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Paris EA, Bahr JM, Basu S, Barua A. Changes in Nucleolin Expression during Malignant Transformation Leading to Ovarian High-Grade Serous Carcinoma. Cancers (Basel) 2023; 15:cancers15030661. [PMID: 36765618 PMCID: PMC9913361 DOI: 10.3390/cancers15030661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE Ovarian high-grade serous carcinoma (HGSC) is a fatal malignancy of women. Alterations in the expression of nuclear proteins are early steps in malignant transformation; nucleolin is one such protein. Changes in nucleolin expression and circulatory levels during ovarian HGSC development are unknown. The study goal was to determine if tissue and circulatory levels of nucleolin change in response to malignant transformation leading to ovarian HGSC. METHODS Sera, ovaries, and BRCA+ fimbria from healthy subjects, and sera and tumor tissues from patients (n = 10 each), and healthy hens and hens with HGSC were examined in exploratory and prospective studies for nucleolin expression by immunohistochemistry, immunoblotting, gene expression, and immunoassay, and analyzed by analysis of variance (ANOVA). RESULTS Compared with normal, nucleolin expression was higher in patients and hens with ovarian HGSC and in women with a risk of HGSC (P < 0.05). Compared with normal (1400 + 105 pg/mL, n = 8), serum nucleolin levels were 1.5 and 1.7-fold higher in patients with early- (n = 5) and late-stage (n = 5) HGSC, respectively. Additionally, serum nucleolin levels increased significantly (P < 0.05) prior to the formation of detectable masses. CONCLUSION This pilot study concluded that tissue and serum levels of nucleolin increase in association with malignant changes in ovaries and fimbriae leading to ovarian HGSC.
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Affiliation(s)
- Elizabeth A. Paris
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Janice M. Bahr
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sanjib Basu
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Animesh Barua
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Obstetrics and Gynecology, Rush University Medical Center, Chicago, IL 60612, USA
- Correspondence:
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Deng W, Xu JY, Peng H, Huang CZ, Le XC, Zhang H. DNAzyme motor systems and logic gates facilitated by toehold exchange translators. Biosens Bioelectron 2022; 217:114704. [PMID: 36113301 DOI: 10.1016/j.bios.2022.114704] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
DNAzyme motor systems using gold nanoparticles (AuNPs) as scaffolds are useful for biosensing and in situ amplification because these systems are free of protein enzymes, isothermal, homogeneous, and sensitive. However, detecting different targets using the available DNAzyme motor techniques requires redesigns of the DNAzyme motor. We report here a toehold-exchange translator and the translator-mediated DNAzyme motor systems, which enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator is able to efficiently convert different nucleic acid targets into a specific output DNA that further activates the pre-silenced DNAzyme motor and consequently initiates the autonomous walking of the DNAzyme motor. Simply adjusting the target-binding region of the translator enables the same DNAzyme motor system to respond to various nucleic acid targets. The translator-mediated DNAzyme motor system is able to detect as low as 2.5 pM microRNA-10b and microRNA-21 under room temperature without the need of separation or washing. We further demonstrate the versatility of the translator and the DNAzyme motor by successful construction and operation of four logic gates, including OR, AND, NOR, and NAND logic gates. These logic gates use two microRNA targets as inputs and generate amplified fluorescence signals from the operation of the same DNAzyme motor. Incorporation of the toehold-exchange translator into the DNAzyme motor technology improves the biosensing applications of DNA motors to diverse nucleic acid targets.
