1
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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [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: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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2
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Statello L, Fernandez-Justel JM, González J, Montes M, Ranieri A, Goñi E, Mas AM, Huarte M. The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors. Nat Commun 2024; 15:978. [PMID: 38302450 PMCID: PMC10834948 DOI: 10.1038/s41467-024-45183-5] [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: 06/12/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Besides the well-characterized protein network involved in the replication stress response, several regulatory RNAs have been shown to play a role in this critical process. However, it has remained elusive whether they act locally at the stressed forks. Here, by investigating the RNAs localizing on chromatin upon replication stress induced by hydroxyurea, we identified a set of lncRNAs upregulated in S-phase and controlled by stress transcription factors. Among them, we demonstrate that the previously uncharacterized lncRNA lncREST (long non-coding RNA REplication STress) is transcriptionally controlled by p53 and localizes at stressed replication forks. LncREST-depleted cells experience sustained replication fork progression and accumulate un-signaled DNA damage. Under replication stress, lncREST interacts with the protein NCL and assists in engaging its interaction with RPA. The loss of lncREST is associated with a reduced NCL-RPA interaction and decreased RPA on chromatin, leading to defective replication stress signaling and accumulation of mitotic defects, resulting in apoptosis and a reduction in tumorigenic potential of cancer cells. These findings uncover the function of a lncRNA in favoring the recruitment of replication proteins to sites of DNA replication.
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Affiliation(s)
- Luisa Statello
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain.
| | - José Miguel Fernandez-Justel
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Marta Montes
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Alessia Ranieri
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Aina M Mas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 11 31008, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain.
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3
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Dzhumashev D, Anton-Joseph S, Morel VJ, Timpanaro A, Bordon G, Piccand C, Aleandri S, Luciani P, Rössler J, Bernasconi M. Rapid liposomal formulation for nucleolin targeting to rhabdomyosarcoma cells. Eur J Pharm Biopharm 2024; 194:49-61. [PMID: 38029941 DOI: 10.1016/j.ejpb.2023.11.020] [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: 08/31/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. More effective and less toxic therapies are urgently needed for high-risk patients. Peptide-guided targeted drug delivery can increase the therapeutic index of encapsulated drugs and improve patients' well-being. To apply this strategy to RMS, we identified the peptide F3 in a screening for peptides binding to RMS cells surface. F3 binds to nucleolin, which is present on the surface of RMS cells and is abundantly expressed at the mRNA level in RMS patients' biopsies compared to healthy tissues. We developed a rapid microfluidic formulation of F3-decorated PEGylated liposomes and remote loading of the chemotherapeutic drug vincristine. Size, surface charge, drug loading and retention of targeted and control liposomes were studied. Enhanced cellular binding and uptake were observed in three different nucleolin-positive RMS cell lines. Importantly, F3-functionalized liposomes loaded with vincristine were up to 11 times more cytotoxic than non-targeted liposomes for RMS cell lines. These results demonstrate that F3-functionalized liposomes are promising for targeted drug delivery to RMS and warrant further in vivo investigations.
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Affiliation(s)
- Dzhangar Dzhumashev
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Stenija Anton-Joseph
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Victoria J Morel
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Andrea Timpanaro
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gregor Bordon
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Caroline Piccand
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Simone Aleandri
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Paola Luciani
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Jochen Rössler
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Michele Bernasconi
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland; Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.
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4
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Peggion C, Massimino ML, Pereira D, Granuzzo S, Righetto F, Bortolotto R, Agostini J, Sartori G, Bertoli A, Lopreiato R. Structural Integrity of Nucleolin Is Required to Suppress TDP-43-Mediated Cytotoxicity in Yeast and Human Cell Models. Int J Mol Sci 2023; 24:17466. [PMID: 38139294 PMCID: PMC10744044 DOI: 10.3390/ijms242417466] [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: 10/03/2023] [Revised: 11/28/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Transactivating response (TAR) element DNA-binding of 43 kDa (TDP-43) is mainly implicated in the regulation of gene expression, playing multiple roles in RNA metabolism. Pathologically, it is implicated in amyotrophic lateral sclerosis and in a class of neurodegenerative diseases broadly going under the name of frontotemporal lobar degeneration (FTLD). A common hallmark of most forms of such diseases is the presence of TDP-43 insoluble inclusions in the cell cytosol. The molecular mechanisms of TDP-43-related cell toxicity are still unclear, and the contribution to cell damage from either loss of normal TDP-43 function or acquired toxic properties of protein aggregates is yet to be established. Here, we investigate the effects on cell viability of FTLD-related TDP-43 mutations in both yeast and mammalian cell models. Moreover, we focus on nucleolin (NCL) gene, recently identified as a genetic suppressor of TDP-43 toxicity, through a thorough structure/function characterization aimed at understanding the role of NCL domains in rescuing TDP-43-induced cytotoxicity. Using functional and biochemical assays, our data demonstrate that the N-terminus of NCL is necessary, but not sufficient, to exert its antagonizing effects on TDP-43, and further support the relevance of the DNA/RNA binding central region of the protein. Concurrently, data suggest the importance of the NCL nuclear localization for TDP-43 trafficking, possibly related to both TDP-43 physiology and toxicity.
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Affiliation(s)
- Caterina Peggion
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Daniel Pereira
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Sara Granuzzo
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Righetto
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Raissa Bortolotto
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Jessica Agostini
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Neuroscience Institute, Consiglio Nazionale Delle Ricerche, 35131 Padova, Italy
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
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5
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Kumar C, Mylavarapu SVS. Nucleolin is required for multiple centrosome-associated functions in early vertebrate mitosis. Chromosoma 2023; 132:305-315. [PMID: 37615728 DOI: 10.1007/s00412-023-00808-4] [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: 02/07/2023] [Revised: 06/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Nucleolin is a multifunctional RNA-binding protein that resides predominantly not only in the nucleolus, but also in multiple other subcellular pools in the cytoplasm in mammalian cells, and is best known for its roles in ribosome biogenesis, RNA stability, and translation. During early mitosis, nucleolin is required for equatorial mitotic chromosome alignment prior to metaphase. Using high resolution fluorescence imaging, we reveal that nucleolin is required for multiple centrosome-associated functions at the G2-prophase boundary. Nucleolin depletion led to dissociation of the centrosomes from the G2 nuclear envelope, a delay in the onset of nuclear envelope breakdown, reduced inter-centrosome separation, and longer metaphase spindles. Our results reveal novel roles for nucleolin in early mammalian mitosis, establishing multiple important functions for nucleolin during mammalian cell division.
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Affiliation(s)
- Chandan Kumar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, -121001, India
| | - Sivaram V S Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, -121001, India.
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6
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Abeesh P, Bouvet P, Guruvayoorappan C. AS1411 aptamer tagged PEGylated liposomes as a smart nanocarrier for tumor-specific delivery of Withaferin A for mitigating pulmonary metastasis. BIOMATERIALS ADVANCES 2023; 154:213661. [PMID: 37879185 DOI: 10.1016/j.bioadv.2023.213661] [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: 03/28/2023] [Revised: 08/17/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Metastasis is the most challenging health problem contributing to about 90 % of cancer-related deaths worldwide. Metastatic tumors are highly aggressive and resistant to the most available therapeutic options. Hence, innovative therapeutic approaches are required to target metastatic tumors selectively. In this study, we prepared AS1411 functionalized Withaferin A loaded PEGylated nanoliposomes (ALW) and investigated its therapeutic effect in B16F10 induced in pulmonary metastasis mice models. The prepared formulations' size and morphological properties were evaluated using dynamic light scattering system and Transmission electron microscope. ALW had spherical-shaped nanosized particles with a size of 118 nm and an encapsulation efficacy of 82.5 %. TEM analysis data indicated that ALW has excellent dispersibility and uniform spherical nano-size particles. ALW inhibited cell viability, and induced cell apoptosis of B16F10. In vivo, the pulmonary metastasis study in C57BL/6 mice revealed that the ALW significantly (p < 0.01) improved the encapsulated WA anti-metastatic activity and survival rate compared to WA or LW treated groups. ALW significantly (p < 0.01) downregulated the levels of IL-6, TNF-α, and IL-1β and significantly reduced the lung collagen hydroxyproline, hexosamine, and uronic acid content in metastatic tumor bearing animals compared to WA or LW. Gene expression levels of MMPs and NF-κB were downregulated in ALW treated metastatic pulmonary tumor-bearing mice. These findings demonstrate that the AS1411 functionalized Withaferin A loaded PEGylated nanoliposomes could be a promising nanoliposomal formulation for targeting metastatic tumors.
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Affiliation(s)
- Prathapan Abeesh
- Laboratory of Immunopharmacology and Experimental Therapeutics, Division of Cancer Research, Regional Cancer Centre, Medical College post, Thiruvananthapuram 695011, Kerala, India (Recognized Research Centre, University of Kerala)
| | - Phillipe Bouvet
- Centre de Recherche en Cancerologie de Lyon, Universite de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Leon Berard, CEDEX 08, F-69373 Lyon, France; Ecole Normale Superieur de Lyon, Universite de Lyon 1, F-69007 Lyon, France
| | - Chandrasekaran Guruvayoorappan
- Laboratory of Immunopharmacology and Experimental Therapeutics, Division of Cancer Research, Regional Cancer Centre, Medical College post, Thiruvananthapuram 695011, Kerala, India (Recognized Research Centre, University of Kerala).
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7
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Ruan P, Wang M, Cheng A, Zhao X, Yang Q, Wu Y, Zhang S, Tian B, Huang J, Ou X, Gao Q, Sun D, He Y, Wu Z, Zhu D, Jia R, Chen S, Liu M. Mechanism of herpesvirus UL24 protein regulating viral immune escape and virulence. Front Microbiol 2023; 14:1268429. [PMID: 37808279 PMCID: PMC10559885 DOI: 10.3389/fmicb.2023.1268429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Herpesviruses have evolved a series of abilities involved in the process of host infection that are conducive to virus survival and adaptation to the host, such as immune escape, latent infection, and induction of programmed cell death for sustainable infection. The herpesvirus gene UL24 encodes a highly conserved core protein that plays an important role in effective viral infection. The UL24 protein can inhibit the innate immune response of the host by acting on multiple immune signaling pathways during virus infection, and it also plays a key role in the proliferation and pathogenicity of the virus in the later stage of infection. This article reviews the mechanism by which the UL24 protein mediates herpesvirus immune escape and its effects on viral proliferation and virulence by influencing syncytial formation, DNA damage and the cell cycle. Reviewing these studies will enhance our understanding of the pathogenesis of herpesvirus infection and provide evidence for new strategies to combat against viral infection.
