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Thongchot S, Aksonnam K, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Nucleolin‑based targeting strategies in cancer treatment: Focus on cancer immunotherapy (Review). Int J Mol Med 2023; 52:81. [PMID: 37477132 PMCID: PMC10555485 DOI: 10.3892/ijmm.2023.5284] [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: 03/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The benefits of treating several types of cancers using immunotherapy have recently been established. The overexpression of nucleolin (NCL) in a number of types of cancer provides an attractive antigen target for the development of novel anticancer immunotherapeutic treatments. NCL is a multifunctional protein abundantly distributed in the nucleus, cytoplasm and cell membrane. It influences carcinogenesis, and the proliferation, survival and metastasis of cancer cells, leading to cancer progression. Additionally, the meta‑analysis of total and cytoplasmic NCL overexpression indicates a poor prognosis of patients with breast cancer. The AS1411 aptamers currently appear to have therapeutic action in the phase II clinical trial. The authors' research group has recently explored the anticancer function of NCL through the activation of T cells by dendritic cell‑based immunotherapy. The present review describes and discusses the mechanisms through which the multiple functions of NCL can participate in the progression of cancer. In addition, the studies that define the utility of NCL‑dependent anticancer therapies are summarized, with specific focus being paid to cancer immunotherapeutic approaches.
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Affiliation(s)
- Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Krittaya Aksonnam
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
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Structural Characteristics of the 5′-Terminal Region of Mouse p53 mRNA and Identification of Proteins That Bind to This mRNA Region. Int J Mol Sci 2022; 23:ijms23179709. [PMID: 36077109 PMCID: PMC9456389 DOI: 10.3390/ijms23179709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/15/2022] Open
Abstract
A mouse model has often been used in studies of p53 gene expression. Detailed interpretation of functional studies is, however, hampered by insufficient knowledge of the impact of mouse p53 mRNA’s structure and its interactions with proteins in the translation process. In particular, the 5′-terminal region of mouse p53 mRNA is an important region which takes part in the regulation of the synthesis of p53 protein and its N-truncated isoform Δ41p53. In this work, the spatial folding of the 5′-terminal region of mouse p53 mRNA and its selected sub-fragments was proposed based on the results of the SAXS method and the RNAComposer program. Subsequently, RNA-assisted affinity chromatography was used to identify proteins present in mouse fibroblast cell lysates that are able to bind the RNA oligomer, which corresponds to the 5′-terminal region of mouse p53 mRNA. Possible sites to which the selected, identified proteins can bind were proposed. Interestingly, most of these binding sites coincide with the sites determined as accessible to hybridization of complementary oligonucleotides. Finally, the high binding affinity of hnRNP K and PCBP2 to the 5′-terminal region of mouse p53 mRNA was confirmed and their possible binding sites were proposed.
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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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Dash S, Trainor PA. Nucleolin loss of function leads to aberrant Fibroblast Growth Factor signaling and craniofacial anomalies. Development 2022; 149:dev200349. [PMID: 35762670 PMCID: PMC9270975 DOI: 10.1242/dev.200349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/25/2022] [Indexed: 11/23/2022]
Abstract
Ribosomal RNA (rRNA) transcription and ribosome biogenesis are global processes required for growth and proliferation of all cells, yet perturbation of these processes in vertebrates leads to tissue-specific defects termed ribosomopathies. Mutations in rRNA transcription and processing proteins often lead to craniofacial anomalies; however, the cellular and molecular reasons for these defects are poorly understood. Therefore, we examined the function of the most abundant nucleolar phosphoprotein, Nucleolin (Ncl), in vertebrate development. ncl mutant (ncl-/-) zebrafish present with craniofacial anomalies such as mandibulofacial hypoplasia. We observed that ncl-/- mutants exhibited decreased rRNA synthesis and p53-dependent apoptosis, consistent with a role in ribosome biogenesis. However, we found that Nucleolin also performs functions not associated with ribosome biogenesis. We discovered that the half-life of fgf8a mRNA was reduced in ncl-/- mutants, which perturbed Fgf signaling, resulting in misregulated Sox9a-mediated chondrogenesis and Runx2-mediated osteogenesis. Consistent with this model, exogenous FGF8 treatment significantly rescued the cranioskeletal phenotype in ncl-/- zebrafish, suggesting that Nucleolin regulates osteochondroprogenitor differentiation. Our work has therefore uncovered tissue-specific functions for Nucleolin in rRNA transcription and post-transcriptional regulation of growth factor signaling during embryonic craniofacial development.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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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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Kim HR, Kim M, Kim BC. Specific detection of Cronobacter sakazakii in powdered infant formula using ssDNA aptamer. Analyst 2021; 146:3534-3542. [PMID: 33884389 DOI: 10.1039/d1an00118c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cronobacter sakazakii (C. sakazakii) is a foodborne pathogen associated with bacterial meningitis, sepsis, and necrotizing enterocolitis in premature and immuno-compromised infants. C. sakazakii is typically acquired by ingesting contaminated powdered infant formula (PIF). The growing demand for a safe food supply requires rapid detection of foodborne pathogens for delivering safe-to-consume food to consumers. In the present study, we isolated C. sakazakii-specific aptamers using a centrifugation-based partitioning method (CBPM) instead of systematic evolution of ligands by exponential enrichment (SELEX) process. Unlike SELEX, the CBPM reduces the evolution-loop time to obtain enriched probes, allowing the isolation of target-specific aptamers in a shorter time. The two aptamers (SC25 and SC45) isolated using the CBPM showed high affinity and specificity for C. sakazakii (Kd: 34 and 66 nM). Among the two aptamers, SC25 aptamer detected efficiently C. sakazakii in PIF with less cross-reactivity. Our results indicate that the isolated aptamers could be used for detecting C. sakazakii in PIF and reducing the overall testing time compared with the conventional C. sakazakii detection method.
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Affiliation(s)
- Hye Ri Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Myunghee Kim
- Department of Food Science and Technology, Yeungnam University, 280 Daehak-ro, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea
| | - Byoung Chan Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
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Das S, De S, Sengupta S. Post-transcriptional regulation of MMP2 mRNA by its interaction with miR-20a and Nucleolin in breast cancer cell lines. Mol Biol Rep 2021; 48:2315-2324. [PMID: 33788053 DOI: 10.1007/s11033-021-06261-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/03/2021] [Indexed: 11/25/2022]
Abstract
Matrix-metalloproteinase-2 (MMP2) is a foremost MMP, governing invasion of breast cancer cells during metastasis. miR-20a was reported to induce mesenchymal to epithelial transition in MDA-MB-231 cells and its endogenous expression varies directly with invasiveness of breast cancer cells. The inverse and direct correlation of invasiveness with miR-20a and Nucleolin respectively led us to study the post-transcriptional regulation of MMP2 by miR-20a and mRNA stabilizing protein, Nucleolin. Thus, understanding the mechanism of its regulation will enable modification of the invasion potential. MMP2 was found to be higher in MDA-MB-231 than MCF-7 cells both at RNA and protein levels. RNA-protein co-immunoprecipitation assay with Argonaute 2 revealed that MMP2 undergoes miRNA-mediated post-transcriptional regulation. miR-20a decreased MMP2 expression as well as its enzymatic activity as found by zymogram assay. Reporter assay showed that miR-20a directly binds to its putative binding site in MMP2 3'-UTR as per in silico prediction. miR-20a additionally impeded MMP2 mRNA stability, and binding of stabilizing trans-factor Nucleolin to its 3'-UTR was confirmed by RNA-protein co-immunoprecipitation assay. Partial down-regulation of Nucleolin by Si-RNA resulted in the downregulation of MMP2 and Nucleolin over-expression rescued the inhibitory effect of miR-20a on MMP2 expression. Delineating the mechanism of post-transcriptional regulation of MMP2, two of its potent regulators, miR-20a and Nucleolin were identified. It was established for the first time that MMP2 is a direct target of miR-20a. The results also elucidated that Nucleolin binds to MMP2 3' UTR and its abundance affects MMP2 expression.
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Affiliation(s)
- Sayantani Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India
| | - Soumasree De
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India
| | - Sumita Sengupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India.
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Okuwaki M, Saotome-Nakamura A, Yoshimura M, Saito S, Hirawake-Mogi H, Sekiya T, Nagata K. RNA-recognition motifs and glycine and arginine-rich region cooperatively regulate the nucleolar localization of nucleolin. J Biochem 2021; 169:87-100. [PMID: 32785674 DOI: 10.1093/jb/mvaa095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 01/11/2023] Open
Abstract
Nucleolin (NCL) is a nucleolar protein i.e. involved in the regulation of the nucleolar structure and functions, and consists of three distinct regions: the N-terminal region; the middle region, which contains four RNA-recognition motifs (RRMs); and the C-terminal glycine- and arginine-rich (GAR) region. The primary function of the RRMs and GAR is thought to be specific RNA binding. However, it is not well understood how these RNA-binding regions of NCL separately or cooperatively regulate its nucleolar localization and functions. To address this issue, we constructed mutant proteins carrying point mutations at the four RRMs individually or deletion of the C-terminal GAR region. We found that the GAR deletion and the mutations in the fourth RRM (RRM4) decreased the nucleolar localization of NCL. Biochemical analyses showed that NCL interacted directly with ribosomal RNAs (rRNAs) and G-rich oligonucleotides, and that this interaction was decreased by mutations at RRM1 and RRM4 and GAR deletion. Although GAR deletion decreased the rRNA-binding activity of NCL, the mutant was efficiently coprecipitated with rRNAs and nucleolar proteins from cell extracts. These contradictory results suggest that NCL stably localizes to the nucleoli via the interactions with rRNAs and nucleolar proteins via GAR, RRM1 and RRM4.