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Affiliation(s)
- Wenchan Deng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Yang Xu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hanyong Peng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Cheng Zhi Huang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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Ying J, Pan R, Tang Z, Zhu J, Ren P, Lou Y, Zhang E, Huang D, Hu P, Li D, Bao Q, Li P. Downregulation of NCL attenuates tumor formation and growth in HeLa cells by targeting the PI3K/AKT pathway. Cancer Med 2022; 11:1454-1464. [PMID: 35128835 PMCID: PMC8921942 DOI: 10.1002/cam4.4569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/29/2021] [Accepted: 01/03/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Nucleolin (NCL, C23) is a multifunctional phosphoprotein that plays a vital role in modulating the survival, proliferationand apoptosis of cancer cells. However, the effects of NCL on cervical cancer and the underlying mechanisms behind this are poorly understood. METHODS Lentiviral transfection technology was used to construct NCL knockdown cell lines. MTT, colony formation assays, and tumorigenic assays in vivo were performed to observe cell proliferation. HOECHST 33342 staining, flow cytometry, and caspase activity assay were used to test cell apoptosis. RNA-Seq, Western blotting, and RT-PCR were conducted to investigate the specific molecular mechanism. RESULTS NCL knockdown inhibited cell proliferation and promoted apoptosis both in vivo and in vitro. Mechanistic studies revealed that NCL knockdown inhibited the PI3K/AKT pathway by upregulating FGF, ITGA, TNXB, VEGF, Caspase 3, and Bax, as well as by downregulating AKT, GNB4, CDK6, IL6R, LAMA, PDGFD, PPP2RSA and BCL-2. In addition, the expression levels of apoptosis-related genes after using a PI3K inhibitor LY294002 were consistent with shRNA studies, while treatment with a 740Y-P agonist showed the opposite effect. CONCLUSIONS Our findings indicate that downregulation of NCL may be a novel treatment strategy forcervical cancer.
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Affiliation(s)
- Jun Ying
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
- School of Forensic MedicineXi'an Jiaotong UniversityXi'anChina
| | - Ruowang Pan
- No. 906 Hospital of Joint Logistic Support Force of PLAWenzhouChina
| | - Zhouhao Tang
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
- Wenzhou Medical University Renji CollegeWenzhouChina
| | - Jiayin Zhu
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
- Laboratory Animal CenterWenzhou Medical UniversityWenzhouChina
| | - Ping Ren
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
| | - Yang Lou
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
- Wenzhou Medical University Renji CollegeWenzhouChina
| | - Enyong Zhang
- No. 906 Hospital of Joint Logistic Support Force of PLAWenzhouChina
| | - Dadao Huang
- No. 906 Hospital of Joint Logistic Support Force of PLAWenzhouChina
| | - Penghong Hu
- No. 906 Hospital of Joint Logistic Support Force of PLAWenzhouChina
| | - Dong Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
| | - Qiyu Bao
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
| | - Peizhen Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical InformaticsWenzhou Medical UniversityWenzhouChina
- Wenzhou Medical University Renji CollegeWenzhouChina
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4
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Ghosh A, Pandey SP, Ansari AH, Sundar J, Singh P, Khan Y, Ekka MK, Chakraborty D, Maiti S. Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA. Nucleic Acids Res 2022; 50:378-396. [PMID: 34761272 PMCID: PMC8754661 DOI: 10.1093/nar/gkab1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3' region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3' region of MALAT1 orchestrating AS.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
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Shefer K, Boulos A, Gotea V, Arafat M, Ben Chaim Y, Muharram A, Isaac S, Eden A, Sperling J, Elnitski L, Sperling R. A novel role for nucleolin in splice site selection. RNA Biol 2021; 19:333-352. [PMID: 35220879 PMCID: PMC8890436 DOI: 10.1080/15476286.2021.2020455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/10/2021] [Indexed: 01/12/2023] Open
Abstract
Latent 5' splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and specifically with initiator-tRNA in the nucleus, but not in the cytoplasm. Next, we show the association of ini-tRNA and NCL with pre-mRNA. We further show that recovery of suppression of latent splicing by initiator-tRNA complementation is NCL dependent. Finally, upon nucleolin knockdown we show activation of latent splicing in hundreds of coding transcripts having important cellular functions. We thus propose nucleolin, a component of the endogenous spliceosome, through its direct binding to initiator-tRNA and its effect on latent splicing, as the first protein of a nuclear quality control mechanism regulating splice site selection to protect cells from latent splicing that can generate defective mRNAs.