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Affiliation(s)
- Peilin Ruan
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu He
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhen Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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8
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Iannucci LF, D'Erchia AM, Picardi E, Bettio D, Conca F, Surdo NC, Di Benedetto G, Musso D, Arrigoni C, Lolicato M, Vismara M, Grisan F, Salviati L, Milanesi L, Pesole G, Lefkimmiatis K. Cyclic AMP induces reversible EPAC1 condensates that regulate histone transcription. Nat Commun 2023; 14:5521. [PMID: 37684224 PMCID: PMC10491619 DOI: 10.1038/s41467-023-41088-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The second messenger cyclic AMP regulates many nuclear processes including transcription, pre-mRNA splicing and mitosis. While most functions are attributed to protein kinase A, accumulating evidence suggests that not all nuclear cyclic AMP-dependent effects are mediated by this kinase, implying that other effectors may be involved. Here we explore the nuclear roles of Exchange Protein Activated by cyclic AMP 1. We find that it enters the nucleus where forms reversible biomolecular condensates in response to cyclic AMP. This phenomenon depends on intrinsically disordered regions present at its amino-terminus and is independent of protein kinase A. Finally, we demonstrate that nuclear Exchange Protein Activated by cyclic AMP 1 condensates assemble at genomic loci on chromosome 6 in the proximity of Histone Locus Bodies and promote the transcription of a histone gene cluster. Collectively, our data reveal an unexpected mechanism through which cyclic AMP contributes to nuclear spatial compartmentalization and promotes the transcription of specific genes.
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Affiliation(s)
- Liliana Felicia Iannucci
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | - Daniela Bettio
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Filippo Conca
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
| | - Nicoletta Concetta Surdo
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
- Institute of Neuroscience (IN-CNR), National Research Council of Italy, Padova, Italy
| | - Giulietta Di Benedetto
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
- Institute of Neuroscience (IN-CNR), National Research Council of Italy, Padova, Italy
| | - Deborah Musso
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Marco Lolicato
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Mauro Vismara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
| | | | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | - Konstantinos Lefkimmiatis
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy.
- Institute of Neuroscience (IN-CNR), National Research Council of Italy, Padova, Italy.
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9
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Nishino Y, Homma T, Ihara KI, Fujii J, Tachibana T, Yokoyama C. Generation of Rat Monoclonal Antibody for Human Nucleolin. Monoclon Antib Immunodiagn Immunother 2023; 42:145-149. [PMID: 37589992 DOI: 10.1089/mab.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Nucleolin (NCL) is a multifunctional phosphoprotein that is mainly localized in the nucleolus, but it is also found in the nucleoplasm, cytoplasm, and cell membrane. The principal functions of NCL involve DNA and RNA metabolism, gene transcription and translation, ribosome biogenesis, and mRNA stability. It was also reported that the localization of human NCL (hNCL) is related to tumor malignancy. Therefore, analyzing the cellular dynamics of NCL could be useful. In this article, we describe rat monoclonal antibody (mAb) 6F9A6 that was generated against a hNCL peptide. This mAb recognizes endogenous human, monkey, dog, and mouse NCL and was shown to be useful in immunofluorescence staining, immunoprecipitation, and immunoblotting experiments in several cancer cell lines. We anticipate that the mAb 6F9A6 will be useful for functional analyses of hNCL in cancer cells.
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Affiliation(s)
- Yuki Nishino
- Department of Chemistry and Bioengineering, Graduate School of Engineering; and Graduate School of Medicine; Osaka Metropolitan University, Osaka, Japan
| | - Takujiro Homma
- Department of Pharmacology, Graduate School of Medicine; Osaka Metropolitan University, Osaka, Japan
| | - Kan-Ichiro Ihara
- Department of Chemistry and Bioengineering, Graduate School of Engineering; and Graduate School of Medicine; Osaka Metropolitan University, Osaka, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Taro Tachibana
- Department of Chemistry and Bioengineering, Graduate School of Engineering; and Graduate School of Medicine; Osaka Metropolitan University, Osaka, Japan
| | - Chikako Yokoyama
- Department of Chemistry and Bioengineering, Graduate School of Engineering; and Graduate School of Medicine; Osaka Metropolitan University, Osaka, Japan
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10
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Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med 2023:10.1038/s12276-023-01038-5. [PMID: 37430089 PMCID: PMC10393972 DOI: 10.1038/s12276-023-01038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023] Open
Abstract
Transfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
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Affiliation(s)
- Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98115, USA
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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11
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Abeesh P, Guruvayoorappan C. Inhibition of tumor-specific angiogenesis by AS1411 aptamer functionalized Withaferin A loaded PEGylated nanoliposomes by targeting nucleolin. Biochem Biophys Res Commun 2023; 673:106-113. [PMID: 37379799 DOI: 10.1016/j.bbrc.2023.05.056] [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: 04/20/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023]
Abstract
Angiogenesis is a vital process for tumor growth and metastasis. Inhibition of angiogenesis is a promising strategy in cancer treatment. In this study, we analyzed the anti-angiogenic activity of AS1411 functionalized Withaferin A encapsulated PEGylated nanoliposomes (ALW) using both in vitro and in vivo models. AS1411 aptamer functionalized nanoliposomes are an efficient drug delivery system for carrying chemotherapeutic agents to target cancer cells, and Withaferin A (WA) is a steroidal lactone known for potent anti-angiogenic activity. ALW showed significant inhibition in the migration and tube formation of endothelial cells, which are critical events in angiogenesis. In vivo angiogenesis study using ALW showed remarkable inhibition of tumor-directed capillary formation by altered serum cytokines, VEGF, GM-CSF, and NO levels. ALW treatment downregulated the gene expression of Matrix metalloproteinase (MMP)-2, MMP-9, VEGF, NF-kB and upregulated the expression of tissue inhibitor of metalloproteinase (TIMP)-1. Our results demonstrate that ALW inhibits tumor-specific angiogenesis by gene expression of NF-κB, VEGF, MMP-2, and MMP-9. The present study shows that using ALW can offer an attractive strategy for inhibiting tumor angiogenesis.
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Affiliation(s)
- Prathapan Abeesh
- Laboratory of Immunopharmacology and Experimental Therapeutics, Division of Cancer Research, Regional Cancer Centre, Medical College Post, Thiruvananthapuram, Kerala, 695011, India; Research Centre, University of Kerala, India
| | - Chandrasekaran Guruvayoorappan
- Laboratory of Immunopharmacology and Experimental Therapeutics, Division of Cancer Research, Regional Cancer Centre, Medical College Post, Thiruvananthapuram, Kerala, 695011, India; Research Centre, University of Kerala, India.
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12
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Kiliszek A, Rypniewski W, Błaszczyk L. Exploring structural determinants and the role of nucleolin in formation of the long-range interactions between untranslated regions of p53 mRNA. RNA (NEW YORK, N.Y.) 2023; 29:630-643. [PMID: 36653114 PMCID: PMC10158990 DOI: 10.1261/rna.079378.122] [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: 07/24/2022] [Accepted: 01/02/2023] [Indexed: 05/06/2023]
Abstract
p53 protein is a key regulator of cellular homeostasis by coordinating the framework of antiproliferative pathways as a response to various stress factors. Although the main mechanism of stress-dependent induction of p53 protein relies on post-translational modifications influencing its stability and activity, a growing amount of evidence suggests that complex regulation of p53 expression occurs also at the mRNA level. This study explores structural determinants of long-range RNA-RNA interactions in p53 mRNA, crucial for stress-dependent regulation of p53 protein translation. We demonstrate that the 8-nt bulge motif plays a key structural role in base-pairing of complementary sequences from the 5' and 3' untranslated regions of p53 mRNA. We also show that one of the p53 translation regulators, nucleolin, displays an RNA chaperone activity and facilitates the association of sequences involved in the formation of long-range interactions in p53 mRNA. Nucleolin promotes base-pairing of complementary sequences through the bulge motif, because mutations of this region reduce or inhibit pairing while compensatory mutations restore this interaction. Mutational analysis of nucleolin reveals that all four RNA recognition motifs are indispensable for optimal RNA chaperone activity of nucleolin. These observations help to decipher the unique mechanism of p53 protein translation regulation pointing to bulge motif and nucleolin as the critical factors during intramolecular RNA-RNA recognition in p53 mRNA.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
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13
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Guo J, Peng Y. A tRF oligomerizes Nucleolin to stabilize metastasis-favoring transcripts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:646-648. [PMID: 36422759 DOI: 10.1007/s11427-022-2234-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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15
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Yokoyama C, Kobayashi S, Harada Y, Nishino Y, Fujii J, Tachibana T. Generation of Rat Monoclonal Antibody for Mouse Nucleolin by Immunization of Ferroptosis-Induced Hepa 1-6 Cells. Monoclon Antib Immunodiagn Immunother 2022; 41:255-259. [PMID: 36269321 DOI: 10.1089/mab.2022.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nucleolin is a multifunctional phosphoprotein that is ubiquitously distributed in the nucleus, nucleoplasm, cytoplasm, and cell membrane. The principal functions of nucleolin involve DNA and RNA metabolism, gene transcription and translation, ribosome biogenesis, and mRNA stability. Ferroptosis is a type of regulated cell death that is characterized by the iron-dependent accumulation of lipid peroxidation products. In a previous study, we produced monoclonal antibodies (mAbs) against lysates prepared from ferroptosis-induced Hepa 1-6 cells. In this study, we describe one of those rat mAbs, 4B5, which was generated against mouse nucleolin. This mAb was useful in immunofluorescence staining, immunoblotting, and immunoprecipitation experiments, and was confirmed to recognize endogenous nucleolin in mouse cell lines and tissues. We anticipate that mAb 4B5 will be useful for functional analyses of nucleolin.