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Affiliation(s)
- Mitsuru Okuwaki
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Ai Saotome-Nakamura
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Masashi Yoshimura
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shoko Saito
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Hiroko Hirawake-Mogi
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takeshi Sekiya
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
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Cancer Stem Cells and Nucleolin as Drivers of Carcinogenesis. Pharmaceuticals (Basel) 2021; 14:ph14010060. [PMID: 33451077 PMCID: PMC7828541 DOI: 10.3390/ph14010060] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer, one of the most mortal diseases worldwide, is characterized by the gain of specific features and cellular heterogeneity. Clonal evolution is an established theory to explain heterogeneity, but the discovery of cancer stem cells expanded the concept to include the hierarchical growth and plasticity of cancer cells. The activation of epithelial-to-mesenchymal transition and its molecular players are widely correlated with the presence of cancer stem cells in tumors. Moreover, the acquisition of certain oncological features may be partially attributed to alterations in the levels, location or function of nucleolin, a multifunctional protein involved in several cellular processes. This review aims at integrating the established hallmarks of cancer with the plasticity of cancer cells as an emerging hallmark; responsible for tumor heterogeneity; therapy resistance and relapse. The discussion will contextualize the involvement of nucleolin in the establishment of cancer hallmarks and its application as a marker protein for targeted anticancer therapies
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de Breyne S, Vindry C, Guillin O, Condé L, Mure F, Gruffat H, Chavatte L, Ohlmann T. Translational control of coronaviruses. Nucleic Acids Res 2020; 48:12502-12522. [PMID: 33264393 PMCID: PMC7736815 DOI: 10.1093/nar/gkaa1116] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.
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Affiliation(s)
- Sylvain de Breyne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Caroline Vindry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Olivia Guillin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Lionel Condé
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Fabrice Mure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurent Chavatte
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
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Fabbiano F, Corsi J, Gurrieri E, Trevisan C, Notarangelo M, D'Agostino VG. RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins? J Extracell Vesicles 2020; 10:e12043. [PMID: 33391635 PMCID: PMC7769857 DOI: 10.1002/jev2.12043] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous membranous particles released from the cells through different biogenetic and secretory mechanisms. We now conceive EVs as shuttles mediating cellular communication, carrying a variety of molecules resulting from intracellular homeostatic mechanisms. The RNA is a widely detected cargo and, impressively, a recognized functional intermediate that elects EVs as modulators of cancer cell phenotypes, determinants of disease spreading, cell surrogates in regenerative medicine, and a source for non-invasive molecular diagnostics. The mechanistic elucidation of the intracellular events responsible for the engagement of RNA into EVs will significantly improve the comprehension and possibly the prediction of EV "quality" in association with cell physiology. Interestingly, the application of multidisciplinary approaches, including biochemical as well as cell-based and computational strategies, is increasingly revealing an active RNA-packaging process implicating RNA-binding proteins (RBPs) in the sorting of coding and non-coding RNAs. In this review, we provide a comprehensive view of RBPs recently emerging as part of the EV biology, considering the scenarios where: (i) individual RBPs were detected in EVs along with their RNA substrates, (ii) RBPs were detected in EVs with inferred RNA targets, and (iii) EV-transcripts were found to harbour sequence motifs mirroring the activity of RBPs. Proteins so far identified are members of the hnRNP family (hnRNPA2B1, hnRNPC1, hnRNPG, hnRNPH1, hnRNPK, and hnRNPQ), as well as YBX1, HuR, AGO2, IGF2BP1, MEX3C, ANXA2, ALIX, NCL, FUS, TDP-43, MVP, LIN28, SRP9/14, QKI, and TERT. We describe the RBPs based on protein domain features, current knowledge on the association with human diseases, recognition of RNA consensus motifs, and the need to clarify the functional significance in different cellular contexts. We also summarize data on previously identified RBP inhibitor small molecules that could also be introduced in EV research as potential modulators of vesicular RNA sorting.
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Affiliation(s)
- Fabrizio Fabbiano
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Jessica Corsi
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Elena Gurrieri
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Caterina Trevisan
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Vito G. D'Agostino
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
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12
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Kim HR, Song MY, Chan Kim B. Rapid isolation of bacteria-specific aptamers with a non-SELEX-based method. Anal Biochem 2019; 591:113542. [PMID: 31837967 DOI: 10.1016/j.ab.2019.113542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 02/08/2023]
Abstract
Usually, isolation of bacteria-specific aptamers by SELEX is a time-consuming process due to the required repeated rounds of binding, separation, and amplification of the probes to target bacteria. Here, we show that it is possible to isolate bacteria-specific DNA aptamers omitting the repeated rounds of binding incubation, separation, and amplification that are indispensable for SELEX. The serial removal of unbound DNAs to the bacterial cells from an initial mixture of bacteria and DNA libraries through serial centrifugation, one-time separation, and further one-time amplification of DNA bound to the target bacterial cells applied in this non-SELEX-based method allows successful aptamer isolation.
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Affiliation(s)
- Hye Ri Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Min Yong Song
- Seoul Institute of Technology, Maebongsan-ro 37, Mapo-gu, Seoul, 03909, Republic of Korea
| | - Byoung Chan Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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13
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Falconi M, Giangrossi M, Zabaleta ME, Wang J, Gambini V, Tilio M, Bencardino D, Occhipinti S, Belletti B, Laudadio E, Galeazzi R, Marchini C, Amici A. A novel 3'-tRNA Glu-derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin. FASEB J 2019; 33:13228-13240. [PMID: 31560576 DOI: 10.1096/fj.201900382rr] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
tRNA-derived fragments (tRFs) have been defined as a novel class of small noncoding RNAs. tRFs have been reported to be deregulated in cancer, but their biologic function remains to be fully understood. We have identified a new tRF (named tRF3E), derived from mature tRNAGlu, that is specifically expressed in healthy mammary glands but not in breast cancer (BC). Consistently, tRF3E levels significantly decrease in the blood of patients with epidermal growth factor receptor 2 (HER2)-positive BC reflecting tumor status (control > early cancer > metastatic cancer). tRF3E down-regulation was recapitulated in Δ16HER2 transgenic mice, representing a BC preclinical model. Pulldown assays, used to search for proteins capable to selectively bind tRF3E, have shown that this tRF specifically interacts with nucleolin (NCL), an RNA-binding protein overexpressed in BC and able to repress the translation of p53 mRNA. The binding properties of NCL-tRF3E complex, predicted in silico and analyzed by EMSA assays, are congruent with a competitive displacement of p53 mRNA by tRF3E, leading to an increased p53 expression and consequently to a modulation of cancer cell growth. Here, we provide evidence that tRF3E plays an important role in the pathogenesis of BC displaying tumor-suppressor functions through a NCL-mediated mechanism.-Falconi, M., Giangrossi, M., Elexpuru Zabaleta, M., Wang, J., Gambini, V., Tilio, M., Bencardino, D., Occhipinti, S., Belletti, B., Laudadio, E., Galeazzi, R., Marchini, C., Amici, A. A novel 3'-tRNAGlu-derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin.
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Affiliation(s)
- Maurizio Falconi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Mara Giangrossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | - Junbiao Wang
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Valentina Gambini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Martina Tilio
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Daniela Bencardino
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sergio Occhipinti
- Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Torino, Torino, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Emiliano Laudadio
- Dipartimento Scienze e Ingegneria della Materia, dell'Ambiente ed Urbanistica, Università Politecnica delle Marche, Ancona, Italy
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Cristina Marchini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Augusto Amici
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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14
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Gomez GN, Abrar F, Dodhia MP, Gonzalez FG, Nag A. SARS coronavirus protein nsp1 disrupts localization of Nup93 from the nuclear pore complex. Biochem Cell Biol 2019; 97:758-766. [PMID: 30943371 DOI: 10.1139/bcb-2018-0394] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus nonstructural protein 1 (nsp1) is a key factor in virus-induced down-regulation of host gene expression. In infected cells, nsp1 engages in a multipronged mechanism to inhibit host gene expression by binding to the 40S ribosome to block the assembly of translationally competent ribosome, and then inducing endonucleolytic cleavage and the degradation of host mRNAs. Here, we report a previously undetected mechanism by which nsp1 exploits the nuclear pore complex and disrupts the nuclear-cytoplasmic transport of biomolecules. We identified members of the nuclear pore complex from the nsp1-associated protein assembly and found that the expression of nsp1 in HEK cells disrupts Nup93 localization around the nuclear envelope without triggering proteolytic degradation, while the nuclear lamina remains unperturbed. Consistent with its role in host shutoff, nsp1 alters the nuclear-cytoplasmic distribution of an RNA binding protein, nucleolin. Our results suggest that nsp1, alone, can regulate multiple steps of gene expression including nuclear-cytoplasmic transport.
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Affiliation(s)
- Garret N Gomez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fareeha Abrar
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Maya P Dodhia
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fabiola G Gonzalez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Anita Nag
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
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15
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Gongol B, Marin T, Zhang J, Wang SC, Sun W, He M, Chen S, Chen L, Li J, Liu JH, Martin M, Han Y, Kang J, Johnson DA, Lytle C, Li YS, Huang PH, Chien S, Shyy JYJ. Shear stress regulation of miR-93 and miR-484 maturation through nucleolin. Proc Natl Acad Sci U S A 2019; 116:12974-12979. [PMID: 31182601 PMCID: PMC6600934 DOI: 10.1073/pnas.1902844116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pulsatile shear (PS) and oscillatory shear (OS) elicit distinct mechanotransduction signals that maintain endothelial homeostasis or induce endothelial dysfunction, respectively. A subset of microRNAs (miRs) in vascular endothelial cells (ECs) are differentially regulated by PS and OS, but the regulation of the miR processing and its implications in EC biology by shear stress are poorly understood. From a systematic in silico analysis for RNA binding proteins that regulate miR processing, we found that nucleolin (NCL) is a major regulator of miR processing in response to OS and essential for the maturation of miR-93 and miR-484 that target mRNAs encoding Krüppel-like factor 2 (KLF2) and endothelial nitric oxide synthase (eNOS). Additionally, anti-miR-93 and anti-miR-484 restore KLF2 and eNOS expression and NO bioavailability in ECs under OS. Analysis of posttranslational modifications of NCL identified that serine 328 (S328) phosphorylation by AMP-activated protein kinase (AMPK) was a major PS-activated event. AMPK phosphorylation of NCL sequesters it in the nucleus, thereby inhibiting miR-93 and miR-484 processing and their subsequent targeting of KLF2 and eNOS mRNA. Elevated levels of miR-93 and miR-484 were found in sera collected from individuals afflicted with coronary artery disease in two cohorts. These findings provide translational relevance of the AMPK-NCL-miR-93/miR-484 axis in miRNA processing in EC health and coronary artery disease.