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Affiliation(s)
- Kinneret Shefer
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Ayub Boulos
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Yair Ben Chaim
- Department of Natural Sciences, The Open University, RaananaIsrael
| | - Aya Muharram
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Amir Eden
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, RehovotIsrael
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
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Chalabi-Dchar M, Cruz E, Mertani HC, Diaz JJ, Courty J, Cascone I, Bouvet P. Nucleolin Aptamer N6L Reprograms the Translational Machinery and Acts Synergistically with mTORi to Inhibit Pancreatic Cancer Proliferation. Cancers (Basel) 2021; 13:cancers13194957. [PMID: 34638443 PMCID: PMC8508287 DOI: 10.3390/cancers13194957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Pancreatic cancer is an aggressive disease characterized by its invasiveness, rapid progression, and resistance to conventional therapy. There is a need to identify new molecules to improve current therapies. The aim of this study was to analyze how the pancreatic cancer cells react to the treatment with an inhibitor of nucleolin, N6L. To this end, we analyzed how the translation was affected in the cells during the treatment. We discovered that in response to N6L, a signaling pathway called the mTOR pathway was activated and was involved in the activation of translation of a subset of mRNA that could be involved in the resistance of the cells to the treatment. Indeed, we showed that the combined action of inhibitors of the mTOR pathway with N6L synergistically inhibited the cancer cells’ proliferation. We propose that this new combination of molecules could be a novel therapeutic option for pancreatic cancer. Abstract We previously showed that N6L, a pseudopeptide that targets nucleolin, impairs pancreatic ductal adenocarcinoma (PDAC) growth and normalizes tumor vessels in animal models. In this study, we analyzed the translatome of PDAC cells treated with N6L to identify the pathways that were either repressed or activated. We observed a strong decrease in global protein synthesis. However, about 6% of the mRNAs were enriched in the polysomes. We identified a 5′TOP motif in many of these mRNAs and demonstrated that a chimeric RNA bearing a 5‘TOP motif was up-regulated by N6L. We demonstrated that N6L activates the mTOR pathway, which is required for the translation of these mRNAs. An inhibitory synergistic effect in PDAC cell lines, including patient-derived xenografts and tumor-derived organoids, was observed when N6L was combined with mTOR inhibitors. In conclusion, N6L reduces pancreatic cells proliferation, which then undergoes translational reprogramming through activation of the mTOR pathway. N6L and mTOR inhibitors act synergistically to inhibit the proliferation of PDAC and human PDX cell lines. This combotherapy of N6L and mTOR inhibitors could constitute a promising alternative to treat pancreatic cancer.
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Affiliation(s)
- Mounira Chalabi-Dchar
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.C.-D.); (E.C.); (H.C.M.); (J.-J.D.)
| | - Elisabeth Cruz
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.C.-D.); (E.C.); (H.C.M.); (J.-J.D.)
| | - Hichem C. Mertani
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.C.-D.); (E.C.); (H.C.M.); (J.-J.D.)
| | - Jean-Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.C.-D.); (E.C.); (H.C.M.); (J.-J.D.)
| | - José Courty
- INSERM, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil, F-94010 Créteil, France; (J.C.); (I.C.)
| | - Ilaria Cascone
- INSERM, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil, F-94010 Créteil, France; (J.C.); (I.C.)
| | - Philippe Bouvet
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.C.-D.); (E.C.); (H.C.M.); (J.-J.D.)
- Ecole Normale Supérieure de Lyon, Université de Lyon 1, F-69007 Lyon, France
- Correspondence:
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Noto D, Giammanco A, Spina R, Fayer F, Cefalù AB, Averna MR. DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis. PLoS One 2021; 16:e0247402. [PMID: 33661949 PMCID: PMC7932541 DOI: 10.1371/journal.pone.0247402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/06/2021] [Indexed: 11/19/2022] Open
Abstract
SREBP1 and 2, are cholesterol sensors able to modulate cholesterol-related gene expression responses. SREBPs binding sites are characterized by the presence of multiple target sequences as SRE, NFY and SP1, that can be arranged differently in different genes, so that it is not easy to identify the binding site on the basis of direct DNA sequence analysis. This paper presents a complete workflow based on a one-dimensional Convolutional Neural Network (CNN) model able to detect putative SREBPs binding sites irrespective of target elements arrangements. The strategy is based on the recognition of SRE linked (less than 250 bp) to NFY sequences according to chromosomal localization derived from TF Immunoprecipitation (TF ChIP) experiments. The CNN is trained with several 100 bp sequences containing both SRE and NF-Y. Once trained, the model is used to predict the presence of SRE-NFY in the first 500 bp of all the known gene promoters. Finally, genes are grouped according to biological process and the processes enriched in genes containing SRE-NFY in their promoters are analyzed in details. This workflow allowed to identify biological processes enriched in SRE containing genes not directly linked to cholesterol metabolism and possible novel DNA patterns able to fill in for missing classical SRE sequences.