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Affiliation(s)
- Chikako Yokoyama
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan.,Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Yumi Harada
- Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Yamagata, Japan
| | - Yuki Nishino
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan.,Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Taro Tachibana
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan.,Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
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16
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Liu X, Mei W, Padmanaban V, Alwaseem H, Molina H, Passarelli MC, Tavora B, Tavazoie SF. A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs. Mol Cell 2022; 82:2604-2617.e8. [PMID: 35654044 PMCID: PMC9444141 DOI: 10.1016/j.molcel.2022.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 04/04/2022] [Accepted: 05/05/2022] [Indexed: 01/09/2023]
Abstract
Stress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to humans; yet, its mechanistic underpinnings and pathological consequences remain poorly defined. Small RNA profiling revealed increased abundance of a cysteine tRNA fragment (5'-tRFCys) during breast cancer metastatic progression. 5'-tRFCys was required for efficient breast cancer metastatic lung colonization and cancer cell survival. We identified Nucleolin as the direct binding partner of 5'-tRFCys. 5'-tRFCys promoted the oligomerization of Nucleolin and its bound metabolic transcripts Mthfd1l and Pafah1b1 into a higher-order transcript stabilizing ribonucleoprotein complex, which protected these transcripts from exonucleolytic degradation. Consistent with this, Mthfd1l and Pafah1b1 mediated pro-metastatic and metabolic effects downstream of 5'-tRFCys-impacting folate, one-carbon, and phosphatidylcholine metabolism. Our findings reveal that a tRF can promote oligomerization of an RNA-binding protein into a transcript stabilizing ribonucleoprotein complex, thereby driving specific metabolic pathways underlying cancer progression.
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Affiliation(s)
- Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenbin Mei
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Veena Padmanaban
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Maria C Passarelli
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Bernardo Tavora
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA.
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17
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Yangngam S, Prasopsiri J, Hatthakarnkul P, Thongchot S, Thuwajit P, Yenchitsomanus PT, Edwards J, Thuwajit C. Cellular localization of nucleolin determines the prognosis in cancers: a meta-analysis. J Mol Med (Berl) 2022; 100:1145-1157. [PMID: 35861882 PMCID: PMC9329415 DOI: 10.1007/s00109-022-02228-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Nucleolin (NCL) is a multifunctional protein expressed in the nucleus, cytoplasm, and cell membrane. Overexpression of NCL has a controversial role as a poor prognostic marker in cancers. In this study, a meta-analysis was performed to evaluate the prognostic value of NCL in different subcellular localizations (cytoplasmic (CyNCL) and nuclear (NuNCL)) across a range of cancers. PubMed was searched for relevant publications. Data were extracted and analyzed from 12 studies involving 1221 patients with eight cancer types. The results revealed high total NCL was significantly associated with poor overall survival (OS) (HR = 2.85 (1.94, 4.91), p < 0.00001, I2 = 59%) and short disease-free survival (DFS) (HR = 3.57 (2.76, 4.62), p < 0.00001, I2 = 2%). High CyNCL was significantly associated with poor OS (HR = 4.32 (3.01, 6.19), p < 0.00001, I2 = 0%) and short DFS (HR = 3.00 (2.17, 4.15), p < 0.00001, I2 = 0%). In contrast, high NuNCL correlated with increased patient OS (HR = 0.42 (0.20, 0.86), p = 0.02, I2 = 66%), with no significant correlation to DFS observed (HR = 0.46 (0.19, 1.14), p = 0.09, I2 = 57%). This study supports the role of subcellular NCL as a poor prognostic cancer biomarker.
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Affiliation(s)
- Supaporn Yangngam
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Phimmada Hatthakarnkul
- Biomedical Sciences Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, G61 1QH, UK
| | - Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, G61 1QH, UK
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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18
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Wan N, Wang N, Yu S, Zhang H, Tang S, Wang D, Lu W, Li H, Delafield DG, Kong Y, Wang X, Shao C, Lv L, Wang G, Tan R, Wang N, Hao H, Ye H. Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome. Nat Methods 2022; 19:854-864. [PMID: 35761067 DOI: 10.1038/s41592-022-01523-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/13/2022] [Indexed: 12/18/2022]
Abstract
Lactylation was initially discovered on human histones. Given its nascence, its occurrence on nonhistone proteins and downstream functional consequences remain elusive. Here we report a cyclic immonium ion of lactyllysine formed during tandem mass spectrometry that enables confident protein lactylation assignment. We validated the sensitivity and specificity of this ion for lactylation through affinity-enriched lactylproteome analysis and large-scale informatic assessment of nonlactylated spectral libraries. With this diagnostic ion-based strategy, we confidently determined new lactylation, unveiling a wide landscape beyond histones from not only the enriched lactylproteome but also existing unenriched human proteome resources. Specifically, by mining the public human Meltome Atlas, we found that lactylation is common on glycolytic enzymes and conserved on ALDOA. We also discovered prevalent lactylation on DHRS7 in the draft of the human tissue proteome. We partially demonstrated the functional importance of lactylation: site-specific engineering of lactylation into ALDOA caused enzyme inhibition, suggesting a lactylation-dependent feedback loop in glycolysis.
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Affiliation(s)
- Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Nian Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Siqin Yu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Shuo Tang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dexiang Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Wenjie Lu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Huanhuan Li
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Kong
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xinmiao Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Langlang Lv
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Renxiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nanxi Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. .,School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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19
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Fabre L, Rousset C, Monier K, Da Cruz-Boisson F, Bouvet P, Charreyre MT, Delair T, Fleury E, Favier A. Fluorescent Polymer-AS1411-Aptamer Probe for dSTORM Super-Resolution Imaging of Endogenous Nucleolin. Biomacromolecules 2022; 23:2302-2314. [PMID: 35549176 DOI: 10.1021/acs.biomac.1c01706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleolin is a multifunctional protein involved in essential biological processes. To precisely localize it and unravel its different roles in cells, fluorescence imaging is a powerful tool, especially super-resolution techniques. Here, we developed polymer-aptamer probes, both small and bright, adapted to direct stochastic optical reconstruction microscopy (dSTORM). Well-defined fluorescent polymer chains bearing fluorophores (AlexaFluor647) and a reactive end group were prepared via RAFT polymerization. The reactive end-group was then used for the oriented conjugation with AS1411, a DNA aptamer that recognizes nucleolin with high affinity. Conjugation via strain-promoted alkyne/azide click chemistry (SPAAC) between dibenzylcyclooctyne-ended fluorescent polymer chains and 3'-azido-functionalized nucleic acids proved to be the most efficient approach. In vitro and in cellulo evaluations demonstrated that selective recognition for nucleolin was retained. Their brightness and small size make these polymer-aptamer probes an appealing alternative to immunofluorescence, especially for super-resolution (10-20 nm) nanoscopy. dSTORM imaging demonstrated the ability of our fluorescent polymer-aptamer probe to provide selective and super-resolved detection of cell surface nucleolin.
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Affiliation(s)
- Laura Fabre
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
| | - Corentin Rousset
- Univ Lyon, Centre Léon Bérard, UMR INSERM 1052 CNRS 5286, Centre de recherche en cancérologie de Lyon, Lyon F-69008, France
| | - Karine Monier
- Univ Lyon, Centre Léon Bérard, UMR INSERM 1052 CNRS 5286, Centre de recherche en cancérologie de Lyon, Lyon F-69008, France
| | - Fernande Da Cruz-Boisson
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
| | - Philippe Bouvet
- Univ Lyon, Centre Léon Bérard, UMR INSERM 1052 CNRS 5286, Centre de recherche en cancérologie de Lyon, Lyon F-69008, France
| | - Marie-Thérèse Charreyre
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
| | - Thierry Delair
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
| | - Etienne Fleury
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
| | - Arnaud Favier
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Université Claude Bernard Lyon 1, INSA Lyon, F-69622 Villeurbanne Cédex, France
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20
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Barzilova VD, Drury J, Rogers B, Thomas E, Ahmed F, Bradfield A, Al-Lamee H, Hapangama DK. Role of Nucleolin in Endometrial Precancerous Hyperplasia and Carcinogenesis: Ex Vivo and In Silico Study. Int J Mol Sci 2022; 23:6228. [PMID: 35682908 PMCID: PMC9181237 DOI: 10.3390/ijms23116228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 12/04/2022] Open
Abstract
Endometrial cancer (EC) is the most common gynaecological malignancy. Nucleolin (NCL) is involved in rDNA transcription, cell proliferation, and apoptosis, with high expression associated with worse overall survival (OS) in other adenocarcinomas. Our aims were to assess NCL gene and protein expression and explore the differential expression of NCL-associated genes (NAGs) in endometrial carcinogenesis. Endometrial samples were obtained from 157 women to include healthy, hyperplastic (EH), EC, and metastatic groups. RT-qPCR and immunohistochemistry were employed to assess NCL gene and protein levels. In silico analysis of NAGs in TCGA and GEO datasets was performed, with the prognostic value determined via Human Protein Atlas. NCL mRNA level of EC was lower than in healthy post-menopausal endometrium (p < 0.01). EH samples had lower NCL immuno-expression scores than healthy pre-menopausal (p < 0.001), benign post-menopausal (p < 0.01), and EC (p < 0.0001) samples. Metastatic lesions demonstrated higher NCL quick scores than primary tissue (p = 0.04). Higher NCL Immuno quick scores carried a worse OS in high-grade EC (p = 0.01). Interrogating Uterine Corpus Endometrial Carcinoma (TCGA-UCEC) and Uterine Carcinosarcoma (TCGA-UCS) cohorts revealed NCL to be the most highly upregulated gene in carcinosarcoma, with S100A11, LMNB2, RERG, E2F1 and CCNA2 representing key dysregulated NAGs in EC. Since NCL is implicated in transforming hyperplastic glands into cancer, with further involvement in metastasis, it is suggested to be a promising target for better-informed diagnosis, risk stratification, and management of EC.