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Affiliation(s)
- Brendan Gongol
- Department of Medicine, University of California, San Diego, CA 92093
| | - Traci Marin
- Department of Health Sciences, Victor Valley College, Victorville, CA 92395
| | - Jiao Zhang
- Department of Medicine, University of California, San Diego, CA 92093
| | - Shen-Chih Wang
- Department of Anesthesiology, Taipei Veterans General Hospital, 115 Taipei, Taiwan
| | - Wei Sun
- Division of Biomedical Sciences, University of California, Riverside, CA 92521
| | - Ming He
- Department of Medicine, University of California, San Diego, CA 92093
| | - Shanshan Chen
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China Xi'an, 710029 Xi'an, China
| | - Lili Chen
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China Xi'an, 710029 Xi'an, China
| | - Jie Li
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China Xi'an, 710029 Xi'an, China
| | - Jun-Hui Liu
- Department of Clinical Laboratory, First Affiliated Hospital of the Medical School, Xi'an Jiaotong University, 710029 Xi'an, China
| | - Marcy Martin
- Department of Medicine, University of California, San Diego, CA 92093
| | - Yue Han
- Institute of Mechanobiology and Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jian Kang
- Department of Medicine, University of California, San Diego, CA 92093
| | - David A Johnson
- Division of Biomedical Sciences, University of California, Riverside, CA 92521
| | - Christian Lytle
- Division of Biomedical Sciences, University of California, Riverside, CA 92521
| | - Yi-Shuan Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Po-Hsun Huang
- Cardiovascular Research Center, National Yang-Ming University, 112 Taipei, Taiwan
- Department of Critical Care Medicine, Taipei Veterans General Hospital, 115 Taipei, Taiwan
| | - Shu Chien
- Department of Medicine, University of California, San Diego, CA 92093;
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, CA 92093;
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China Xi'an, 710029 Xi'an, China
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16
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Expression of CPNE7 during mouse dentinogenesis. J Mol Histol 2019; 50:179-188. [DOI: 10.1007/s10735-019-09816-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
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17
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Meng W, Wang XJ, Wang HCR. Targeting nuclear proteins for control of viral replication. Crit Rev Microbiol 2019; 45:495-513. [DOI: 10.1080/1040841x.2018.1553848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wen Meng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hwa-Chain Robert Wang
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, The University of Tennessee, Knoxville, USA
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18
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Olson CO, Pejhan S, Kroft D, Sheikholeslami K, Fuss D, Buist M, Ali Sher A, Del Bigio MR, Sztainberg Y, Siu VM, Ang LC, Sabourin-Felix M, Moss T, Rastegar M. MECP2 Mutation Interrupts Nucleolin-mTOR-P70S6K Signaling in Rett Syndrome Patients. Front Genet 2018; 9:635. [PMID: 30619462 PMCID: PMC6305968 DOI: 10.3389/fgene.2018.00635] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/27/2018] [Indexed: 01/26/2023] Open
Abstract
Rett syndrome (RTT) is a severe and rare neurological disorder that is caused by mutations in the X-linked MECP2 (methyl CpG-binding protein 2) gene. MeCP2 protein is an important epigenetic factor in the brain and in neurons. In Mecp2-deficient neurons, nucleoli structures are compromised. Nucleoli are sites of active ribosomal RNA (rRNA) transcription and maturation, a process mainly controlled by nucleolin and mechanistic target of rapamycin (mTOR)-P70S6K signaling. Currently, it is unclear how nucleolin-rRNA-mTOR-P70S6K signaling from RTT cellular model systems translates into human RTT brain. Here, we studied the components of nucleolin-rRNA-mTOR-P70S6K signaling in the brain of RTT patients with common T158M and R255X mutations. Immunohistochemical examination of T158M brain showed disturbed nucleolin subcellular localization, which was absent in Mecp2-deficient homozygous male or heterozygote female mice, compared to wild type (WT). We confirmed by Western blot analysis that nucleolin protein levels are altered in RTT brain, but not in Mecp2-deficient mice. Further, we studied the expression of rRNA transcripts in Mecp2-deficient mice and RTT patients, as downstream molecules that are controlled by nucleolin. By data mining of published ChIP-seq studies, we showed MeCP2-binding at the multi-copy rRNA genes in the mouse brain, suggesting that rRNA might be a direct MeCP2 target gene. Additionally, we observed compromised mTOR-P70S6K signaling in the human RTT brain, a molecular pathway that is upstream of rRNA-nucleolin molecular conduits. RTT patients showed significantly higher phosphorylation of active mTORC1 or mTORC2 complexes compared to age- and sex-matched controls. Correlational analysis of mTORC1/2-P70S6K signaling pathway identified multiple points of deviation from the control tissues that may result in abnormal ribosome biogenesis in RTT brain. To our knowledge, this is the first report of deregulated nucleolin-rRNA-mTOR-P70S6K signaling in the human RTT brain. Our results provide important insight toward understanding the molecular properties of human RTT brain.
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Affiliation(s)
- Carl O Olson
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Shervin Pejhan
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Kroft
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kimia Sheikholeslami
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - David Fuss
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Marjorie Buist
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Annan Ali Sher
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Marc R Del Bigio
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Yehezkel Sztainberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Victoria Mok Siu
- Division of Medical Genetics, Department of Paediatrics, Schulich School of Medicine, Western University, London, ON, Canada
| | - Lee Cyn Ang
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Marianne Sabourin-Felix
- Cancer Division of the Quebec University Hospital Research Centre, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Tom Moss
- Cancer Division of the Quebec University Hospital Research Centre, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Mojgan Rastegar
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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19
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Sen Gupta A, Joshi G, Pawar S, Sengupta K. Nucleolin modulates compartmentalization and dynamics of histone 2B-ECFP in the nucleolus. Nucleus 2018; 9:350-367. [PMID: 29943658 PMCID: PMC6165600 DOI: 10.1080/19491034.2018.1471936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Eukaryotic cells have 2 to 3 discrete nucleoli required for ribosome synthesis. Nucleoli are phase separated nuclear sub-organelles. Here we examined the role of nuclear Lamins and nucleolar factors in modulating the compartmentalization and dynamics of histone 2B (H2B-ECFP) in the nucleolus. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) of labelled H2B, showed that the depletion of Lamin B1, Fibrillarin (FBL) or Nucleostemin (GNL3), enhances H2B-ECFP mobility in the nucleolus. Furthermore, Nucleolin knockdown significantly decreases H2B-ECFP compartmentalization in the nucleolus, while H2B-ECFP residence and mobility in the nucleolus was prolonged upon Nucleolin overexpression. Co-expression of N-terminal and RNA binding domain (RBD) deletion mutants of Nucleolin or inhibiting 45S rRNA synthesis reduces the sequestration of H2B-ECFP in the nucleolus. Taken together, these studies reveal a crucial role of Nucleolin-rRNA complex in modulating the compartmentalization, stability and dynamics of H2B within the nucleolus.
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Affiliation(s)
- Ayantika Sen Gupta
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Gaurav Joshi
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Sumit Pawar
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
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20
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Li D, Zhang J, Wang M, Li X, Gong H, Tang H, Chen L, Wan L, Liu Q. Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation. Nat Commun 2018; 9:1726. [PMID: 29712923 PMCID: PMC5928123 DOI: 10.1038/s41467-018-04072-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 12/27/2022] Open
Abstract
The ribosome is indispensable for precisely controlling the capacity of protein synthesis. However, how translational machinery is coordinated to meet the translational demands remains elusive. Here, we identify a nucleolar-specific lncRNA (LoNA), its 5' portion binds and sequesters nucleolin to suppress rRNA transcription, and its snoRNA like 3' end recruits and diminishes fibrillarin activity to reduce rRNA methylation. Activity-dependent decrease of LoNA leads to elevated rRNA and ribosome levels, an increased proportion of polysomes, mRNA polysome loading, and protein translation. In addition, transport of ribosomes to synapses is particularly promoted, resulting in increased levels of AMPA/NMDA receptor, enhanced synaptic plasticity, long-term potentiation and consolidated memory. Strikingly, hippocampal LoNA deficiency not only enhances long-term memory in WT mice, but also restores impaired memory function in APP/PS1 transgenic mice. Together, these findings reveal the multifaceted role of LoNA in modulating ribosome biogenesis to meet the translational demands of long-term memory.
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MESH Headings
- 5' Untranslated Regions
- Amyloid beta-Protein Precursor/genetics
- Amyloid beta-Protein Precursor/metabolism
- Animals
- Cell Line, Tumor
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Hippocampus/cytology
- Hippocampus/metabolism
- Long-Term Potentiation/genetics
- Memory, Long-Term/physiology
- Methylation
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Neurons/cytology
- Neurons/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Presenilin-1/genetics
- Presenilin-1/metabolism
- Protein Biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, AMPA/genetics
- Receptors, AMPA/metabolism
- Receptors, N-Methyl-D-Aspartate/genetics
- Receptors, N-Methyl-D-Aspartate/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Synapses/genetics
- Transgenes
- Nucleolin
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Affiliation(s)
- Dingfeng Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Ming Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaohui Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Huarui Gong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Huiping Tang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Lin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Lili Wan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qiang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China.
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China.
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China.