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Affiliation(s)
- Davide Noto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
- * E-mail:
| | - Antonina Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Rossella Spina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Francesca Fayer
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Angelo B. Cefalù
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Maurizio R. Averna
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
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Sonoda Y, Kano F, Murata M. Applications of cell resealing to reconstitute microRNA loading to extracellular vesicles. Sci Rep 2021; 11:2900. [PMID: 33536479 PMCID: PMC7859222 DOI: 10.1038/s41598-021-82452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/20/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are cargo carried by extracellular vesicles (EVs) and are associated with cell-cell interactions. The response to the cellular environment, such as disease states, genetic/metabolic changes, or differences in cell type, highly regulates cargo sorting to EVs. However, morphological features during EV formation and secretion involving miRNA loading are unknown. This study developed a new method of EV loading using cell resealing and reconstituted the elementary miRNA-loading processes. Morphology, secretory response, and cellular uptake ability of EVs obtained from intact and resealed HeLa cells were comparable. Exogenously added soluble factors were introduced into multivesicular endosomes (MVEs) and their subsequent secretion to the extracellular region occurred in resealed HeLa cells. In addition, miRNA transport to MVEs and miRNA encapsulation to EVs followed a distinct pathway regulated by RNA-binding proteins, such as Argonaute and Y-box binding protein 1, depending on miRNA types. Our cell-resealing system can analyze disease-specific EVs derived from disease model cells, where pathological cytosol is introduced into cells. Thus, EV formation in resealed cells can be used not only to create a reconstitution system to give mechanistic insight into EV encapsulation but also for applications such as loading various molecules into EVs and identifying disease-specific EV markers.
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Affiliation(s)
- Yuki Sonoda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Fumi Kano
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Masayuki Murata
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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Single-cell multiomics: technologies and data analysis methods. Exp Mol Med 2020; 52:1428-1442. [PMID: 32929225 PMCID: PMC8080692 DOI: 10.1038/s12276-020-0420-2] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/14/2020] [Accepted: 02/28/2020] [Indexed: 01/31/2023] Open
Abstract
Advances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk multiomics analyses, such as multidimensional genomic and proteogenomic analyses, have proven beneficial for obtaining a comprehensive understanding of cellular events. This benefit has facilitated the development of single-cell multiomics analysis, which enables cell type-specific gene regulation to be examined. The cardinal features of single-cell multiomics analysis include (1) technologies for single-cell isolation, barcoding, and sequencing to measure multiple types of molecules from individual cells and (2) the integrative analysis of molecules to characterize cell types and their functions regarding pathophysiological processes based on molecular signatures. Here, we summarize the technologies for single-cell multiomics analyses (mRNA-genome, mRNA-DNA methylation, mRNA-chromatin accessibility, and mRNA-protein) as well as the methods for the integrative analysis of single-cell multiomics data. The expansion of single-cell profiling technologies will provide unprecedented insights into the molecular mechanisms inherent in disease. Novel technologies known collectively as ‘single-cell multiomics’ enable systematic, high-resolution profiling of DNA, RNA and proteins in individual cells. This provides valuable data about gene regulation and molecular populations, and cellular processes during disease development and progression. Daehee Hwang and co-workers at Seoul National University, Seoul, South Korea, reviewed existing single-cell multiomics technologies and highlighted ways to integrate the data generated. Analytical features of multiomics allow scientists to isolate, sequence and label (or ‘barcode’) multiple molecules in single cells. Different sequencing techniques can be used for different purposes, such as exploring gene mutation coverage or measuring RNA transcripts. Combining these sequencing data will help identify links between significant features during disease.