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Affiliation(s)
- Vanya D. Barzilova
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
| | - Josephine Drury
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
| | - Bryony Rogers
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
| | - Emily Thomas
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
| | - Fareen Ahmed
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
| | - Alice Bradfield
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
| | - Hannan Al-Lamee
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Hewitt Centre for Reproductive Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK
| | - Dharani K. Hapangama
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7SS, UK; (V.D.B.); (J.D.); (B.R.); (E.T.); (F.A.); (H.A.-L.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
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21
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Feng M, Swevers L, Sun J. Hemocyte Clusters Defined by scRNA-Seq in Bombyx mori: In Silico Analysis of Predicted Marker Genes and Implications for Potential Functional Roles. Front Immunol 2022; 13:852702. [PMID: 35281044 PMCID: PMC8914287 DOI: 10.3389/fimmu.2022.852702] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
Within the hemolymph, insect hemocytes constitute a heterogeneous population of macrophage-like cells that play important roles in innate immunity, homeostasis and development. Classification of hemocytes in different subtypes by size, morphology and biochemical or immunological markers has been difficult and only in Drosophila extensive genetic analysis allowed the construction of a coherent picture of hemocyte differentiation from pro-hemocytes to granulocytes, crystal cells and plasmatocytes. However, the advent of high-throughput single cell technologies, such as single cell RNA sequencing (scRNA-seq), is bound to have a high impact on the study of hemocytes subtypes and their phenotypes in other insects for which a sophisticated genetic toolbox is not available. Instead of averaging gene expression across all cells as occurs in bulk-RNA-seq, scRNA-seq allows high-throughput and specific visualization of the differentiation status of individual cells. With scRNA-seq, interesting cell types can be identified in heterogeneous populations and direct analysis of rare cell types is possible. Next to its ability to profile the transcriptomes of individual cells in tissue samples, scRNA-seq can be used to propose marker genes that are characteristic of different hemocyte subtypes and predict their functions. In this perspective, the identities of the different marker genes that were identified by scRNA-seq analysis to define 13 distinct cell clusters of hemocytes in larvae of the silkworm, Bombyx mori, are discussed in detail. The analysis confirms the broad division of hemocytes in granulocytes, plasmatocytes, oenocytoids and perhaps spherulocytes but also reveals considerable complexity at the molecular level and highly specialized functions. In addition, predicted hemocyte marker genes in Bombyx generally show only limited convergence with the genes that are considered characteristic for hemocyte subtypes in Drosophila.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research "Demokritos", Aghia Paraskevi, Athens, Greece
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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22
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Tonello F, Massimino ML, Peggion C. Nucleolin: a cell portal for viruses, bacteria, and toxins. Cell Mol Life Sci 2022; 79:271. [PMID: 35503380 PMCID: PMC9064852 DOI: 10.1007/s00018-022-04300-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/18/2022]
Abstract
The main localization of nucleolin is the nucleolus, but this protein is present in multiple subcellular sites, and it is unconventionally secreted. On the cell surface, nucleolin acts as a receptor for various viruses, some bacteria, and some toxins. Aim of this review is to discuss the characteristics that make nucleolin able to act as receptor or co-receptor of so many and different pathogens. The important features that emerge are its multivalence, and its role as a bridge between the cell surface and the nucleus. Multiple domains, short linear motifs and post-translational modifications confer and modulate nucleolin ability to interact with nucleic acids, with proteins, but also with carbohydrates and lipids. This modular multivalence allows nucleolin to participate in different types of biomolecular condensates and to move to various subcellular locations, where it can act as a kind of molecular glue. It moves from the nucleus to the cell surface and can accompany particles in the reverse direction, from the cell surface into the nucleus, which is the destination of several pathogens to manipulate the cell in their favour.
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Affiliation(s)
- Fiorella Tonello
- CNR of Italy, Neuroscience Institute, viale G. Colombo 3, 35131, Padua, Italy.
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi, 58/B, 35131, Padua, Italy
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23
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Song J, Quan R, Wang D, Liu J. Seneca Valley Virus 3C pro Mediates Cleavage and Redistribution of Nucleolin To Facilitate Viral Replication. Microbiol Spectr 2022; 10:e0030422. [PMID: 35357201 PMCID: PMC9045095 DOI: 10.1128/spectrum.00304-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 11/21/2022] Open
Abstract
Seneca Valley virus (SVV) is a recently discovered pathogen that poses a significant threat to the global pig industry. It has been shown that many viruses are reliant on nucleocytoplasmic trafficking of nucleolin (NCL) for their own replication. Here, we demonstrate that NCL, a critical protein component of the nucleolus, is cleaved and translocated out of the nucleoli following SVV infection. Furthermore, our data suggest that SVV 3C protease (3Cpro) is responsible for this cleavage and subsequent delocalization from the nucleoli, and that inactivation of this protease activity abolished this cleavage and translocation. SVV 3Cpro cleaved NCL at residue Q545, and the cleavage fragment (aa 1 to 545) facilitated viral replication, which was similar to the activities described for full-length NCL. Small interfering RNA-mediated knockdown indicated that NCL is required for efficient viral replication and viral protein expression. In contrast, lentivirus-mediated overexpression of NCL significantly enhanced viral replication. Taken together, these results indicate that SVV 3Cpro targets NCL for its cleavage and redistribution, which contributes to efficient viral replication, thereby emphasizing the potential target of antiviral strategies for the control of SVV infection. IMPORTANCE The nucleolus is a subnuclear cellular compartment, and nucleolin (NCL) resides predominantly in the nucleolus. NCL participates in viral replication, translation, internalization, and also serves as a receptor for virus entry. The interaction between NCL and SVV is still unknown. Here, we demonstrate that SVV 3Cpro targets NCL for its cleavage and nucleocytoplasmic transportation, which contributes to efficient viral replication. Our results reveal novel function of SVV 3Cpro and provide further insight into the mechanisms by which SVV utilizes nucleoli for efficient replication.
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Affiliation(s)
- Jiangwei Song
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Rong Quan
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dan Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
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24
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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25
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Lopes R, Shi K, Fonseca NA, Gama A, Ramalho JS, Almeida L, Moura V, Simões S, Tidor B, Moreira JN. Modelling the impact of nucleolin expression level on the activity of F3 peptide-targeted pH-sensitive pegylated liposomes containing doxorubicin. Drug Deliv Transl Res 2022; 12:629-646. [PMID: 33860446 DOI: 10.1007/s13346-021-00972-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 01/06/2023]
Abstract
Strategies targeting nucleolin have enabled a significant improvement in intracellular bioavailability of their encapsulated payloads. In this respect, assessment of the impact of target cell heterogeneity and nucleolin homology across species (structurally and functionally) is of major importance. This work also aimed at mathematically modelling the nucleolin expression levels at the cell membrane, binding and internalization of pH-sensitive pegylated liposomes encapsulating doxorubicin and functionalized with the nucleolin-binding F3 peptide (PEGASEMP), and resulting cytotoxicity against cancer cells from mouse, rat, canine, and human origin. Herein, it was shown that nucleolin expression levels were not a limitation on the continuous internalization of F3 peptide-targeted liposomes, despite the saturable nature of the binding mechanism. Modeling enabled the prediction of nucleolin-mediated total doxorubicin exposure provided by the experimental settings of the assessment of PEGASEMP's impact on cell death. The former increased proportionally with nucleolin-binding sites, a measure relevant for patient stratification. This pattern of variation was observed for the resulting cell death in nonsaturating conditions, depending on the cancer cell sensitivity to doxorubicin. This approach differs from standard determination of cytotoxic concentrations, which normally report values of incubation doses rather than the actual intracellular bioactive drug exposure. Importantly, in the context of development of nucleolin-based targeted drug delivery, the structural nucleolin homology (higher than 84%) and functional similarity across species presented herein, emphasized the potential to use toxicological data and other metrics from lower species to infer the dose for a first-in-human trial.
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Affiliation(s)
- Rui Lopes
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Kevin Shi
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nuno A Fonseca
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD), Quinta de Prados, Apartado 1013, 5000-801, Vila Real, Portugal
| | - José S Ramalho
- Laboratory of Cellular and Molecular Biology, NOVA Medical School, New University of Lisbon, Campo Mártires da Pátria, 130, 1169-056, Lisboa, Portugal
| | - Luís Almeida
- Blueclinical, Ltd, 4460-439, Senhora da Hora, Matosinhos, Portugal
| | - Vera Moura
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Sérgio Simões
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
| | - Bruce Tidor
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - João N Moreira
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
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26
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Zhu J, Miao Q, Guo H, Tang A, Dong D, Tang J, Wang F, Tong G, Liu G. Nucleolin interacts with the rabbit hemorrhagic disease virus replicase RdRp, nonstructural proteins p16 and p23, playing a role in virus replication. Virol Sin 2022; 37:48-59. [PMID: 35234629 PMCID: PMC8922422 DOI: 10.1016/j.virs.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022] Open
Abstract
Rabbit hemorrhagic disease virus (RHDV) is a member of the Caliciviridae family and cannot be propagated in vitro, which has impeded the progress of investigating its replication mechanism. Construction of an RHDV replicon system has recently provided a platform for exploring RHDV replication in host cells. Here, aided by this replicon system and using two-step affinity purification, we purified the RHDV replicase and identified its associated host factors. We identified rabbit nucleolin (NCL) as a physical link, which mediating the interaction between other RNA-dependent RNA polymerase (RdRp)-related host proteins and the viral replicase RdRp. We found that the overexpression or knockdown of NCL significantly increased or severely impaired RHDV replication in RK-13 cells, respectively. NCL was identified to directly interact with RHDV RdRp, p16, and p23. Furthermore, NCL knockdown severely impaired the binding of RdRp to RdRp-related host factors. Collectively, these results indicate that the host protein NCL is essential for RHDV replication and acts as a physical link between viral replicase and host proteins.
