignored in the cGAS-mediated innate antiviral response. It will be important to identify RNAs that can bind and regulate the activity of cGAS in cells with or without virus infection. Our review provides novel insight into the regulation of cGAS by its RNA-binding activity and extends beyond its DNA-binding activity. Our review would be significant for understanding the precise modulation of cGAS activity, providing the foundation for the future development of drugs against cGAS-triggering autoimmune diseases such as Aicardi-Gourtières syndrome.
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Affiliation(s)
- Yuying Ma
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Xiaohui Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Weisheng Luo
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Ji Xiao
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Xiaowei Song
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Hanlin Shuai
- Department of Obstetrics and Gynecology, The Fifth Affiliated Hospital of Jinan University, Heyuan, China
| | - Zhe Ren
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Yiliang Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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31
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Dubinski A, Vande Velde C. Altered stress granule disassembly: links to neurodegenerative disease? Trends Neurosci 2021; 44:765-766. [PMID: 34429216 DOI: 10.1016/j.tins.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/06/2021] [Indexed: 10/20/2022]
Abstract
A recent study by Gwon et al. identified context-specific ubiquitination of G3BP1 as critical for stress granule disassembly via VCP and the adaptor FAF2. This study provides new insights into stress granule dynamics, with potential implications for neurodegenerative disease.
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Affiliation(s)
- Alicia Dubinski
- Department of Neurosciences, Université de Montréal & Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal & Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.
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Sidibé H, Dubinski A, Vande Velde C. The multi-functional RNA-binding protein G3BP1 and its potential implication in neurodegenerative disease. J Neurochem 2021; 157:944-962. [PMID: 33349931 PMCID: PMC8248322 DOI: 10.1111/jnc.15280] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
Ras-GTPase-activating protein (GAP)-binding protein 1 (G3BP1) is a multi-functional protein that is best known for its role in the assembly and dynamics of stress granules. Recent studies have highlighted that G3BP1 also has other functions related to RNA metabolism. In the context of disease, G3BP1 has been therapeutically targeted in cancers because its over-expression is correlated with proliferation of cancerous cells and metastasis. However, evidence suggests that G3BP1 is essential for neuronal development and possibly neuronal maintenance. In this review, we will examine the many functions that are carried out by G3BP1 in the context of neurons and speculate how these functions are critical to the progression of neurodegenerative diseases. Additionally, we will highlight the similarities and differences between G3BP1 and the closely related protein G3BP2, which is frequently overlooked. Although G3BP1 and G3BP2 have both been deemed important for stress granule assembly, their roles may differ in other cellular pathways, some of which are specific to the CNS, and presents an opportunity for further exploration.
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Affiliation(s)
- Hadjara Sidibé
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Alicia Dubinski
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Christine Vande Velde
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
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