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Fang L, Wang KK, Huang Q, Cheng F, Huang F, Liu WW. Nucleolin Mediates LPS-induced Expression of Inflammatory Mediators and Activation of Signaling Pathways. Curr Med Sci 2020; 40:646-653. [PMID: 32862374 DOI: 10.1007/s11596-020-2229-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
In this study, we investigated the effects of nucleolin on lipopolysaccharide (LPS)-induced activation of MAPK and NF-KappaB (NF-κB) signaling pathways and secretion of TNF-α, IL-1β and HMGB1 in THP-1 monocytes. Immunofluorescence assay and Western blotting were used to identify the nucleolin expression in cell membrane, cytoplasm and nucleus of THP-1 monocytes. Inactivation of nucleolin was induced by neutralizing antibody against nucleolin. THP-1 monocytes were pretreated with anti-nucleolin antibody for 1 h prior to LPS challenge. The irrelevant IgG group was used as control. Secretion of inflammatory mediators (TNF-α, IL-1β and HMGB1) and activation of MAPK and NF-κB/I-κB signaling pathways were examined to assess the effects of nucleolin on LPS-mediated inflammatory response. Nucleolin existed in cell membrane, cytoplasm and nucleus of THP-1 monocytes. Pretreatment of anti-nucleolin antibody significantly inhibited the LPS-induced secretion of TNF-α, IL-1β and HMGB1. P38, JNK, ERK and NF-κB subunit p65 inhibitors could significantly inhibit the secretion of IL-1β, TNF-α and HMGB1 induced by LPS. Moreover, the phosphorylation of p38, JNK, ERK and p65 (or nuclear translocation of p65) was significantly increased after LPS challenge. In contrast, pretreatment of anti-nucleolin antibody could significantly inhibit the LPS-induced phosphorylation of p38, JNK, ERK and p65 (or nuclear translocation of p65). However, the irrelevant IgG, as a negative control, had no effect on LPS-induced secretion of TNF-α and IL-1β and phosphorylation of p38, JNK, ERK and p65 (or nuclear translocation of p65). We demonstrated that nucleolin mediated the LPS-induced activation of MAPK and NF-κB signaling pathways, and regulated the secretion of inflammatory mediators (TNF-α, IL-1β and HMGB1).
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Affiliation(s)
- Li Fang
- Department of Cardiology, the First Hospital of Changsha, Changsha, 410008, China.
| | - Kang-Kai Wang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, 410008, China
| | - Qing Huang
- Department of Cardiology, the First Hospital of Changsha, Changsha, 410008, China
| | - Feng Cheng
- Department of Cardiology, the First Hospital of Changsha, Changsha, 410008, China
| | - Fang Huang
- Department of Cardiology, the First Hospital of Changsha, Changsha, 410008, China
| | - Wei-Wei Liu
- Department of Cardiology, the First Hospital of Changsha, Changsha, 410008, China
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11
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Kabirian-Dehkordi S, Chalabi-Dchar M, Mertani HC, Le Guellec D, Verrier B, Diaz JJ, Mehrgardi MA, Bouvet P. AS1411-conjugated gold nanoparticles affect cell proliferation through a mechanism that seems independent of nucleolin. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2019; 21:102060. [PMID: 31336175 DOI: 10.1016/j.nano.2019.102060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/11/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
G-rich oligonucleotide, AS1411, has been shown to interact with nucleolin and to inhibit cancer cell proliferation and tumor growth. This antiproliferative action is increased when AS1411 is conjugated to different types of nanoparticles. However, the molecular mechanisms are not known. In this work, we show in several cell lines that optimized AS1411-conjugated gold nanoparticles (GNS-AS1411) inhibit nucleolin expression at the RNA and protein levels. We observed an alteration of the nucleolar structure with a decrease of ribosomal RNA accumulation comparable to what is observed upon nucleolin knock down. However, the expression of genes involved in cell cycle and the cell cycle blockage by GNS-AS1411 are not regulated in the same way as that in cells where nucleolin has been knocked down. These data suggest that the anti-proliferative activity of GNS-AS1411 is not the only consequence of nucleolin targeting and down-regulation.