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21
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Sen Gupta A, Sengupta K. Lamin B2 Modulates Nucleolar Morphology, Dynamics, and Function. Mol Cell Biol 2017; 37:e00274-17. [PMID: 28993479 PMCID: PMC5705821 DOI: 10.1128/mcb.00274-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/05/2017] [Accepted: 09/29/2017] [Indexed: 01/11/2023] Open
Abstract
The nucleolus is required for ribosome biogenesis. Human cells have 2 or 3 nucleoli associated with nucleolar organizer region (NOR)-bearing chromosomes. An increase in number and altered nucleolar morphology define cancer cells. However, the mechanisms that modulate nucleolar morphology and function are unclear. Here we show that in addition to localizing at the nuclear envelope, lamin B2 localizes proximal to nucleolin at the granular component (GC) of the nucleolus and associates with the nucleolar proteins nucleolin and nucleophosmin. Lamin B2 knockdown severely disrupted the nucleolar morphology, which was rescued to intact and discrete nucleoli upon lamin B2 overexpression. Furthermore, two mutually exclusive lamin B2 deletion mutants, ΔHead and ΔSLS, rescued nuclear and nucleolar morphology defects, respectively, induced upon lamin B2 depletion, suggesting independent roles for lamin B2 at the nucleolus and nuclear envelope. Lamin B2 depletion increased nucleolin aggregation in the nucleoplasm, implicating lamin B2 in stabilizing nucleolin within the nucleolus. Lamin B2 knockdown upregulated nucleolus-specific 45S rRNA and upstream intergenic sequence (IGS) transcripts. The IGS transcripts colocalized with aggregates of nucleolin speckles, which were sustained in the nucleoplasm upon lamin B2 depletion. Taken together, these studies uncover a novel role for lamin B2 in modulating the morphology, dynamics, and function of the nucleolus.
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Affiliation(s)
- Ayantika Sen Gupta
- Biology, Indian Institute of Science Education and Research, Pune, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research, Pune, India
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22
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Ugrinova I, Petrova M, Chalabi-Dchar M, Bouvet P. Multifaceted Nucleolin Protein and Its Molecular Partners in Oncogenesis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 111:133-164. [PMID: 29459030 DOI: 10.1016/bs.apcsb.2017.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Discovered in 1973, nucleolin is one of the most abundant phosphoproteins of the nucleolus. The ability of nucleolin to be involved in many cellular processes is probably related to its structural organization and its capability to form many different interactions with other proteins. Many functions of nucleolin affect cellular processes involved in oncogenesis-for instance: in ribosome biogenesis; in DNA repair, remodeling, and genome stability; in cell division and cell survival; in chemokine and growth factor signaling pathways; in angiogenesis and lymphangiogenesis; in epithelial-mesenchymal transition; and in stemness. In this review, we will describe the different functions of nucleolin in oncogenesis through its interaction with other proteins.
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Affiliation(s)
- Iva Ugrinova
- "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Maria Petrova
- "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Mounira Chalabi-Dchar
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, Lyon, France
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
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23
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Jia W, Yao Z, Zhao J, Guan Q, Gao L. New perspectives of physiological and pathological functions of nucleolin (NCL). Life Sci 2017; 186:1-10. [PMID: 28751161 DOI: 10.1016/j.lfs.2017.07.025] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/21/2017] [Accepted: 07/23/2017] [Indexed: 12/13/2022]
Abstract
Nucleolin (NCL) is a multifunctional protein that mainly localized in the nucleolus, it is also found in the nucleoplasm, cytoplasm and cell membrane. The three main structural domains allow the interaction of NCL with different proteins and RNA sequences. Moreover, specific post-translational modifications and its shuttling property also contribute to its multifunctionality. NCL has been demonstrated to be involved in a variety of aspects such as ribosome biogenesis, chromatin organization and stability, DNA and RNA metabolism, cytokinesis, cell proliferation, angiogenesis, apoptosis regulation, stress response and microRNA processing. NCL has been increasingly implicated in several pathological processes, especially in tumorigenesis and viral infection, which makes NCL a potential target for the development of anti-tumor and anti-viral strategies. In this review, we present an overview on the structure, localizations and various functions of NCL, and further describe how the multiple functions of NCL are correlated to its multiple cellular distributions.
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Affiliation(s)
- Wenyu Jia
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong Province, PR China; Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong Province, PR China; Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong Province, PR China
| | - Zhenyu Yao
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong Province, PR China; Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong Province, PR China; Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong Province, PR China
| | - Jiajun Zhao
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong Province, PR China; Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong Province, PR China; Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong Province, PR China
| | - Qingbo Guan
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong Province, PR China; Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong Province, PR China; Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong Province, PR China
| | - Ling Gao
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong Province, PR China; Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong Province, PR China; Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong Province, PR China.
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24
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Kumar S, Gomez EC, Chalabi-Dchar M, Rong C, Das S, Ugrinova I, Gaume X, Monier K, Mongelard F, Bouvet P. Integrated analysis of mRNA and miRNA expression in HeLa cells expressing low levels of Nucleolin. Sci Rep 2017; 7:9017. [PMID: 28827664 PMCID: PMC5567140 DOI: 10.1038/s41598-017-09353-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Nucleolin is an essential protein that plays important roles in the regulation of cell cycle and cell proliferation. Its expression is up regulated in many cancer cells but its molecular functions are not well characterized. Nucleolin is present in the nucleus where it regulates gene expression at the transcriptional and post-transcriptional levels. Using HeLa cells depleted in nucleolin we performed an mRNA and miRNA transcriptomics analysis to identify biological pathways involving nucleolin. Bioinformatic analysis strongly points to a role of nucleolin in lipid metabolism, and in many signaling pathways. Down regulation of nucleolin is associated with lower level of cholesterol while the amount of fatty acids is increased. This could be explained by the decreased and mis-localized expression of the transcription factor SREBP1 and the down-regulation of enzymes involved in the beta-oxidation and degradation of fatty acids. Functional classification of the miRNA-mRNA target genes revealed that deregulated miRNAs target genes involved in apoptosis, proliferation and signaling pathways. Several of these deregulated miRNAs have been shown to control lipid metabolism. This integrated transcriptomic analysis uncovers new unexpected roles for nucleolin in metabolic regulation and signaling pathways paving the way to better understand the global function of nucleolin within the cell.
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Affiliation(s)
- Sanjeev Kumar
- BioCOS Life Sciences Private Limited, AECS Layout, B-Block, Singasandra Hosur Road SAAMI Building, 851/A, 3rd Floor, Bengaluru, Karnataka, India.
| | - Elizabhet Cruz Gomez
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Mounira Chalabi-Dchar
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Cong Rong
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Iva Ugrinova
- Institute of Molecular Biology "Acad. Roumen Tsanev" Bulgarian Academy of Sciences "Acad. G Bonchev str. bl. 21, 1113, Sofia, Bulgaria
| | - Xavier Gaume
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Karine Monier
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Fabien Mongelard
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Philippe Bouvet
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France.
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.
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25
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Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD. RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection. Methods 2017; 126:18-28. [PMID: 28651966 DOI: 10.1016/j.ymeth.2017.06.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/16/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.
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Affiliation(s)
- Kate B Cook
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Shankar Vembu
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Kevin C H Ha
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada.
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26
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Conlon EG, Lu L, Sharma A, Yamazaki T, Tang T, Shneider NA, Manley JL. The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains. eLife 2016; 5. [PMID: 27623008 PMCID: PMC5050020 DOI: 10.7554/elife.17820] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022] Open
Abstract
An expanded GGGGCC hexanucleotide in C9ORF72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It has been proposed that expanded transcripts adopt G-quadruplex (G-Q) structures and associate with proteins, but whether this occurs and contributes to disease is unknown. Here we show first that the protein that predominantly associates with GGGGCC repeat RNA in vitro is the splicing factor hnRNP H, and that this interaction is linked to G-Q formation. We then show that G-Q RNA foci are more abundant in C9 ALS patient fibroblasts and astrocytes compared to those without the expansion, and more frequently colocalize with hnRNP H. Importantly, we demonstrate dysregulated splicing of multiple known hnRNP H-target transcripts in C9 patient brains, which correlates with elevated insoluble hnRNP H/G-Q aggregates. Together, our data implicate C9 expansion-mediated sequestration of hnRNP H as a significant contributor to neurodegeneration in C9 ALS/FTD. DOI:http://dx.doi.org/10.7554/eLife.17820.001
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Affiliation(s)
- Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, United States
| | - Lei Lu
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Aarti Sharma
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, United States
| | - Timothy Tang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Neil A Shneider
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, United States
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27
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Bjerregaard N, Andreasen PA, Dupont DM. Expected and unexpected features of protein-binding RNA aptamers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:744-757. [PMID: 27173731 DOI: 10.1002/wrna.1360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022]
Abstract
RNA molecules with high affinity to specific proteins can be isolated from libraries of up to 1016 different RNA sequences by systematic evolution of ligands by exponential enrichment (SELEX). These so-called protein-binding RNA aptamers are often interesting, e.g., as modulators of protein function for therapeutic use, for probing the conformations of proteins, for studies of basic aspects of nucleic acid-protein interactions, etc. Studies on the interactions between RNA aptamers and proteins display a number of expected and unexpected features, including the chemical nature of the interacting RNA-protein surfaces, the conformation of protein-bound aptamer versus free aptamer, the conformation of aptamer-bound protein versus free protein, and the effects of aptamers on protein function. Here, we review current insights into the details of RNA aptamer-protein interactions. WIREs RNA 2016, 7:744-757. doi: 10.1002/wrna.1360 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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28
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Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A. Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches. J Proteome Res 2016; 15:1659-69. [PMID: 27049334 DOI: 10.1021/acs.jproteome.6b00126] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein.