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Affiliation(s)
- Jie Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Qiuhong Miao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Laboratory of Virology, Wageningen University and Research, Wageningen, 6708 PB, the Netherlands
| | - Hongyuan Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Aoxing Tang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Dandan Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jingyu Tang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Fang Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Guangqing Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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27
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Targeted liposomal doxorubicin/ceramides combinations: the importance to assess the nature of drug interaction beyond bulk tumor cells. Eur J Pharm Biopharm 2022; 172:61-77. [PMID: 35104605 DOI: 10.1016/j.ejpb.2022.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
One of the major assets of anticancer nanomedicine is the ability to co-deliver drug combinations, as it enables targeting of different cellular populations and/or signaling pathways implicated in tumorigenesis and thus tackling tumor heterogeneity. Moreover, drug resistance can be circumvented, for example, upon co-encapsulation and delivery of doxorubicin and sphingolipids, as ceramides. Herein, the impact of short (C6) and long (C18) alkyl chain length ceramides on the nature of drug interaction, within the scope of combination with doxorubicin, was performed in bulk triple-negative breast cancer (TNBC) cells, as well as on the density of putative cancer stem cells and phenotype, including live single-cell tracking. C6- or C18-ceramide enabled a synergistic drug interaction in all conditions and (bulk) cell lines tested. However, differentiation among these two ceramides was reflected on the migratory potential of cancer cells, particularly significant against the highly motile MDA-MB-231 cells. This effect was supported by the downregulation of the PI3K/Akt pathway enabled by C6-ceramide and in contrast with C18-ceramide. The decrease of the migratory potential enabled by the targeted liposomal combinations is of high relevance in the context of TNBC, due to the underlying metastatic potential. Surprisingly, the nature of the drug interaction assessed at the level of bulk cancer cells revealed to be insufficient to predict whether a drug combination enables a decrease in the percentage of the master regulators of tumor relapse as ALDH+/high putative TNBC cancer stem cells, suggesting, for the first time, that it should be extended further down to this level.
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28
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Yu Y, Wang X, Jia X, Feng Z, Zhang L, Li H, He J, Shen G, Ding X. Aptamer Probes Labeled with Lanthanide-Doped Carbon Nanodots Permit Dual-Modal Fluorescence and Mass Cytometric Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102812. [PMID: 34719883 PMCID: PMC8693039 DOI: 10.1002/advs.202102812] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/07/2021] [Indexed: 05/11/2023]
Abstract
High-dimensional imaging mass cytometry (IMC) enables simultaneous quantification of over 35 biomarkers on one tissue section. However, its limited resolution and ultralow acquisition speed remain major issues for general clinical application. Meanwhile, conventional immunofluorescence microscopy (IFM) allows sub-micrometer resolution and rapid identification of the region of interest (ROI), but only operates with low multiplicity. Herein, a series of lanthanide-doped blue-, green-, and red-fluorescent carbon nanodots (namely, B-Cdots(Ln1 ), G-Cdots(Ln2 ), and R-Cdots(Ln3 )) as fluorescence and mass dual-modal tags are developed. Coupled with aptamers, B-Cdots(159 Tb)-A10-3.2, G-Cdots(165 Ho)-AS1411, and R-Cdots(169 Tm)-SYL3C dual-functional aptamer probes, which are then multiplexed with commercially available Maxpar metal-tagged antibodies for analyzing clinical formalin-fixed, paraffin-embedded (FFPE) prostatic adenocarcinoma (PaC) tissue, are further synthesized. The rapid identification of ROI with IFM using fluorescence signals and subsequent multiplexed detection of in situ ROI with IMC using the same tissue section is demonstrated. Dual-modal probes save up to 90% IMC blind scanning time for a standard 3.5 mm × 3.5 mm overall image. Meanwhile, the IFM provides refined details and topological spatial distributions for the functional proteins at optical resolution, which compensates for the low resolution of the IMC imaging.
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Affiliation(s)
- Youyi Yu
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xin Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xiaolong Jia
- Department of UrologyNingbo First HospitalNingbo Hospital of Zhejiang UniversityNingboZhejiang Province315700China
| | - Zijian Feng
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lulu Zhang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Hongxia Li
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jie He
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Guangxia Shen
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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29
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Gabanella F, Barbato C, Fiore M, Petrella C, de Vincentiis M, Greco A, Minni A, Corbi N, Passananti C, Di Certo MG. Fine-Tuning of mTOR mRNA and Nucleolin Complexes by SMN. Cells 2021; 10:3015. [PMID: 34831238 PMCID: PMC8616268 DOI: 10.3390/cells10113015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence points to the Survival Motor Neuron (SMN) protein as a key determinant of translation pathway. Besides its role in RNA processing and sorting, several works support a critical implication of SMN in ribosome biogenesis. We previously showed that SMN binds ribosomal proteins (RPs) as well as their encoding transcripts, ensuring an appropriate level of locally synthesized RPs. SMN impacts the translation machinery in both neural and non-neural cells, in agreement with the concept that SMN is an essential protein in all cell types. Here, we further assessed the relationship between SMN and translation-related factors in immortalized human fibroblasts. We focused on SMN-nucleolin interaction, keeping in mind that nucleolin is an RNA-binding protein, highly abundant within the nucleolus, that exhibits a central role in ribosomes production. Nucleolin may also affects translation network by binding the mammalian target of rapamycin (mTOR) mRNA and promoting its local synthesis. In this regard, for the first time we provided evidence that SMN protein itself associates with mTOR transcript. Collectively, we found that: (1) SMN coexists with nucleolin-mTOR mRNA complexes at subcellular level; (2) SMN deficiency impairs nucleolar compartmentalization of nucleolin, and (3) this event correlates with the nuclear retention of mTOR mRNA. These findings suggest that SMN may regulate not only structural components of translation machinery, but also their upstream regulating factors.
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Affiliation(s)
- Francesca Gabanella
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Christian Barbato
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Marco Fiore
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Carla Petrella
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Marco de Vincentiis
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Antonio Greco
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Antonio Minni
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Nicoletta Corbi
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Claudio Passananti
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Maria Grazia Di Certo
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
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Manzano A, Pereda-Loth V, de Bures A, Sáez-Vásquez J, Herranz R, Medina FJ. Light signals counteract alterations caused by simulated microgravity in proliferating plant cells. AMERICAN JOURNAL OF BOTANY 2021; 108:1775-1792. [PMID: 34524692 DOI: 10.1002/ajb2.1728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Light and gravity are fundamental cues for plant development. Our understanding of the effects of light stimuli on plants in space, without gravity, is key to providing conditions for plants to acclimate to the environment. Here we tested the hypothesis that the alterations caused by the absence of gravity in root meristematic cells can be counteracted by light. METHODS Seedlings of wild-type Arabidopsis thaliana and two mutants of the essential nucleolar protein nucleolin (nuc1, nuc2) were grown in simulated microgravity, either under a white light photoperiod or under continuous darkness. Key variables of cell proliferation (cell cycle regulation), cell growth (ribosome biogenesis), and auxin transport were measured in the root meristem using in situ cellular markers and transcriptomic methods and compared with those of a 1 g control. RESULTS The incorporation of a photoperiod regime was sufficient to attenuate or suppress the effects caused by gravitational stress at the cellular level in the root meristem. In all cases, values for variables recorded from samples receiving light stimuli in simulated microgravity were closer to values from the controls than values from samples grown in darkness. Differential sensitivities were obtained for the two nucleolin mutants. CONCLUSIONS Light signals may totally or partially replace gravity signals, significantly improving plant growth and development in microgravity. Despite that, molecular alterations are still compatible with the expected acclimation mechanisms, which need to be better understood. The differential sensitivity of nuc1 and nuc2 mutants to gravitational stress points to new strategies to produce more resilient plants to travel with humans in new extraterrestrial endeavors.
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Affiliation(s)
- Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | | | - Anne de Bures
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, 66860, France
- Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, 66860, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, 66860, France
- Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, 66860, France
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - F Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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31
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Li Y, Wang WX. Integrated transcriptomics and proteomics revealed the distinct toxicological effects of multi-metal contamination on oysters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117533. [PMID: 34261227 DOI: 10.1016/j.envpol.2021.117533] [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: 04/22/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
The Pearl River Estuary (PRE) is the largest estuary in southern China and under high metal stress. In the present study, we employed an integrated method of transcriptomics and proteomics to investigate the ecotoxicological effects of trace metals on the Hong Kong oyster Crassostrea hongkongensis. Three oyster populations with distinct spatial distributions of metals were sampled, including the Control (Station QA, the lowest metal levels), the High Cd (Station JZ, the highest Cd), and the High Zn-Cu-Cr-Ni (Station LFS, with the highest levels of zinc, copper, chromium, and nickel). Dominant metals in oysters were differentiated by principal component analysis (PCA), and theirgene and protein profiles were studied using RNA-seq and iTRAQ techniques. Of the 2250 proteins identified at both protein and RNA levels, 70 proteins exhibited differential expressions in response to metal stress in oysters from the two contaminated stations. There were 8 proteins altered at both stations, with the potential effects on mitochondria and endoplasmic reticulum by Ag. The genotoxicity, including impaired DNA replication and transcription, was specifically observed in the High Cd oysters with the dominating influence of Cd. The structural components (cytoskeleton and chromosome-associated proteins) were impaired by the over-accumulated Cu, Zn, Cr, and Ni at Station LFS. However, enhanced tRNA biogenesis and exosome activity might help the oysters to alleviate the toxicities resulting from their exposure to these metals. Our study provided comprehensive information on the molecular changes in oysters at both protein and RNA levels in responding to multi-levels of trace metal stress.
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Affiliation(s)
- Yunlong Li
- Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China; School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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32
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Zhang W, Zhou R, Yang Y, Peng S, Xiao D, Kong T, Cai X, Zhu B. Aptamer-mediated synthesis of multifunctional nano-hydroxyapatite for active tumour bioimaging and treatment. Cell Prolif 2021; 54:e13105. [PMID: 34382270 PMCID: PMC8450118 DOI: 10.1111/cpr.13105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The nano-hydroxyapatite (nHAp) is widely used to develop imaging probes and drug carriers due to its excellent bioactivity and biocompatibility. However, traditional methods usually need cumbersome and stringent conditions such as high temperature and post-modification to prepare the functionalized nHAp, which do not benefit the particles to enter cells due to the increased particle size. Herein, a biomimetic synthesis strategy was explored to achieve the AS1411-targeted tumour dual-model bioimaging using DNA aptamer AS1411 as a template. Then, the imaging properties and the biocompatibility of the synthesized AS-nFAp:Gd/Tb were further investigated. MATERIALS AND METHODS The AS-nFAp:Gd/Tb was prepared under mild conditions through a one-pot procedure with AS1411 as a template. Besides, the anticancer drug DOX was loaded to AS-nFAp:Gd/Tb so as to achieve the establishment of a multifunctional nano-probe that integrated the tumour diagnosis and treatment. The AS-nFAp:Gd/Tb was characterized by transmission electron microscopy (TEM), energy disperse X-ray Spectroscopy (EDS) mapping, X-ray photoelectron spectroscopy (XPS) spectrum, X-ray diffraction (XRD), fourier-transformed infrared (FTIR) spectroscopy, capillary electrophoresis analyses, zeta potential and particle sizes. The in vitro magnetic resonance imaging (MRI) and fluorescence imaging were performed on an MRI system and a confocal laser scanning microscope, respectively. The potential of the prepared multifunctional nHAp for a targeted tumour therapy was investigated by a CCK-8 kit. And the animal experiments were conducted on the basis of the guidelines approved by the Animal Care and Use Committee of Sichuan University, China. RESULTS In the presence of AS1411, the as-prepared AS-nFAp:Gd/Tb presented a needle-like morphology with good monodispersity and improved imaging performance. Furthermore, due to the specific binding between AS1411 and nucleolin up-expressed in cancer cells, the AS-nFAp:Gd/Tb possessed excellent AS1411-targeted fluorescence and MRI imaging properties. Moreover, after loading chemotherapy drug DOX, in vitro and in vivo studies showed that DOX@AS-nFAp:Gd/Tb could effectively deliver DOX to tumour tissues and exert a highly effective tumour inhibition without systemic toxicity compared with pure DOX. CONCLUSIONS The results indicated that the prepared multifunctional nHAp synthesized by a novel biomimetic strategy had outstanding capabilities of recognition and treatment for the tumour and had good biocompatibility; hence, it might have a potential clinical application in the future.