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Affiliation(s)
- Samaneh Kabirian-Dehkordi
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre, Léon Bérard, Lyon, France; Department of chemistry, University of Isfahan, Isfahan, Iran
| | - 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
| | - Hichem C Mertani
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre, Léon Bérard, Lyon, France
| | - Dominique Le Guellec
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, Université Claude Bernard Lyon 1, Centre, National de la Recherche Scientifique (CNRS), Lyon, France
| | - Bernard Verrier
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, Université Claude Bernard Lyon 1, Centre, National de la Recherche Scientifique (CNRS), Lyon, France
| | - Jean-Jacques Diaz
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre, Léon Bérard, 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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12
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Singh S, Kumar M, Kumar S, Sen S, Upadhyay P, Bhattacharjee S, M N, Tomar VS, Roy S, Dutt A, Kundu TK. The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis. J Biol Chem 2019; 294:14081-14095. [PMID: 31366730 PMCID: PMC6755804 DOI: 10.1074/jbc.ra118.007265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 06/21/2019] [Indexed: 02/05/2023] Open
Abstract
TP53 is the most frequently mutated tumor suppressor gene in many cancers, yet biochemical characterization of several of its reported mutations with probable biological significance have not been accomplished enough. Specifically, missense mutations in TP53 can contribute to tumorigenesis through gain-of-function of biochemical and biological properties that stimulate tumor growth. Here, we identified a relatively rare mutation leading to a proline to leucine substitution (P152L) in TP53 at the very end of its DNA-binding domain (DBD) in a sample from an Indian oral cancer patient. Although the P152Lp53 DBD alone bound to DNA, the full-length protein completely lacked binding ability at its cognate DNA motifs. Interestingly, P152Lp53 could efficiently tetramerize, and the mutation had only a limited impact on the structure and stability of full-length p53. Significantly, when we expressed this variant in a TP53-null cell line, it induced cell motility, proliferation, and invasion compared with a vector-only control. Also, enhanced tumorigenic potential was observed when P152Lp53-expressing cells were xenografted into nude mice. Investigating the effects of P152Lp53 expression on cellular pathways, we found that it is associated with up-regulation of several pathways, including cell-cell and cell-extracellular matrix signaling, epidermal growth factor receptor signaling, and Rho-GTPase signaling, commonly active in tumorigenesis and metastasis. Taken together, our findings provide a detailed account of the biochemical and cellular alterations associated with the cancer-associated P152Lp53 variant and establish it as a gain-of-function TP53 variant.
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Affiliation(s)
- Siddharth Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | | | - Shrinka Sen
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Sayan Bhattacharjee
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Naveen M
- BioCOS Life Sciences Pvt. Ltd., Bengaluru, India
| | - Vivek Singh Tomar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Amit Dutt
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
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13
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Nguyen Van Long F, Lardy-Cleaud A, Bray S, Chabaud S, Dubois T, Diot A, Jordan LB, Thompson AM, Bourdon JC, Perol D, Bouvet P, Diaz JJ, Marcel V. Druggable Nucleolin Identifies Breast Tumours Associated with Poor Prognosis That Exhibit Different Biological Processes. Cancers (Basel) 2018; 10:cancers10100390. [PMID: 30360377 PMCID: PMC6210205 DOI: 10.3390/cancers10100390] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/12/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Nucleolin (NCL) is a multifunctional protein with oncogenic properties. Anti-NCL drugs show strong cytotoxic effects, including in triple-negative breast cancer (TNBC) models, and are currently being evaluated in phase II clinical trials. However, few studies have investigated the clinical value of NCL and whether NCL stratified cancer patients. Here, we have investigated for the first time the association of NCL with clinical characteristics in breast cancers independently of the different subtypes. Methods: Using two independent series (n = 216; n = 661), we evaluated the prognostic value of NCL in non-metastatic breast cancers using univariate and/or multivariate Cox-regression analyses. Results: We reported that NCL mRNA expression levels are markers of poor survivals independently of tumour size and lymph node invasion status (n = 216). In addition, an association of NCL expression levels with poor survival was observed in TNBC (n = 40, overall survival (OS) p = 0.0287, disease-free survival (DFS) p = 0.0194). Transcriptomic analyses issued from The Cancer Genome Atlas (TCGA) database (n = 661) revealed that breast tumours expressing either low or high NCL mRNA expression levels exhibit different gene expression profiles. These data suggest that tumours expressing high NCL mRNA levels are different from those expressing low NCL mRNA levels. Conclusions: NCL is an independent marker of prognosis in breast cancers. We anticipated that anti-NCL is a promising therapeutic strategy that could rapidly be evaluated in high NCL-expressing tumours to improve breast cancer management.
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Affiliation(s)
- Flora Nguyen Van Long
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, 69373 Lyon, France; (F.N.V.L.); (P.B.)
| | - Audrey Lardy-Cleaud
- Department of Clinical Research, Léon Bérard Cancer Centre, 28 rue Laennec, 69008 Lyon, France; (A.L.-C.); (S.C.); (D.P.)
| | - Susan Bray
- Tayside Tissue Bank, Ninewells Hospital and Medical School, NHS Tayside, Dundee DD1 9SY, Scotland, UK;
| | - Sylvie Chabaud
- Department of Clinical Research, Léon Bérard Cancer Centre, 28 rue Laennec, 69008 Lyon, France; (A.L.-C.); (S.C.); (D.P.)
| | - Thierry Dubois
- Breast Cancer Biology Group, Translational Research Department, PSL Research University, Institut Curie, 26 rue d’Ulm, 75005 Paris, France;
| | - Alexandra Diot
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK; (A.D.); (A.M.T.); (J.-C.B.)
| | - Lee B. Jordan
- Department of Pathology, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Alastair M. Thompson
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK; (A.D.); (A.M.T.); (J.-C.B.)