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Affiliation(s)
- Anna Salvetti
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Alberto Epstein
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Loredana Arata
- Subdepartment of Molecular Genetics, Public Health Institute of Chile , Santiago, Chile
| | - Alexandra Kraut
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Vincent Navratil
- Pôle Rhône Alpes de Bioinformatique (PRABI), Université Lyon 1 , 69100 Villeurbanne, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286 , 69003 Lyon, France
| | - Anna Greco
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
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29
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Tasdemir S, Eroz R, Dogan H, Erdem HB, Sahin I, Kara M, Engin RI, Turkez H. Association Between Human Hair Loss and the Expression Levels of Nucleolin, Nucleophosmin, and UBTF Genes. Genet Test Mol Biomarkers 2016; 20:197-202. [PMID: 26866305 DOI: 10.1089/gtmb.2015.0246] [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: 11/13/2022] Open
Abstract
AIMS Nucleolar organizer regions, also known as argyrophilic nucleolar organizer regions, are associated with ribosomal genes. The main function of the nucleolus is the rapid production of ribosomal subunits, a process that must be highly regulated to provide the appropriate levels for cellular proliferation and cell growth. There are no studies in the literature addressing the expression and function of nucleolar component proteins, including nucleophosmin, nucleolin and the upstream binding transcription factor (UBTF), in human follicular hair cells. METHODS Nineteen healthy males who had normal and sufficient hair follicles on the back of the head, but exhibited hair loss on the frontal/vertex portions of the head and 14 healthy males without hair loss were included in the current study. Gene expression levels were measured by relative quantitative real time polymerase chain reaction. RESULTS In the individuals suffering from alopecia, the total expression levels of nucleolin, nucleophosmin, and UBTF were lower in normal sites than in hair loss sites. Strong expression level correlations were detected between: nucleophosmin and nucleolin; nucleophosmin and UBTF, and nucleolin and UBTF for both groups. CONCLUSIONS There was an association between human hair loss and the expression levels of nucleolin, nucleophosmin, and UBTF genes.
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Affiliation(s)
- Sener Tasdemir
- 1 Department of Medical Genetics, Faculty of Medicine, Ataturk University , Erzurum, Turkey
| | - Recep Eroz
- 2 Department of Medical Genetics, Faculty of Medicine, Duzce University , Duzce, Turkey
| | - Hasan Dogan
- 3 Department of Medical Biology, Faculty of Medicine, Ataturk University , Erzurum, Turkey
| | - Haktan Bagis Erdem
- 1 Department of Medical Genetics, Faculty of Medicine, Ataturk University , Erzurum, Turkey
| | - Ibrahim Sahin
- 1 Department of Medical Genetics, Faculty of Medicine, Ataturk University , Erzurum, Turkey
| | - Murat Kara
- 4 Department of Medical Genetics, Faculty of Medicine, Mugla Sitki Kocaman University , Mugla, Turkey
| | - Ragip Ismail Engin
- 5 Department of Dermatology, Regional Training and Research Hospital , Erzurum, Turkey
| | - Hasan Turkez
- 6 Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University , Erzurum, Turkey
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30
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Saha S, Chakraborty A, Bandyopadhyay SS. Stabilization of Oncostatin-M mRNA by Binding of Nucleolin to a GC-Rich Element in Its 3'UTR. J Cell Biochem 2016; 117:988-99. [PMID: 26399567 DOI: 10.1002/jcb.25384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/22/2015] [Indexed: 12/23/2022]
Abstract
Oncostatin-M (OSM) is a patho-physiologically important pleiotropic, multifunctional cytokine. OSM mRNA sequence analysis revealed that its 3'UTR contains three highly conserved GC-rich cis-elements (GCREs) whose role in mRNA stability is unidentified. In the present study, the functional role of the proximal GC-rich region of osm 3'-UTR (GCRE-1) in post-transcriptional regulation of osm expression in U937 cells was assessed by transfecting construct containing GCRE-1 at 3'-end of a fairly stable reporter gene followed by analysis of the expression of the reporter. GCRE-1 showed mRNA destabilizing activity; however, upon PMA treatment the reporter message containing GCRE-1 was stabilized. This stabilization is owing to a time-dependent progressive binding of trans-factors (at least five proteins) to GCRE-1 post-PMA treatment. Nucleolin was identified as one of the proteins in the RNP complex of GCRE-1 with PMA-treated U937 cytosolic extracts by oligo-dT affinity chromatography of poly-adenylated GCRE-1. Immuno-blot revealed time-dependent enhancement of nucleolin in the cytoplasm which in turn directly binds GCRE-1. RNA co-immunoprecipitation confirmed the GCRE-1-nucleolin interaction in vivo. To elucidate the functional role of nucleolin in stabilization of osm mRNA, nucleolin was overexpressed in U937 cells and found to stabilize the intrinsic osm mRNA, where co-transfection with the reporter containing GCRE-1 confirms the role of GCRE-1 in stabilization of the reporter mRNA. Thus, in conclusion, the results asserted that PMA treatment in U937 cells leads to cytoplasmic translocation of nucleolin that directly binds GCRE-1, one of the major GC-rich instability elements, thereby stabilizing the osm mRNA.
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Affiliation(s)
- Sucharita Saha
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India
| | - Alina Chakraborty
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India
| | - Sumita Sengupta Bandyopadhyay
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 A.P.C. Road, Kolkata, 700009, India
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31
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Abstract
A technique is described for the identification of nucleic acid sequences bound with high affinity by proteins or by other molecules suitable for a partitioning assay. Here, a histidine-tagged protein is allowed to interact with a pool of nucleic acids and the protein-nucleic acid complexes formed are retained on a Ni-NTA matrix. Nucleic acids with a low level of recognition by the protein are washed away. The pool of recovered nucleic acids is amplified by the polymerase chain reaction and is submitted to further rounds of selection. Each round of selection increases the proportion of sequences that are avidly bound by the protein of interest. The cloning and sequencing of these sequences finally completes their identification.
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32
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DeBoer J, Jagadish T, Haverland NA, Madson CJ, Ciborowski P, Belshan M. Alterations in the nuclear proteome of HIV-1 infected T-cells. Virology 2014; 468-470:409-420. [PMID: 25240327 DOI: 10.1016/j.virol.2014.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/17/2023]
Abstract
Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein-protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection.
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Affiliation(s)
- Jason DeBoer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christian J Madson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA.
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33
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Lima WF, Vickers TA, Nichols J, Li C, Crooke ST. Defining the factors that contribute to on-target specificity of antisense oligonucleotides. PLoS One 2014; 9:e101752. [PMID: 25072142 PMCID: PMC4114480 DOI: 10.1371/journal.pone.0101752] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/11/2014] [Indexed: 11/18/2022] Open
Abstract
To better understand the factors that influence the activity and specificity of antisense oligonucleotides (ASOs), we designed a minigene encoding superoxide dismutase 1 (SOD-1) and cloned the minigene into vectors for T7 transcription of pre-mRNA and splicing in a nuclear extract or for stable integration in cells. We designed a series of ASOs that covered the entire mRNA and determined the binding affinities and activities of the ASOs in a cell-free system and in cells. The mRNA bound known RNA-binding proteins on predicted binding sites in the mRNA. The higher order structure of the mRNA had a significantly greater effect than the RNA-binding proteins on ASO binding affinities as the ASO activities in cells and in the cell-free systems were consistent. We identified several ASOs that exhibited off-target hybridization to the SOD-1 minigene mRNA in the cell-free system. Off-target hybridization occurred only at highly accessible unstructured sites in the mRNA and these interactions were inhibited by both the higher order structure of the mRNA and by RNA-binding proteins. The same off-target hybridization interactions were identified in cells that overexpress E. coli RNase H1. No off-target activity was observed for cells expressing only endogenous human RNase H1. Neither were these off-target heteroduplexes substrates for recombinant human RNase H1 under multiple-turnover kinetics suggesting that the endogenous enzyme functions under similar kinetic parameters in cells and in the cell-free system. These results provide a blueprint for design of more potent and more specific ASOs.
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Affiliation(s)
- Walt F. Lima
- Isis Pharmaceuticals Inc., Carlsbad, California, United States of America
- * E-mail:
| | - Timothy A. Vickers
- Isis Pharmaceuticals Inc., Carlsbad, California, United States of America
| | - Josh Nichols
- Isis Pharmaceuticals Inc., Carlsbad, California, United States of America
| | - Cheryl Li
- Isis Pharmaceuticals Inc., Carlsbad, California, United States of America
| | - Stanley T. Crooke
- Isis Pharmaceuticals Inc., Carlsbad, California, United States of America
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von Hacht A, Seifert O, Menger M, Schütze T, Arora A, Konthur Z, Neubauer P, Wagner A, Weise C, Kurreck J. Identification and characterization of RNA guanine-quadruplex binding proteins. Nucleic Acids Res 2014; 42:6630-44. [PMID: 24771345 PMCID: PMC4041461 DOI: 10.1093/nar/gku290] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Guanine quadruplex (G-quadruplex) motifs in the 5′ untranslated region (5′-UTR) of mRNAs were recently shown to influence the efficiency of translation. In the present study, we investigate the interaction between cellular proteins and the G-quadruplexes located in two mRNAs (MMP16 and ARPC2). Formation of the G-quadruplexes was confirmed by biophysical characterization and the inhibitory activity on translation was shown by luciferase reporter assays. In experiments with whole cell extracts from different eukaryotic cell lines, G-quadruplex-binding proteins were isolated by pull-down assays and subsequently identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The binding partners of the RNA G-quadruplexes we discovered included several heterogenous nuclear ribonucleoproteins, ribosomal proteins, and splicing factors, as well as other proteins that have previously not been described to interact with nucleic acids. While most of the proteins were specific for either of the investigated G-quadruplexes, some of them bound to both motifs. Selected candidate proteins were subsequently produced by recombinant expression and dissociation constants for the interaction between the proteins and RNA G-quadruplexes in the low nanomolar range were determined by surface plasmon resonance spectroscopy. The present study may thus help to increase our understanding of the mechanisms by which G-quadruplexes regulate translation.