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Affiliation(s)
- Wenqing Zhang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ronghui Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuting Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shuanglin Peng
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Southwest Medical University, Luzhou, China
| | - Dexuan Xiao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tingting Kong
- Department of Stomatology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bofeng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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33
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Sun Z, Yu H, Zhao J, Tan T, Pan H, Zhu Y, Chen L, Zhang C, Zhang L, Lei A, Xu Y, Bi X, Huang X, Gao B, Wang L, Correia C, Chen M, Sun Q, Feng Y, Shen L, Wu H, Wang J, Shen X, Daley GQ, Li H, Zhang J. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein Cell 2021; 13:490-512. [PMID: 34331666 PMCID: PMC9226220 DOI: 10.1007/s13238-021-00864-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/15/2021] [Indexed: 01/21/2023] Open
Abstract
LIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs, and few have addressed LIN28's role within the nucleus. Here, we show that LIN28 displays dynamic temporal and spatial expression during murine embryo development. Maternal LIN28 expression drops upon exit from the 2-cell stage, and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blastocyst stage development, to become dominantly expressed in the cytosol after implantation. In cultured pluripotent stem cells (PSCs), loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus genes. Mechanistically, LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity, and its loss leads to nucleolar phase separation defects, ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor Dux. LIN28 also resides in a complex containing the nucleolar factor Nucleolin (NCL) and the transcriptional repressor TRIM28, and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci, and thus de-repressed Dux and reduced rRNA expression. Lin28 knockout cells with nucleolar stress are more likely to assume a slowly cycling, translationally inert and anabolically inactive state, which is a part of previously unappreciated 2C-like transcriptional program. These findings elucidate novel roles for nucleolar LIN28 in PSCs, and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.
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Affiliation(s)
- Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Tianyu Tan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Li Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Anhua Lei
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xianju Bi
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100085, China
| | - Xin Huang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bo Gao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Cristina Correia
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiming Sun
- Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu Feng
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li Shen
- Institute of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100085, China
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, 310058, China.
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Rovira-Clavé X, Jiang S, Bai Y, Zhu B, Barlow G, Bhate S, Coskun AF, Han G, Ho CMK, Hitzman C, Chen SY, Bava FA, Nolan GP. Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging. Nat Commun 2021; 12:4628. [PMID: 34330905 PMCID: PMC8324837 DOI: 10.1038/s41467-021-24822-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses. Multiplexed ion beam imaging can provide subcellular localisation information but with limited resolution. Here the authors report an ion beam imaging method with nanoscale resolution which they use to assess the subcellular distribution of cisplatin.
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Affiliation(s)
- Xavier Rovira-Clavé
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sizun Jiang
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham Barlow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Salil Bhate
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ahmet F Coskun
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Guojun Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Chin-Min Kimmy Ho
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chuck Hitzman
- Stanford Nano Shared Facility, Stanford University, Stanford, CA, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Felice-Alessio Bava
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. .,Department of Pathology, Stanford University, Stanford, CA, USA.
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35
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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far. Noncoding RNA 2021; 7:ncrna7030042. [PMID: 34287370 PMCID: PMC8293466 DOI: 10.3390/ncrna7030042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 12/26/2022] Open
Abstract
Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.
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36
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Figueiredo J, Miranda A, Lopes-Nunes J, Carvalho J, Alexandre D, Valente S, Mergny JL, Cruz C. Targeting nucleolin by RNA G-quadruplex-forming motif. Biochem Pharmacol 2021; 189:114418. [PMID: 33460627 DOI: 10.1016/j.bcp.2021.114418] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/27/2022]
Abstract
A high level of nucleolin (NCL) expression is often associated with a poor prognosis of patients with lung cancer (LC), suggesting that NCL can be used as a possible biomarker. NCL has been shown to display a marked preference for the binding to G-quadruplexes (G4). Here, we investigate the formation of an RNA quadruplex structure in a sequence found in the human precursor pre-MIR150 with the potential to recognize NCL. Circular dichroism (CD) spectra of pre-MIR150 G4-forming sequence (designated by rG4) indicate the formation of a parallel quadruplex structure in KCl or when complexed with the well-known G4 ligand PhenDC3. The thermal stability of rG4 is very high, and further increases in the presence of PhenDC3. The binding affinities of rG4 to PhenDC3 and NCL RBD1,2 are similar with KD values in the nanomolar range. PAGE results suggest the formation of a ternary quadruplex-ligand-protein complex (rG4-PhenDC3-NCL RBD1,2), indicative that PhenDC3 does not prevent the binding of rG4 to NCL RBD1,2. Finally, rG4 can recognize NCL-positive cells and, when fluorescently labeled, can be used as a probe for this protein. ELISA experiments indicate altered NCL expression patterns in liquid biopsies of LC patients in a non-invasive manner, potentially helping the diagnosis, prognosis, and patient response to treatment. Hence, labeled rG4 could be used as a detection probe of LC in liquid biopsies.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Jéssica Lopes-Nunes
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Daniela Alexandre
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Salete Valente
- Serviço de Pneumologia do Centro Hospitalar Universitário Cova da Beira (CHUCB), Covilhã, Portugal
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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Santos T, Miranda A, Campello MPC, Paulo A, Salgado G, Cabrita EJ, Cruz C. Recognition of nucleolin through interaction with RNA G-quadruplex. Biochem Pharmacol 2021; 189:114208. [PMID: 32860827 DOI: 10.1016/j.bcp.2020.114208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The development of novel biomarkers for early-stage diagnosis of prostate cancer (PCa) has attracted the attention of researchers in the last decade. Nucleolin (NCL) has emerged as a possible biomarker of PCa due to its high expression levels in the surface of PCa cells and affinity towards parallel G4s since it contains four RNA-binding domains (RBDs). Herein, we developed a novel strategy based on a microfluidic platform for the detection of NCL in biological samples, such as human plasma. The RNA G4 (rG4) sequence found in human precursor microRNA 92b (pre-miR-92b) was used as a molecular recognition probe since it forms a single dominant parallel rG4 conformation in the presence of 0.1 mM K+ as confirmed by NMR spectroscopy. The additional stability of the rG4 structure was provided by the acridine orange derivative ligand C8, which stabilizes the pre-miR-92b rG4 structure, as denoted by an increase in more than 30 °C of its melting temperature. FRET-melting assay revealed a remarkable synergistic effect of NCL RBD1,2 and C8 on the stabilization of the pre-miR-92b rG4. The binding of pre-miR-92b to NCL RBD1,2 was determined by in silico studies, which revealed a binding pocket formed by a 12-residue linker between RBD1 and RBD2. Both, pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex demonstrated high affinity towards NCL RBD1,2, as proved by fluorimetric titrations (KD range between 10-12 and 10-9 M). The stability and nuclease resistance of pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex were evaluated as molecular recognition probes to capture and detect NCL. Finally, the microfluidic platform detects NCL in complex biological samples, such as human plasma. Overall, this work demonstrates the usefulness of the microfluidic platform based on the pre-miR-92b to detect NCL and the possibility to be used as a valuable biomedical tool in PCa diagnosis.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Maria P C Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - Gilmar Salgado
- Univ. Bordeaux, ARNA Laboratory, INSERM, U1212, CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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Wu S, Teo BHD, Wee SYK, Chen J, Lu J. The GAR/RGG motif defines a family of nuclear alarmins. Cell Death Dis 2021; 12:477. [PMID: 33980825 PMCID: PMC8116331 DOI: 10.1038/s41419-021-03766-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 02/03/2023]
Abstract
The nucleus is the target of autoantibodies in many diseases, which suggests intrinsic nuclear adjuvants that confer its high autoimmunogenicity. Nucleolin (NCL) is one abundant nucleolar autoantigen in systemic lupus erythematosus (SLE) patients and, in lupus-prone mice, it elicits autoantibodies early. With purified NCL, we observed that it was a potent alarmin that activated monocytes, macrophages and dendritic cells and it was a ligand for TLR2 and TLR4. NCL released by necrotic cells also exhibited alarmin activity. The NCL alarmin activity resides in its glycine/arginine-rich (GAR/RGG) motif and can be displayed by synthetic GAR/RGG peptides. Two more GAR/RGG-containing nucleolar proteins, fibrillarin (FBRL) and GAR1, were also confirmed to be novel alarmins. Therefore, the GAR/RGG alarmin motif predicts a family of nucleolar alarmins. The apparent prevalence of nucleolar alarmins suggests their positive contribution to tissue homeostasis by inducing self-limiting tissue inflammation with autoimmunity only occurring when surveillance is broken down.