- Olga Keith Wiess Chair of Surgery, Dan L. Duncan Breast Center, Division of Surgical Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Christophe Bourdon
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK; (A.D.); (A.M.T.); (J.-C.B.)
| | - David Perol
- Department of Clinical Research, Léon Bérard Cancer Centre, 28 rue Laennec, 69008 Lyon, France; (A.L.-C.); (S.C.); (D.P.)
| | - Philippe Bouvet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, 69373 Lyon, France; (F.N.V.L.); (P.B.)
- Ecole Normale Supérieure de Lyon, Université de Lyon, CEDEX 07, 69342 Lyon, France
| | - Jean-Jacques Diaz
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, 69373 Lyon, France; (F.N.V.L.); (P.B.)
- Correspondence: (J.-J.D.); (V.M.); Tel.: +33-42655-2819 (J.-J.D.); +33-42655-6745 (V.M.)
| | - Virginie Marcel
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, 69373 Lyon, France; (F.N.V.L.); (P.B.)
- Correspondence: (J.-J.D.); (V.M.); Tel.: +33-42655-2819 (J.-J.D.); +33-42655-6745 (V.M.)
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14
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Xu W, Yin P, Dai M. Super-resolution Geometric Barcoding for Multiplexed miRNA Profiling. Angew Chem Int Ed Engl 2018; 57:14075-14079. [PMID: 30182521 DOI: 10.1002/anie.201807956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/21/2018] [Indexed: 01/07/2023]
Abstract
MicroRNA (miRNA) expression profiles hold promise as biomarkers for diagnostics and prognosis of complex diseases. Herein, we report a super-resolution fluorescence imaging-based digital profiling method for specific, sensitive, and multiplexed detection of miRNAs. In particular, we applied the DNA-PAINT (point accumulation for imaging in nanoscale topography) method to implement a super-resolution geometric barcoding scheme for multiplexed single-molecule miRNA capture and digital counting. Using synthetic DNA nanostructures as a programmable miRNA capture nano-array, we demonstrated high-specificity (single nucleotide mismatch discrimination), multiplexed (8-plex, 2 panels), and sensitive measurements on synthetic miRNA samples, as well as applied one 8-plex panel to measure endogenous miRNAs levels in total RNA extract from HeLa cells.
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Affiliation(s)
- Weidong Xu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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15
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Xu W, Yin P, Dai M. Super‐resolution Geometric Barcoding for Multiplexed miRNA Profiling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Weidong Xu
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
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16
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Das S, Reddy MA, Senapati P, Stapleton K, Lanting L, Wang M, Amaram V, Ganguly R, Zhang L, Devaraj S, Schones DE, Natarajan R. Diabetes Mellitus-Induced Long Noncoding RNA Dnm3os Regulates Macrophage Functions and Inflammation via Nuclear Mechanisms. Arterioscler Thromb Vasc Biol 2018; 38:1806-1820. [PMID: 29930005 PMCID: PMC6202204 DOI: 10.1161/atvbaha.117.310663] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Objective- Macrophages play key roles in inflammation and diabetic vascular complications. Emerging evidence implicates long noncoding RNAs in inflammation, but their role in macrophage dysfunction associated with inflammatory diabetic complications is unclear and was therefore investigated in this study. Approach and Results- RNA-sequencing and real-time quantitative PCR demonstrated that a long noncoding RNA Dnm3os (dynamin 3 opposite strand) is upregulated in bone marrow-derived macrophages from type 2 diabetic db/db mice, diet-induced insulin-resistant mice, and diabetic ApoE-/- mice, as well as in monocytes from type 2 diabetic patients relative to controls. Diabetic conditions (high glucose and palmitic acid) induced Dnm3os in mouse and human macrophages. Promoter reporter analysis and chromatin immunoprecipitation assays demonstrated that diabetic conditions induce Dnm3os via NF-κB activation. RNA fluorescence in situ hybridization and real-time quantitative PCRs of subcellular fractions demonstrated nuclear localization and chromatin enrichment of Dnm3os in macrophages. Stable overexpression of Dnm3os in macrophages altered global histone modifications and upregulated inflammation and immune response genes and phagocytosis. Conversely, RNAi-mediated knockdown of Dnm3os attenuated these responses. RNA pull-down assays with macrophage nuclear lysates identified nucleolin and ILF-2 (interleukin enhancer-binding factor 2) as protein binding partners of Dnm3os, which was further confirmed by RNA fluorescence in situ hybridization immunofluorescence. Furthermore, nucleolin levels were decreased in diabetic conditions, and its knockdown enhanced Dnm3os-induced inflammatory gene expression and histone H3K9-acetylation at their promoters. Conclusions- These results demonstrate novel mechanisms involving upregulation of long noncoding RNA Dnm3os, disruption of its interaction with nucleolin, and epigenetic modifications at target genes that promote macrophage inflammatory phenotype in diabetes mellitus. The data could lead to long noncoding RNA-based therapies for inflammatory diabetes mellitus complications.