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Affiliation(s)
- Annekathrin von Hacht
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Oliver Seifert
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | | | - Tatjana Schütze
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Amit Arora
- Institute for Molecular Biosciences, University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Department of Bioprocess Engineering, ACK-24, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Anke Wagner
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jens Kurreck
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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Monte E, Mouillesseaux K, Chen H, Kimball T, Ren S, Wang Y, Chen JN, Vondriska TM, Franklin S. Systems proteomics of cardiac chromatin identifies nucleolin as a regulator of growth and cellular plasticity in cardiomyocytes. Am J Physiol Heart Circ Physiol 2013; 305:H1624-38. [PMID: 24077883 PMCID: PMC3882469 DOI: 10.1152/ajpheart.00529.2013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/10/2013] [Indexed: 11/22/2022]
Abstract
Myocyte hypertrophy antecedent to heart failure involves changes in global gene expression, although the preceding mechanisms to coordinate DNA accessibility on a genomic scale are unknown. Chromatin-associated proteins alter chromatin structure by changing their association with DNA, thereby altering the gene expression profile. Little is known about the global changes in chromatin subproteomes that accompany heart failure, and the mechanisms by which these proteins alter chromatin structure. The present study tests the fundamental hypothesis that cardiac growth and plasticity in the setting of disease recapitulates conserved developmental chromatin remodeling events. We used quantitative proteomics to identify chromatin-associated proteins extracted via detergent and to quantify changes in their abundance during disease. Our study identified 321 proteins in this subproteome, demonstrating it to have modest conservation (37%) with that revealed using strong acid. Of these proteins, 176 exhibited altered expression during cardiac hypertrophy and failure; we conducted extensive functional characterization of one of these proteins, Nucleolin. Morpholino-based knockdown of nucleolin nearly abolished protein expression but surprisingly had little impact on gross morphological development. However, hearts of fish lacking Nucleolin displayed severe developmental impairment, abnormal chamber patterning and functional deficits, ostensibly due to defects in cardiac looping and myocyte differentiation. The mechanisms underlying these defects involve perturbed bone morphogenetic protein 4 expression, decreased rRNA transcription, and a shift to more heterochromatic chromatin. This study reports the quantitative analysis of a new chromatin subproteome in the normal and diseased mouse heart. Validation studies in the complementary model system of zebrafish examine the role of Nucleolin to orchestrate genomic reprogramming events shared between development and disease.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, California
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Chen S, Seiler J, Santiago-Reichelt M, Felbel K, Grummt I, Voit R. Repression of RNA Polymerase I upon Stress Is Caused by Inhibition of RNA-Dependent Deacetylation of PAF53 by SIRT7. Mol Cell 2013; 52:303-13. [DOI: 10.1016/j.molcel.2013.10.010] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/09/2013] [Accepted: 09/24/2013] [Indexed: 11/25/2022]
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Das S, Cong R, Shandilya J, Senapati P, Moindrot B, Monier K, Delage H, Mongelard F, Kumar S, Kundu TK, Bouvet P. Characterization of nucleolin K88 acetylation defines a new pool of nucleolin colocalizing with pre-mRNA splicing factors. FEBS Lett 2013; 587:417-24. [PMID: 23353999 DOI: 10.1016/j.febslet.2013.01.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/17/2012] [Accepted: 01/14/2013] [Indexed: 11/22/2022]
Abstract
Nucleolin is a multifunctional protein that carries several post-translational modifications. We characterized nucleolin acetylation and developed antibodies specific to nucleolin K88 acetylation. Using this antibody we show that nucleolin is acetylated in vivo and is not localized in the nucleoli, but instead is distributed throughout the nucleoplasm. Immunofluorescence studies indicate that acetylated nucleolin is co-localized with the splicing factor SC35 and partially with Y12. Acetylated nucleolin is expressed in all tested proliferating cell types. Our findings show that acetylation defines a new pool of nucleolin which support a role for nucleolin in the regulation of mRNA maturation and transcription by RNA polymerase II.
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Affiliation(s)
- Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, France
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Molineros JE, Maiti AK, Sun C, Looger LL, Han S, Kim-Howard X, Glenn S, Adler A, Kelly JA, Niewold TB, Gilkeson GS, Brown EE, Alarcón GS, Edberg JC, Petri M, Ramsey-Goldman R, Reveille JD, Vilá LM, Freedman BI, Tsao BP, Criswell LA, Jacob CO, Moore JH, Vyse TJ, Langefeld CL, Guthridge JM, Gaffney PM, Moser KL, Scofield RH, Alarcón-Riquelme ME, Williams SM, Merrill JT, James JA, Kaufman KM, Kimberly RP, Harley JB, Nath SK. Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production. PLoS Genet 2013; 9:e1003222. [PMID: 23441136 PMCID: PMC3575474 DOI: 10.1371/journal.pgen.1003222] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/20/2012] [Indexed: 01/22/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22–24 (LOD = 6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio ∼1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [Pmeta = 5.20×10−14; odds ratio, 95% confidence interval = 0.82 (0.78–0.87)], and two missense variants, rs1990760 (Ala946Thr) [Pmeta = 3.08×10−7; 0.88 (0.84–0.93)] and rs10930046 (Arg460His) [Pdom = 1.16×10−8; 0.70 (0.62–0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis. African-Americans (AA) are at increased risk of systemic lupus erythematosus (SLE), but the genetic basis of this risk increase is largely unknown. We used admixture mapping to localize disease-causing genetic variants that differ in frequency across populations. This approach is advantageous for localizing susceptibility genes in recently admixed populations like AA. Our genome-wide admixture scan identified seven admixture signals, and we followed the best signal at 2q22–24 with fine-mapping, imputation-based association analysis and experimental validation. We identified two independent coding variants and a non-coding variant within the IFIH1 gene associated with SLE. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.
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Affiliation(s)
- Julio E. Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Amit K. Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
| | - Shizhong Han
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Stuart Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Timothy B. Niewold
- Mayo Clinic, Division of Rheumatology and Department of Immunology, Rochester, Minnesota, United States of America
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Elizabeth E. Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Graciela S. Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - John D. Reveille
- Department of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Luis M. Vilá
- Department of Medicine, Division of Rheumatology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Betty P. Tsao
- Division of Rheumatology, Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lindsey A. Criswell
- Rosalind Russell Medical Research Center for Arthritis, University of California San Francisco, San Francisco, California, United States of America
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jason H. Moore
- Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
| | - Timothy J. Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
- Division of Immunology, Infection and Inflammatory Diseases, Kings College London, London, United Kingdom
| | - Carl L. Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kathy L. Moser
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - R. Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Centro de Genómica e Investigación Oncológica (GENyO)–Pfizer/Universidad de Granada/Junta de Andalucía, Granada, Spain
| | | | - Scott M. Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Joan T. Merrill
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Kenneth M. Kaufman
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John B. Harley
- Cincinnati Children's Hospital Medical Center and the U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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Birmpas C, Briand JP, Courty J, Katsoris P. The pseudopeptide HB-19 binds to cell surface nucleolin and inhibits angiogenesis. Vasc Cell 2012; 4:21. [PMID: 23265284 PMCID: PMC3606460 DOI: 10.1186/2045-824x-4-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/30/2012] [Indexed: 12/31/2022] Open
Abstract
Background Nucleolin is a protein over-expressed on the surface of tumor and endothelial cells. Recent studies have underlined the involvement of cell surface nucleolin in tumor growth and angiogenesis. This cell surface molecule serves as a receptor for various ligands implicated in pathophysiological processes such as growth factors, cell adhesion molecules like integrins, selectins or laminin-1, lipoproteins and viruses (HIV and coxsackie B). HB-19 is a synthetic multimeric pseudopeptide that binds cell surface expressed nucleolin and inhibits both tumor growth and angiogenesis. Methodology/principal findings In the present work, we further investigated the biological actions of pseudopeptide HB-19 on HUVECs. In a previous work, we have shown that HB-19 inhibits the in vivo angiogenesis on the chicken embryo CAM assay. We now provide evidence that HB-19 inhibits the in vitro adhesion, migration and proliferation of HUVECs without inducing their apoptosis. The above biological actions seem to be regulated by SRC, ERK1/2, AKT and FAK kinases as we found that HB-19 inhibits their activation in HUVECs. Matrix metalloproteinases (MMPs) play crucial roles in tumor growth and angiogenesis, so we investigated the effect of HB-19 on the expression of MMP-2 and we found that HB-19 downregulates MMP-2 in HUVECs. Finally, down regulation of nucleolin using siRNA confirmed the implication of nucleolin in the biological actions of these peptides. Conclusions/significance Taken together, these results indicate that HB-19 could constitute an interesting tool for tumor therapy strategy, targeting cell surface nucleolin.
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Segerstolpe Å, Granneman S, Björk P, de Lima Alves F, Rappsilber J, Andersson C, Högbom M, Tollervey D, Wieslander L. Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome. Nucleic Acids Res 2012. [PMID: 23193268 PMCID: PMC3553979 DOI: 10.1093/nar/gks1129] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ribosomal subunit biogenesis in eukaryotes is a complex multistep process. Mrd1 is an essential and conserved small (40S) ribosomal subunit synthesis factor that is required for early cleavages in the 35S pre-ribosomal RNA (rRNA). Yeast Mrd1 contains five RNA-binding domains (RBDs), all of which are necessary for optimal function of the protein. Proteomic data showed that Mrd1 is part of the early pre-ribosomal complexes, and deletion of individual RBDs perturbs the pre-ribosomal structure. In vivo ultraviolet cross-linking showed that Mrd1 binds to the pre-rRNA at two sites within the 18S region, in helix 27 (h27) and helix 28. The major binding site lies in h27, and mutational analyses shows that this interaction requires the RBD1-3 region of Mrd1. RBD2 plays the dominant role in h27 binding, but other RBDs also contribute directly. h27 and helix 28 are located close to the sequences that form the central pseudoknot, a key structural feature of the mature 40S subunit. We speculate that the modular structure of Mrd1 coordinates pseudoknot formation with pre-rRNA processing and subunit assembly.