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Affiliation(s)
- Shan Wu
- grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore, 117545 Singapore ,grid.4280.e0000 0001 2180 6431Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Boon Heng Dennis Teo
- grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore, 117545 Singapore ,grid.4280.e0000 0001 2180 6431Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Seng Yin Kelly Wee
- grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore, 117545 Singapore ,grid.4280.e0000 0001 2180 6431Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Junjie Chen
- grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore, 117545 Singapore ,grid.4280.e0000 0001 2180 6431Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Jinhua Lu
- grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore, 117545 Singapore ,grid.4280.e0000 0001 2180 6431Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
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Miranda A, Santos T, Carvalho J, Alexandre D, Jardim A, Caneira CF, Vaz V, Pereira B, Godinho R, Brito D, Chu V, Conde JP, Cruz C. Aptamer-based approaches to detect nucleolin in prostate cancer. Talanta 2021; 226:122037. [PMID: 33676639 DOI: 10.1016/j.talanta.2020.122037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
We have investigated the expression of nucleolin (NCL) in liquid biopsies of prostate cancer (PCa) patients and healthy controls to determine its correlation with tumor prognosis. To detect NCL we used a modified AS1411 aptamer designated by AS1411-N5. In presence of NCL, AS1411-N5 increases the fluorescence by assuming a G-quadruplex (G4) structure, while in the absence of NCL the fluorescence signal remains quenched. The structural characterization of AS1411-N5 was performed by biophysical studies, which demonstrated the formation of G4 parallel conformation in the presence of 100 mM K+ and the ability to recognize NCL with high affinity (KD = 138.1 ± 5.5 nM). Furthermore, the clinical relevance of NCL in PCa liquid biopsies was assessed by using an NCL-based ELISA assay. The protein was measured in the peripheral blood mononuclear cells (PBMCs) cell lysate of 158 individuals, including PCa patients and healthy individuals. The results depicted a remarkable increase of NCL levels in the PBMC's lysate of PCa patients (mean of 626.1 pg/mL whole blood) when compared to healthy individuals (mean of 198.5 pg/mL whole blood). The ELISA results also provided evidence for the usefulness of determining NCL levels in advanced PCa stages. Furthermore, a microfluidic assay showed the ability of AS1411-N5 in recognizing NCL in spiked human plasma samples.
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Affiliation(s)
- André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Daniela Alexandre
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Andreia Jardim
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal; Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - CatarinaR F Caneira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Vírgilio Vaz
- Serviço de Urologia do Centro Hospitalar Universitário Cova da Beira (CHUCB), Covilhã, Portugal
| | - Bruno Pereira
- Faculdade de Ciências da Saúde, Universidade da Beira Interior (FCS-UBI), Covilhã, Portugal; Instituto Português de Oncologia (IPO), Coimbra, Portugal
| | | | - Duarte Brito
- Instituto Português de Oncologia (IPO), Coimbra, Portugal
| | - Virgínia Chu
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - João P Conde
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Blood 2021; 137:190-202. [PMID: 32756943 DOI: 10.1182/blood.2020005219] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Nascent hematopoietic stem and progenitor cells (HSPCs) acquire definitive hematopoietic characteristics only when they develop into fetal HSPCs; however, the mechanisms underlying fetal HSPC development are poorly understood. Here, we profiled the chromatin accessibility and transcriptional features of zebrafish nascent and fetal HSPCs using ATAC-seq and RNA-seq and revealed dynamic changes during HSPC transition. Functional assays demonstrated that chromatin remodeler-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Systematical screening of chromatin remodeler-related genes identified that smarca5 is responsible for the maintenance of chromatin accessibility at promoters of hematopoiesis-related genes in fetal HSPCs. Mechanistically, Smarca5 interacts with nucleolin to promote chromatin remodeling, thereby facilitating genomic binding of transcription factors to regulate expression of hematopoietic regulators such as bcl11ab. Our results unravel a new role of epigenetic regulation and reveal that Smarca5-mediated epigenetic programming is responsible for fetal HSPC development, which will provide new insights into the generation of functional HSPCs both in vivo and in vitro.
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Li X, Li J, Xu J, Chen K, Zhang Z, Duan J, Luo Q, Du Y, Chen S, Xie Y, Lu W. Nanostructure of Functional Larotaxel Liposomes Decorated with Guanine-Rich Quadruplex Nucleotide-Lipid Derivative for Treatment of Resistant Breast Cancer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007391. [PMID: 33522108 DOI: 10.1002/smll.202007391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Breast cancer is the most common malignant disease in women all over the world and its chemotherapy outcome is restricted by multidrug resistance. Here, a nanostructure by functional larotaxel liposomes decorated with guanine-rich quadruplex nucleotide-lipid derivative for treatment of resistant breast cancer is developed. The studies are performed on the resistant breast cancer cells and the cancer-bearing mice. The nucleotide-lipid derivative (DSPE-PEG2000 -C6 -GT28nt) is synthesized by introducing a hydrophobic hexyl linkage between GT-28nt (containing 17 guanines and 11 thymidines) and DSPE-PEG2000 -NHS, and is incorporated on the functional larotaxel liposomes for specific binding with nucleolin receptor on the resistant cancer cells. The studies demonstrate that the liposomes had long circulatory effect, targeted capability, and significant anticancer efficacy in resistant cancer-bearing mice. The studies further reveal their action mechanism, consisting of blocking depolymerization of microtubules, arresting cell cycle, blocking JAK-STAT signaling pathway, and inhibiting activity of antiapoptotic proteins. In conclusion, the functional larotaxel liposomes can be used for effective treatment of drug-resistant breast cancer, and this study also offers a novel targeted nanomedicine based on nucleotide-lipid derivative.
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Affiliation(s)
- Xueqi Li
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jianwei Li
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100875, China
| | - Jiarui Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Kun Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhan Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jialun Duan
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Qian Luo
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yafei Du
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Songyue Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Ying Xie
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Wanliang Lu
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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Shafiei F, Saberi RS, Mehrgardi MA. A label-free electrochemical aptasensor for breast cancer cell detection based on a reduced graphene oxide-chitosan-gold nanoparticle composite. Bioelectrochemistry 2021; 140:107807. [PMID: 33845441 DOI: 10.1016/j.bioelechem.2021.107807] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/18/2021] [Accepted: 03/21/2021] [Indexed: 12/11/2022]
Abstract
Regarding the cancer fatal consequences, early detection and progression monitoring are the most vital issues in patients' treatment and mortality reduction. Therefore, there is a great demand for fast, inexpensive, and selective detection methods. Herein, a graphene-based aptasensor was designed for sensitive human breast cancer cell detection. A reduced graphene oxide-chitosan-gold nanoparticles composite was used as a biocompatible substrate for the receptor stabilization. The significant function of the aptamer on this composite is due to the synergistic effects of the components in improving the properties of the composite, including increasing the electrical conductivity and effective surface area. After the aptasensor incubation in MCF-7 cancer cells, the cell membrane proteins interacted specifically with the three dimensional-structure of the AS1411 aptamer, resulting in the cell capture on the aptasensor. The aptasensor fabrication steps were investigated by cyclic voltammetry and electrochemical impedance spectroscopy. The higher cell concentrations concluded to the higher captured cells on the aptasensor which blocked the Ferro/Ferricyanide access to the sensor, causing increases in the charge transfer resistances. This aptasensor shows a linear relationship with the cell concentration logarithm, high selectivity, a wide linear range of 1 × 101-1 × 106 cells/mL, and a low detection limit of 4 cells/mL.
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Affiliation(s)
- Fatemeh Shafiei
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | | | - Masoud A Mehrgardi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
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43
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Copp W, Pontarelli A, Wilds CJ. Recent Advances of DNA Tetrahedra for Therapeutic Delivery and Biosensing. Chembiochem 2021; 22:2237-2246. [PMID: 33506614 DOI: 10.1002/cbic.202000835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/16/2021] [Indexed: 11/11/2022]
Abstract
The chemical and self-assembly properties of nucleic acids make them ideal for the construction of discrete structures and stimuli-responsive devices for a diverse array of applications. Amongst the various three-dimensional assemblies, DNA tetrahedra are of particular interest, as these structures have been shown to be readily taken up by the cell, by the process of caveolin-mediated endocytosis, without the need for transfection agents. Moreover, these structures can be readily modified with a diverse range of pendant groups to confer greater functionality. This minireview highlights recent advances related to applications of this interesting DNA structure including the delivery of therapeutic agents ranging from small molecules to oligonucleotides in addition to its use for sensing and imaging various species within the cell.
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Affiliation(s)
- William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
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Cruz C, Pedro AQ, Carvalho J, Santos T, Talhada D, Paiva A, Queiroz JA, Andrade M, Pinto M, Montenegro L, Delgado L, Pereira P. Nucleolin as a potential biomarker for canine malignant neoplasia. Res Vet Sci 2021; 135:297-303. [PMID: 33077166 DOI: 10.1016/j.rvsc.2020.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 01/03/2023]
Abstract
Human nucleolin (NCL) is a multifunctional protein that is involved in diverse pathological processes. Recent evidences have shown that NCL is markedly overexpressed on the surface of most human cancer cells when compared to normal cells, being overexpressed in several malignant cells. Based on the exposed, the purpose of this pilot study is to investigate the expression pattern of NCL in canine malignant neoplasia and control groups. NCL expression at both messenger RNA and protein levels in the subcellular fractions were respectively detected by RT-PCR and western blotting, allowing to infer the NCL positivity rate in canine neoplasia. The identity of NCL amplicons obtained by RT-PCR was confirmed by Sanger sequencing and found to correspond to Canis lupus familiaris. Using flow cytometry, the blood cells expressing NCL from canine neoplasms were also identified using several cell surface markers and their levels quantified. These results showed that NCL expressed in lymphocytes, monocytes and neutrophils in dogs with malignant neoplasia is higher (> 50%) when compared with the control group. We found an increased expression of surface and cytoplasmic NCL in canine malignant neoplasia group, while nuclear NCL is predominantly found in the control group. Overall, this study discloses and identifies for the first time the presence of NCL in canine blood.