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MESH Headings
- Animals
- Case-Control Studies
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 1/chemically induced
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Epigenesis, Genetic
- Female
- Humans
- Inflammation/genetics
- Inflammation/metabolism
- Inflammation Mediators/metabolism
- Macrophage Activation
- Macrophages/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Phagocytosis
- Phenotype
- Phosphoproteins/metabolism
- Protein Binding
- RAW 264.7 Cells
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Binding Proteins/metabolism
- Signal Transduction
- Streptozocin
- Up-Regulation
- Nucleolin
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Affiliation(s)
- Sadhan Das
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Marpadga A Reddy
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Kenneth Stapleton
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Vishnu Amaram
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Rituparna Ganguly
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Lingxiao Zhang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Sridevi Devaraj
- Pathology and Immunology, Texas Children’s Hospital, Houston, Houston, TX
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, United States
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17
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Massimino ML, Simonato M, Spolaore B, Franchin C, Arrigoni G, Marin O, Monturiol-Gross L, Fernández J, Lomonte B, Tonello F. Cell surface nucleolin interacts with and internalizes Bothrops asper Lys49 phospholipase A 2 and mediates its toxic activity. Sci Rep 2018; 8:10619. [PMID: 30006575 PMCID: PMC6045611 DOI: 10.1038/s41598-018-28846-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 06/20/2018] [Indexed: 01/01/2023] Open
Abstract
Phospholipases A2 are a major component of snake venoms. Some of them cause severe muscle necrosis through an unknown mechanism. Phospholipid hydrolysis is a possible explanation of their toxic action, but catalytic and toxic properties of PLA2s are not directly connected. In addition, viperid venoms contain PLA2-like proteins, which are very toxic even if they lack catalytic activity due to a critical mutation in position 49. In this work, the PLA2-like Bothrops asper myotoxin-II, conjugated with the fluorophore TAMRA, was found to be internalized in mouse myotubes, and in RAW264.7 cells. Through experiments of protein fishing and mass spectrometry analysis, using biotinylated Mt-II as bait, we found fifteen proteins interacting with the toxin and among them nucleolin, a nucleolar protein present also on cell surface. By means of confocal microscopy, Mt-II and nucleolin were shown to colocalise, at 4 °C, on cell membrane where they form Congo-red sensitive assemblies, while at 37 °C, 20 minutes after the intoxication, they colocalise in intracellular spots going from plasmatic membrane to paranuclear and nuclear area. Finally, nucleolin antagonists were found to inhibit the Mt-II internalization and toxic activity and were used to identify the nucleolin regions involved in the interaction with the toxin.
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Affiliation(s)
| | - Morena Simonato
- Istituto di Neuroscienze, CNR, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Barbara Spolaore
- Dipartimento di Scienze del Farmaco, Università di Padova, Via F. Marzolo, 5, 35131, Padova, Italy
| | - Cinzia Franchin
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
- Centro di Proteomica, Università di Padova e Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129, Padova, Italy
| | - Giorgio Arrigoni
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
- Centro di Proteomica, Università di Padova e Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129, Padova, Italy
| | - Oriano Marin
- Dipartimento di Scienze Biomediche, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Laura Monturiol-Gross
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Julián Fernández
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 11501, San José, Costa Rica
| | - Fiorella Tonello
- Istituto di Neuroscienze, CNR, Via Ugo Bassi 58/B, 35131, Padova, Italy.
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18
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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: 48] [Impact Index Per Article: 6.9] [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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