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Affiliation(s)
- Åsa Segerstolpe
- Department of Molecular Biology and Functional Genomics, Stockholm University SE-106 91, Stockholm, Sweden
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Greco A, Arata L, Soler E, Gaume X, Couté Y, Hacot S, Callé A, Monier K, Epstein AL, Sanchez JC, Bouvet P, Diaz JJ. Nucleolin interacts with US11 protein of herpes simplex virus 1 and is involved in its trafficking. J Virol 2012; 86:1449-57. [PMID: 22130536 PMCID: PMC3264372 DOI: 10.1128/jvi.06194-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/18/2011] [Indexed: 02/06/2023] Open
Abstract
Herpes simplex virus type 1 (HSV-1) infection induces profound nucleolar modifications at the functional and organizational levels, including nucleolar invasion by several viral proteins. One of these proteins is US11, which exhibits several different functions and displays both cytoplasmic localization and clear nucleolar localization very similar to that of the major multifunctional nucleolar protein nucleolin. To determine whether US11 interacts with nucleolin, we purified US11 protein partners by coimmunoprecipitations using a tagged protein, Flag-US11. From extracts of cells expressing Flag-US11 protein, we copurified a protein of about 100 kDa that was further identified as nucleolin. In vitro studies have demonstrated that nucleolin interacts with US11 and that the C-terminal domain of US11, which is required for US11 nucleolar accumulation, is sufficient for interaction with nucleolin. This association was confirmed in HSV-1-infected cells. We found an increase in the nucleolar accumulation of US11 in nucleolin-depleted cells, thereby revealing that nucleolin could play a role in US11 nucleocytoplasmic trafficking through one-way directional transport out of the nucleolus. Since nucleolin is required for HSV-1 nuclear egress, the interaction of US11 with nucleolin may participate in the outcome of infection.
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Affiliation(s)
- Anna Greco
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
| | - Loredana Arata
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
| | - Eric Soler
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
| | - Xavier Gaume
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, France
| | - Yohann Couté
- Geneva Proteomics Center, Central Clinical Chemistry Laboratory, Geneva University Hospital, Genève, Switzerland
| | - Sabine Hacot
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
- CRCL Inserm U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
| | - Aleth Callé
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
| | - Karine Monier
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, France
| | - Alberto L. Epstein
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
| | - Jean-Charles Sanchez
- Human Protein Sciences, Faculty of Medicine, Geneva University, Geneva, Switzerland
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, France
| | - Jean-Jacques Diaz
- Université de Lyon and Université Lyon 1, Lyon, France, and CNRS, UMR5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Villeurbanne, France
- CRCL Inserm U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
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Wang SA, Li HY, Hsu TI, Chen SH, Wu CJ, Chang WC, Hung JJ. Heat shock protein 90 stabilizes nucleolin to increase mRNA stability in mitosis. J Biol Chem 2011; 286:43816-43829. [PMID: 21998300 PMCID: PMC3243509 DOI: 10.1074/jbc.m111.310979] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Indexed: 11/06/2022] Open
Abstract
Most studies on heat shock protein 90 (Hsp90) have focused on the involvement of Hsp90 in the interphase, whereas the role of this protein in the nucleus during mitosis remains largely unclear. In this study, we found that the level of the acetylated form of Hsp90 decreased dramatically during mitosis, which indicates more chaperone activity during mitosis. We thus probed proteins that interacted with Hsp90 by liquid chromatography/mass spectrometry (LC/MS) and found that nucleolin was one of those interacting proteins during mitosis. The nucleolin level decreased upon geldanamycin treatment, and Hsp90 maintained the cyclin-dependent kinase 1 (CDK1) activity to phosphorylate nucleolin at Thr-641/707. Mutation of Thr-641/707 resulted in the destabilization of nucleolin in mitosis. We globally screened the level of mitotic mRNAs and found that 229 mRNAs decreased during mitosis in the presence of geldanamycin. Furthermore, a bioinformatics tool and an RNA immunoprecipitation assay found that 16 mRNAs, including cadherin and Bcl-xl, were stabilized through the recruitment of nucleolin to the 3'-untranslated regions (3'-UTRs) of those genes. Overall, strong correlations exist between the up-regulation of Hsp90, nucleolin, and the mRNAs related to tumorigenesis of the lung. Our findings thus indicate that nucleolin stabilized by Hsp90 contributes to the lung tumorigenesis by increasing the level of many tumor-related mRNAs during mitosis.
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Affiliation(s)
- Shao-An Wang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan
| | - Hao-Yi Li
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan
| | - Tsung-I Hsu
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, National Cheng-Kung University, Tainan 701, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, College of Science, National Cheng-Kung University, Tainan 701, Taiwan
| | - Chin-Jen Wu
- Department of Chemistry, College of Science, National Cheng-Kung University, Tainan 701, Taiwan
| | - Wen-Chang Chang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, National Cheng-Kung University, Tainan 701, Taiwan; Center for Infection Disease and Signal Transduction Research, National Cheng-Kung University, Tainan 701, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Jan-Jong Hung
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, National Cheng-Kung University, Tainan 701, Taiwan; Center for Infection Disease and Signal Transduction Research, National Cheng-Kung University, Tainan 701, Taiwan; Department of Pharmacology, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan.
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Cancio-Lonches C, Yocupicio-Monroy M, Sandoval-Jaime C, Galvan-Mendoza I, Ureña L, Vashist S, Goodfellow I, Salas-Benito J, Gutiérrez-Escolano AL. Nucleolin interacts with the feline calicivirus 3' untranslated region and the protease-polymerase NS6 and NS7 proteins, playing a role in virus replication. J Virol 2011; 85:8056-68. [PMID: 21680514 PMCID: PMC3147956 DOI: 10.1128/jvi.01878-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 05/29/2011] [Indexed: 12/19/2022] Open
Abstract
Cellular proteins play many important roles during the life cycle of all viruses. Specifically, host cell nucleic acid-binding proteins interact with viral components of positive-stranded RNA viruses and regulate viral translation, as well as RNA replication. Here, we report that nucleolin, a ubiquitous multifunctional nucleolar shuttling phosphoprotein, interacts with the Norwalk virus and feline calicivirus (FCV) genomic 3' untranslated regions (UTRs). Nucleolin can also form a complex in vitro with recombinant Norwalk virus NS6 and -7 (NS6/7) and can be copurified with the analogous protein from feline calicivirus (p76 or NS6/7) from infected feline kidney cells. Nucleolin RNA levels or protein were not modified during FCV infection; however, as a consequence of the infection, nucleolin was seen to relocalize from the nucleoli to the nucleoplasm, as well as to the perinuclear area where it colocalizes with the feline calicivirus NS6/7 protein. In addition, antibodies to nucleolin were able to precipitate viral RNA from feline calicivirus-infected cells, indicating a direct or indirect association of nucleolin with the viral RNA during virus replication. Small interfering RNA (siRNA)-mediated knockdown of nucleolin resulted in a reduction of the cytopathic effect and virus yield in CrFK cells. Taken together, these results demonstrate that nucleolin is a nucleolar component that interacts with viral RNA and NS6/7 and is required for feline calicivirus replication.
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Affiliation(s)
- Clotilde Cancio-Lonches
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Distrito Federal, México
| | - Carlos Sandoval-Jaime
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Iván Galvan-Mendoza
- Laboratorios Centrales, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Luis Ureña
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Surender Vashist
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Ian Goodfellow
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Juan Salas-Benito
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Ana Lorena Gutiérrez-Escolano
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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Ishimaru D, Zuraw L, Ramalingam S, Sengupta TK, Bandyopadhyay S, Reuben A, Fernandes DJ, Spicer EK. Mechanism of regulation of bcl-2 mRNA by nucleolin and A+U-rich element-binding factor 1 (AUF1). J Biol Chem 2010; 285:27182-27191. [PMID: 20571027 PMCID: PMC2930717 DOI: 10.1074/jbc.m109.098830] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/28/2010] [Indexed: 11/06/2022] Open
Abstract
The antiapoptotic Bcl-2 protein is overexpressed in a variety of cancers, particularly leukemias. In some cell types this is the result of enhanced stability of bcl-2 mRNA, which is controlled by elements in its 3'-untranslated region. Nucleolin is one of the proteins that binds to bcl-2 mRNA, thereby increasing its half-life. Here, we examined the site on the bcl-2 3'-untranslated region that is bound by nucleolin as well as the protein binding domains important for bcl-2 mRNA recognition. RNase footprinting and RNA fragment binding assays demonstrated that nucleolin binds to a 40-nucleotide region at the 5' end of the 136-nucleotide bcl-2 AU-rich element (ARE(bcl-2)). The first two RNA binding domains of nucleolin were sufficient for high affinity binding to ARE(bcl-2). In RNA decay assays, ARE(bcl-2) transcripts were protected from exosomal decay by the addition of nucleolin. AUF1 has been shown to recruit the exosome to mRNAs. When MV-4-11 cell extracts were immunodepleted of AUF1, the rate of decay of ARE(bcl-2) transcripts was reduced, indicating that nucleolin and AUF1 have opposing roles in bcl-2 mRNA turnover. When the function of nucleolin in MV-4-11 cells was impaired by treatment with the nucleolin-targeting aptamer AS1411, association of AUF1 with bcl-2 mRNA was increased. This suggests that the degradation of bcl-2 mRNA induced by AS1411 results from both interference with nucleolin protection of bcl-2 mRNA and recruitment of the exosome by AUF1. Based on our findings, we propose a model that illustrates the opposing roles of nucleolin and AUF1 in regulating bcl-2 mRNA stability.
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Affiliation(s)
- Daniella Ishimaru
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Lisa Zuraw
- Department of Chemistry, The Citadel, Charleston, South Carolina 29409
| | - Sivakumar Ramalingam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Tapas K Sengupta
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Sumita Bandyopadhyay
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Adrian Reuben
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Daniel J Fernandes
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Eleanor K Spicer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425.