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Affiliation(s)
- Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - Augusto Q Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Daniela Talhada
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Artur Paiva
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Portugal; Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Instituto Politécnico de Coimbra, ESTESC-Coimbra Health School, Ciências Biomédicas Laboratoriais, Portugal
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | | | | | | | - Leonor Delgado
- Pathology Department, INNO Serviços Especializados em Veterinária, Braga, Portugal; Cancer Research Group, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS), Instituto Universitário de Ciências da Saúde (IUCS), CESPU, Gandra, Portugal
| | - Patrícia Pereira
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
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Liu J, Li C, Xue H, Li L, Liu Q, Wang H, Wen T, Qian H. Cancer metastasis-associated protein 1 localizes to the nucleolus and regulates pre-rRNA synthesis in cancer cells. J Cell Biochem 2021; 122:180-188. [PMID: 32786109 DOI: 10.1002/jcb.29837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 04/07/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Abstract
Metastasis-associated protein 1 (MTA1) is a critical component of the nucleosome remodeling and histone deacetylase (NuRD) complex. MTA1 has several biological functions, and it is closely associated with the malignant properties of human cancers; however, the mechanisms and subcellular localization of MTA1 in cells remain unclear. Some initial studies indicated that MTA1 was absent from the nucleolus; however, several NuRD components were recently found to be present in the nucleolus, where they regulate preribosomal RNA (pre-rRNA) transcription. In this study, we demonstrated that MTA1 is definitely localized to the nucleolus and regulates pre-rRNA transcription, which is consistent with the recent reports on NuRD. To determine if MTA1 was present in the nucleolus, we utilized the following complementary molecular approaches: immunofluorescence, GFP-tag tracking, immunoelectron microscopy, and immunoprecipitation (IP). To examine the role of MTA1 in rRNA synthesis, we performed quantitative polymerase chain reaction analysis. We revealed that both endogenous and exogenous MTA1 showed apparent granule-like nucleolar subcellular localization. MTA1 interacts with two major resident nucleolar proteins, nucleolin and nucleophosmin. Immunofluorescent colocalization analyses showed that MTA1 localizes to the fibrillarin-deficient regions of the nucleolus, and Co-IP experiments indicated that there was no interaction between MTA1 and fibrillarin; further, fibrillarin was not identified in the MTA1 interactome. Loss- and gain-of-function studies indicated that MTA1 promotes pre-rRNA transcription in cancer cells. Collectively, our data identify MTA1 as a novel nucleolar protein, and activation of pre-rRNA transcription in cancer cells may be an alternative mechanism by which MTA1 promotes malignancies.
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Affiliation(s)
- Jian Liu
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongsheng Xue
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Lina Li
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Qun Liu
- Department of Gynaecology and Obstetrics, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tao Wen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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46
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Liu Y, Yang Y, Zhang Q, Lu D, Li S, Li J, Yang G, Shan Y. Dynamics of delivering aptamer targeted nano-drugs into cells. J Mater Chem B 2021; 9:952-957. [PMID: 33437980 DOI: 10.1039/d0tb02527e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A targeted nano-drug delivery system has provided great potential and benefits to the diagnosis and therapy of cancers. Cell entry is a critical step for taking effect of the targeted nano-drug. In this report, the dynamics of delivering a single aptamer targeted polyamindoamine-camptothecin-AS1411 (PAMAM-CPT-AS1411) nano-drug into cells was investigated using a force tracing technique based on atomic force microscopy. The results show that the specific interaction of AS1411 and nucleolin, which is overexpressed on cancer cells, enhances the efficiency of the PAMAM-CPT-AS1411 cell entry. Moreover, the specific interaction induced receptor-mediated endocytosis prolongs the duration and decreases the speed of a single PAMAM-CPT-AS1411 cell entry, which is helpful to understand the targeted nano-drugs prolonging the therapeutic drug level. However, the required force for PAMAM-CPT-AS1411 cell entry is not changed. This report will provide a novel and potential method for achieving the precise dynamics of targeted nano-drug delivery.
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Affiliation(s)
- Yulin Liu
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
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47
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Venom peptides in cancer therapy: An updated review on cellular and molecular aspects. Pharmacol Res 2020; 164:105327. [PMID: 33276098 DOI: 10.1016/j.phrs.2020.105327] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023]
Abstract
Based on the high incidence and mortality rates of cancer, its therapy remains one of the most vital challenges in the field of medicine. Consequently, enhancing the efficacy of currently applied treatments and finding novel strategies are of great importance for cancer treatment. Venoms are important sources of a variety of bioactive compounds including salts, small molecules, macromolecules, proteins, and peptides that are defined as toxins. They can exhibit different pharmacological effects, and in recent years, their anti-tumor activities have gained significant attention. Several different compounds are responsible for the anti-tumor activity of venoms, and peptides are one of them. In the present review, we discuss the possible anti-tumor activities of venom peptides by highlighting molecular pathways and mechanisms through which these molecules can act effectively. Venom peptides can induce cell death in cancer cells and can substantially enhance the efficacy of chemotherapy and radiotherapy. Also, the venom peptides can mitigate the migration of cancer cells via suppression of angiogenesis and epithelial-to-mesenchymal transition. Notably, nanoparticles have been applied in enhancing the bioavailability of venom peptides and providing targeted delivery, thereby leading to their elevated anti-tumor activity and potential application for cancer therapy.
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48
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Manzano A, Villacampa A, Sáez-Vásquez J, Kiss JZ, Medina FJ, Herranz R. The Importance of Earth Reference Controls in Spaceflight -Omics Research: Characterization of Nucleolin Mutants from the Seedling Growth Experiments. iScience 2020; 23:101686. [PMID: 33163940 PMCID: PMC7607443 DOI: 10.1016/j.isci.2020.101686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/04/2020] [Accepted: 10/10/2020] [Indexed: 01/23/2023] Open
Abstract
Understanding plant adaptive responses to the space environment is a requisite for enabling space farming. Spaceflight produces deleterious effects on plant cells, particularly affecting ribosome biogenesis, a complex stress-sensitive process coordinated with cell division and differentiation, known to be activated by red light. Here, in a series of ground studies, we have used mutants from the two Arabidopsis nucleolin genes (NUC1 and NUC2, nucleolar regulators of ribosome biogenesis) to better understand their role in adaptive response mechanisms to stress on Earth. Thus, we show that nucleolin stress-related gene NUC2 can compensate for the environmental stress provided by darkness in nuc1 plants, whereas nuc2 plants are not able to provide a complete response to red light. These ground control findings, as part of the ESA/NASA Seedling Growth spaceflight experiments, will determine the basis for the identification of genetic backgrounds enabling an adaptive advantage for plants in future space experiments.
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Affiliation(s)
- Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Univ. Perpignan Via Domitia, LGDP, UMR 5096, 66860 Perpignan, France
| | - John Z. Kiss
- Department of Biology, University of North Carolina-Greensboro, Greensboro, NC 27402, USA
| | - F. Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
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49
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Nait Slimane S, Marcel V, Fenouil T, Catez F, Saurin JC, Bouvet P, Diaz JJ, Mertani HC. Ribosome Biogenesis Alterations in Colorectal Cancer. Cells 2020; 9:E2361. [PMID: 33120992 PMCID: PMC7693311 DOI: 10.3390/cells9112361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
Many studies have focused on understanding the regulation and functions of aberrant protein synthesis in colorectal cancer (CRC), leaving the ribosome, its main effector, relatively underappreciated in CRC. The production of functional ribosomes is initiated in the nucleolus, requires coordinated ribosomal RNA (rRNA) processing and ribosomal protein (RP) assembly, and is frequently hyperactivated to support the needs in protein synthesis essential to withstand unremitting cancer cell growth. This elevated ribosome production in cancer cells includes a strong alteration of ribosome biogenesis homeostasis that represents one of the hallmarks of cancer cells. None of the ribosome production steps escape this cancer-specific dysregulation. This review summarizes the early and late steps of ribosome biogenesis dysregulations described in CRC cell lines, intestinal organoids, CRC stem cells and mouse models, and their possible clinical implications. We highlight how this cancer-related ribosome biogenesis, both at quantitative and qualitative levels, can lead to the synthesis of ribosomes favoring the translation of mRNAs encoding hyperproliferative and survival factors. We also discuss whether cancer-related ribosome biogenesis is a mere consequence of cancer progression or is a causal factor in CRC, and how altered ribosome biogenesis pathways can represent effective targets to kill CRC cells. The association between exacerbated CRC cell growth and alteration of specific steps of ribosome biogenesis is highlighted as a key driver of tumorigenesis, providing promising perspectives for the implementation of predictive biomarkers and the development of new therapeutic drugs.
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Affiliation(s)
- Sophie Nait Slimane
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Virginie Marcel
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Tanguy Fenouil
- Institute of Pathology EST, Hospices Civils de Lyon, Site-Est Groupement Hospitalier- Est, 69677 Bron, France;
| | - Frédéric Catez
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Christophe Saurin
- Gastroenterology and Genetic Department, Edouard Herriot Hospital, Hospices Civils de Lyon, 69008 Lyon, France;
| | - Philippe Bouvet
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Hichem C. Mertani
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
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50
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Pavlova II, Tsvetkov VB, Isaakova EA, Severov VV, Khomyakova EA, Lacis IA, Lazarev VN, Lagarkova MA, Pozmogova GE, Varizhuk AM. Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures. Int J Biol Macromol 2020; 160:1144-1157. [PMID: 32454109 DOI: 10.1016/j.ijbiomac.2020.05.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Affinity for G-quadruplex (G4) structures may be a common feature of transcription-facilitating histone chaperons (HCs). This assumption is based on previous unmatched studies of HCs FACT, nucleolin (NCL), BRD3, and ATRX. We verified this assumption and considered its implications for the therapeutic applications of synthetic (exogenous) G4s and the biological significance of genomic G4s. First, we questioned whether exogenous G4s that recognize cell-surface NCL and could trap other HCs in the nucleus are usable as anticancer agents. We performed in vitro binding assays and selected leading multi-targeted G4s. They exhibited minor effects on cell viability. The presumed NCL-regulated intracellular transport of G4s was inefficient or insufficient for tumor-specific G4 delivery. Next, to clarify whether G4s in the human genome could recruit HCs, we compared available HC ChIP-seq data with G4-seq/G4-ChIP-seq data. Several G4s, including the well-known c-Myc quadruplex structure, were found to be colocalized with HC occupancy sites in cancer cell lines. As evidenced by our molecular modeling data, c-Myc G4 might interfere with the HC function of BRD3 but is unlikely to prevent the BRD3-driven assembly of the chromatin remodeling complex. The c-Myc case illustrates the intricate role of genomic G4s in chromatin remodeling, nucleosome remodeling, and transcription.
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Affiliation(s)
- Iulia I Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow 119146, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow 119991, Russia
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vyacheslav V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ekaterina A Khomyakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ivan A Lacis
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia; Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991, Russia.
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