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Miniard AC, Middleton LM, Budiman ME, Gerber CA, Driscoll DM. Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression. Nucleic Acids Res 2010; 38:4807-20. [PMID: 20385601 PMCID: PMC2919729 DOI: 10.1093/nar/gkq247] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 03/17/2010] [Accepted: 03/24/2010] [Indexed: 01/20/2023] Open
Abstract
Selenium, an essential trace element, is incorporated into selenoproteins as selenocysteine (Sec), the 21st amino acid. In order to synthesize selenoproteins, a translational reprogramming event must occur since Sec is encoded by the UGA stop codon. In mammals, the recoding of UGA as Sec depends on the selenocysteine insertion sequence (SECIS) element, a stem-loop structure in the 3' untranslated region of the transcript. The SECIS acts as a platform for RNA-binding proteins, which mediate or regulate the recoding mechanism. Using UV crosslinking, we identified a 110 kDa protein, which binds with high affinity to SECIS elements from a subset of selenoprotein mRNAs. The crosslinking activity was purified by RNA affinity chromatography and identified as nucleolin by mass spectrometry analysis. In vitro binding assays showed that purified nucleolin discriminates among SECIS elements in the absence of other factors. Based on siRNA experiments, nucleolin is required for the optimal expression of certain selenoproteins. There was a good correlation between the affinity of nucleolin for a SECIS and its effect on selenoprotein expression. As selenoprotein transcript levels and localization did not change in siRNA-treated cells, our results suggest that nucleolin selectively enhances the expression of a subset of selenoproteins at the translational level.
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Affiliation(s)
- Angela C. Miniard
- Department of Cell Biology, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, Agricultural Technical Institute, Ohio State University, Wooster, OH 44691 and Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Lisa M. Middleton
- Department of Cell Biology, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, Agricultural Technical Institute, Ohio State University, Wooster, OH 44691 and Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Michael E. Budiman
- Department of Cell Biology, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, Agricultural Technical Institute, Ohio State University, Wooster, OH 44691 and Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Carri A. Gerber
- Department of Cell Biology, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, Agricultural Technical Institute, Ohio State University, Wooster, OH 44691 and Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Donna M. Driscoll
- Department of Cell Biology, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, Agricultural Technical Institute, Ohio State University, Wooster, OH 44691 and Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
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Characterization of proteins associating with 5' terminus of PGHS-1 mRNA. Cell Mol Biol Lett 2010; 15:196-214. [PMID: 20112001 PMCID: PMC6275937 DOI: 10.2478/s11658-010-0005-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 01/15/2010] [Indexed: 01/21/2023] Open
Abstract
Induction of Prostaglandin Endoperoxide H Synthase-1 (PGHS-1) gene has been previously documented in a few studies during events such as development and cellular differentiation. However, molecular mechanisms governing the regulation of PGHS-1 gene expression and contributing to changes in protein levels are poorly understood. Using the MEG-01 cell model of PGHS-1 gene induction, our laboratory has previously demonstrated that the 5’UTR and the first two exons of PGHS-1 mRNA had a significant impact on decreasing the translational efficiency of a reporter gene and suggested that the presence of a secondary structure is required for conservation of this activity. This 5’end of PGHS-1 mRNA sequence has also been shown to associate with nucleolin protein. In the current study, we set to investigate the protein composition of the mRNP (messenger ribonucleoprotein) associating with the 5’end of PGHS-1 mRNA and to identify its protein members. RNA/protein binding assays coupled with LC-MS analysis identified serpin B1 and NF45 (nuclear factor 45) proteins as potential members of PGHS-1 mRNP complex. Immunoprecipitation experiments using MEG-01 protein extracts validated mass spectrometry data and confirmed binding of nucleolin, serpin B1, NF45 and NF90. The RNA fraction was extracted from immunoprecipitated mRNP complexes and association of RNA binding proteins, serpin B1, NF45 and NF90, to PGHS-1 mRNA target sequence was confirmed by RT-PCR. Together these data suggest that serpin B1, NF45 and NF90 associate with PGHS-1 mRNA and can potentially participate in the formation a single or a number of PGHS-1 ribonucleoprotein complexes, through nucleolin that possibly serves as a docking base for other protein complex members.
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Drygin D, Siddiqui-Jain A, O'Brien S, Schwaebe M, Lin A, Bliesath J, Ho CB, Proffitt C, Trent K, Whitten JP, Lim JKC, Von Hoff D, Anderes K, Rice WG. Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis. Cancer Res 2009; 69:7653-61. [PMID: 19738048 DOI: 10.1158/0008-5472.can-09-1304] [Citation(s) in RCA: 412] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hallmark deregulated signaling in cancer cells drives excessive ribosome biogenesis within the nucleolus, which elicits unbridled cell growth and proliferation. The rate-limiting step of ribosome biogenesis is synthesis of rRNA (building blocks of ribosomes) by RNA Polymerase I (Pol I). Numerous kinase pathways and products of proto-oncogenes can up-regulate Pol I, whereas tumor suppressor proteins can inhibit rRNA synthesis. In tumorigenesis, activating mutations in certain cancer-associated kinases and loss-of-function mutations in tumor suppressors lead to deregulated signaling that stimulates Pol I transcription with resultant increases in ribosome biogenesis, protein synthesis, cell growth, and proliferation. Certain anticancer therapeutics, such as cisplatin and 5-fluorouracil, reportedly exert, at least partially, their activity through disruption of ribosome biogenesis, yet many prime targets for anticancer drugs within the ribosome synthetic machinery of the nucleolus remain largely unexploited. Herein, we describe CX-3543, a small molecule nucleolus-targeting agent that selectively disrupts nucleolin/rDNA G-quadruplex complexes in the nucleolus, thereby inhibiting Pol I transcription and inducing apoptosis in cancer cells. CX-3543 is the first G-quadruplex interactive agent to enter human clinical trials, and it is currently under evaluation against carcinoid/neuroendocrine tumors in a phase II clinical trial.
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Affiliation(s)
- Denis Drygin
- Cylene Pharmaceuticals, Inc., San Diego, CA 92121, USA
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Yang C, Kim MS, Chakravarty D, Indig FE, Carrier F. Nucleolin Binds to the Proliferating Cell Nuclear Antigen and Inhibits Nucleotide Excision Repair. ACTA ACUST UNITED AC 2009; 1:130-137. [PMID: 20336191 DOI: 10.4255/mcpharmacol.09.17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nucleolin is over-expressed in malignant tumors and is used as a marker for cell proliferation and to reliably predict tumor growth rate. However, it is not known whether nucleolin expression is directly involved in or is a consequence of carcinogenesis. Using GST-pull down assays, we have determined that the recombinant nucleolin interacts with the Proliferating Cell Nuclear Antigen (PCNA). Co-immunoprecipitation assays indicate that the nucleolin-PCNA interaction also occurs in intact cells and this interaction increases after exposure of colon carcinoma RKO cells to UV radiation. Moreover, our data indicate that PCNA and nucleolin co-localize in some areas within the RKO cell nuclei. The functional significance of this interaction is evaluated on Nucleotide Excision Repair (NER) since PCNA is a primary mediator of this cellular function. Our data indicate that overexpression of nucleolin decreases the repair efficiency of UV damaged plasmid DNA in RKO cells. Co-transfection with PCNA can rescue this effect in vivo. Furthermore, reduction of nucleolin protein levels increases DNA repair efficiency in RKO and CHO cells and consequently increases cell survival. These data indicate that the direct interaction of nucleolin with PCNA inhibits NER efficiency of UV damaged DNA. This effect could contribute to carcinogenesis and aging in cells over-expressing nucleolin.
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Affiliation(s)
- Chonglin Yang
- Marlene and Stewart Greenebaum Cancer Center and Department of Radiation Oncology, University of Maryland at Baltimore School of Medicine, Baltimore, Maryland
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50
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Song BS, Lee SH, Kim SU, Kim JS, Park JS, Kim CH, Chang KT, Han YM, Lee KK, Lee DS, Koo DB. Nucleologenesis and embryonic genome activation are defective in interspecies cloned embryos between bovine ooplasm and rhesus monkey somatic cells. BMC DEVELOPMENTAL BIOLOGY 2009; 9:44. [PMID: 19635167 PMCID: PMC2734572 DOI: 10.1186/1471-213x-9-44] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 07/28/2009] [Indexed: 01/29/2023]
Abstract
Background Interspecies somatic cell nuclear transfer (iSCNT) has been proposed as a tool to address basic developmental questions and to improve the feasibility of cell therapy. However, the low efficiency of iSCNT embryonic development is a crucial problem when compared to in vitro fertilization (IVF) and intraspecies SCNT. Thus, we examined the effect of donor cell species on the early development of SCNT embryos after reconstruction with bovine ooplasm. Results No apparent difference in cleavage rate was found among IVF, monkey-bovine (MB)-iSCNT, and bovine-bovine (BB)-SCNT embryos. However, MB-iSCNT embryos failed to develop beyond the 8- or 16-cell stages and lacked expression of the genes involved in embryonic genome activation (EGA) at the 8-cell stage. From ultrastructural observations made during the peri-EGA period using transmission electron microscopy (TEM), we found that the nucleoli of MB-iSCNT embryos were morphologically abnormal or arrested at the primary stage of nucleologenesis. Consistent with the TEM analysis, nucleolar component proteins, such as upstream binding transcription factor, fibrillarin, nucleolin, and nucleophosmin, showed decreased expression and were structurally disorganized in MB-iSCNT embryos compared to IVF and BB-SCNT embryos, as revealed by real-time PCR and immunofluorescence confocal laser scanning microscopy, respectively. Conclusion The down-regulation of housekeeping and imprinting genes, abnormal nucleolar morphology, and aberrant patterns of nucleolar proteins during EGA resulted in developmental failure in MB-iSCNT embryos. These results provide insight into the unresolved problems of early embryonic development in iSCNT embryos.
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Affiliation(s)
- Bong-Seok Song
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahangno, Yuseong-gu, Daejeon, Republic of Korea.
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