1
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Kudaibergenova Z, Pany S, Placheril E, Jeremic AM. UTRs and Ago-2/miR-335 Complex Restricts Amylin Translation in Insulinoma and Human Pancreatic β-Cells. Int J Mol Sci 2024; 25:9614. [PMID: 39273561 PMCID: PMC11394793 DOI: 10.3390/ijms25179614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Amylin promoter and transcriptional factors are well-established, inducible factors in the production of the main amyloidogenic pancreatic hormone, human islet amyloid peptide (hIAPP) or amylin. However, posttranscriptional mechanisms driving hIAPP expression in pancreas remain enigmatic, and hence were explored here. The translational assay revealed that both 5' and 3' untranslated regions (UTRs) of hIAPP restricted expression of the luciferase constructs only in constructs driven by the hIAPP promoter. Bioinformatics analysis revealed several putative seed sequences for a dozen micro RNAs (miRNAs) in hIAPP's 3' UTR. miR-182, miR-335, and miR-495 were the most downregulated miRNAs in stressed human islets exposed to endoplasmic reticulum (ER) or metabolic stressors, thapsigargin (TG) or high glucose (HG). Correspondingly, miR-335 mimics alone or in combination with miR-495 and miR-182 mimics significantly and potently (>3-fold) reduced hIAPP protein expression in HG-treated cultured human islets. siRNA-mediated silencing of Ago2 but not Ago1 significantly stimulated hIAPP expression and secretion from transfected, HG-treated human islets. Conversely, ectopic expression of Ago2 in hIAPP-expressing RIN-m5F cell line driven by CMV promoter reduced hIAPP intracellular protein levels. Collectively, the results point to a novel and synergistic role for hIAPP promoter, 5/3' UTRs and Ago-2/miR-335 complex in post-transcriptional regulation of hIAPP gene expression in normal and metabolically active β-cells.
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Affiliation(s)
| | | | | | - Aleksandar M. Jeremic
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA; (Z.K.); (S.P.); (E.P.)
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2
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Zhang T, Sun X, Chen X, Chen W, Tang H, Li CY. Intelligent near-infrared light-activatable DNA machine with DNA wire nano-scaffold-integrated fast domino-like driving amplification for high-performance imaging in live biological samples. Biosens Bioelectron 2024; 259:116412. [PMID: 38795498 DOI: 10.1016/j.bios.2024.116412] [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: 03/12/2024] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
While there is significant potential for DNA machine-built enzyme-free fluorescence biosensors in the imaging analysis of live biological samples, they persist certain shortcomings. These encompass a deficiency of signal enrichment within a singular interface, uncontrolled premature activation during bio-delivery, and a slow reaction rate due to free nucleic acid collisions. In this contribution, we are committed to resolving the above challenges. Firstly, a single-interface-integrated domino-like driving amplification is constructed. In this conception, a specific target acts as the domino promotor (namely the energy source), initiating a cascading chain reaction that grafts onto a singular interface. Next, an 808 nm near-infrared (NIR) light-excited up-converting luminescence-induced light-activatable biosensing technique is introduced. By locking the target-specific identification segment with a photo-cleavage connector, the up-converted ultraviolet emission can activate target binding in a completely controlled manner. Moreover, a fast reaction rate is achieved by confining nucleic acid collisions within the surface of a DNA wire nano-scaffold, leading to a substantial enhancement in local contact concentration (30.8-fold increase, alongside a 15 times elevation in rate). When a non-coding microRNA (miRNA-221) is positioned as the model low-abundance target for proof-of-concept validation, our intelligent DNA machine demonstrates ultra-high sensitivity (with a limit of detection down to 62.65 fM) and good specificity for this hepatic malignant tumor-associated biomarker in solution detection. Going further, it is worth highlighting that the biosensing system can be employed to carry out high-performance imaging analysis in live bio-samples (ranging from the cellular level to the nude mouse body), thereby propelling the field of DNA machines in disease diagnosis.
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Affiliation(s)
- Tiantian Zhang
- School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Xiaoxue Chen
- School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Weilin Chen
- School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Hongwu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Cheng-Yu Li
- School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
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3
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Xin MK, Sun X, Tang HW, Li CY. Near-Infrared Light-Powered and DNA Nanocage-Confined Catalytic Hairpin Assembly Nanobiosensor with a Nucleic Acid Restriction Behavior and Reinforced Enzymatic Resistance for Robust Imaging Assay in Live Biosystems. Anal Chem 2024; 96:7101-7110. [PMID: 38663376 DOI: 10.1021/acs.analchem.4c00473] [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: 05/08/2024]
Abstract
While DNA amplifier-built nanobiosensors featuring a DNA polymerase-free catalytic hairpin assembly (CHA) reaction have shown promise in fluorescence imaging assays within live biosystems, challenges persist due to unsatisfactory precision stemming from premature activation, insufficient sensitivity arising from low reaction kinetics, and poor biostability caused by endonuclease degradation. In this research, we aim to tackle these issues. One aspect involves inserting an analyte-binding unit with a photoinduced cleavage bond to enable a light-powered notion. By utilizing 808 nm near-infrared (NIR) light-excited upconversion luminescence as the ultraviolet source, we achieve entirely a controllable sensing event during the biodelivery phase. Another aspect refers to confining the CHA reaction within the finite space of a DNA self-assembled nanocage. Besides the accelerated kinetics (up to 10-fold enhancement) resulting from the nucleic acid restriction behavior, the DNA nanocage further provides a 3D rigid skeleton to reinforce enzymatic resistance. After selecting a short noncoding microRNA (miRNA-21) as the modeled low-abundance sensing analyte, we have verified that the innovative NIR light-powered and DNA nanocage-confined CHA nanobiosensor possesses remarkably high sensitivity and specificity. More importantly, our sensing system demonstrates a robust imaging capability for this cancer-related universal biomarker in live cells and tumor-bearing mouse bodies, showcasing its potential applications in disease analysis.
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Affiliation(s)
- Meng-Kun Xin
- School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Cheng-Yu Li
- School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
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4
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Garreau M, Weidner J, Hamilton R, Kolosionek E, Toki N, Stavenhagen K, Paris C, Bonetti A, Czechtizky W, Gnerlich F, Rydzik A. Chemical modification patterns for microRNA therapeutic mimics: a structure-activity relationship (SAR) case-study on miR-200c. Nucleic Acids Res 2024; 52:2792-2807. [PMID: 38421619 PMCID: PMC11014349 DOI: 10.1093/nar/gkae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
microRNA (miRNA) mimics are an emerging class of oligonucleotide therapeutics, with a few compounds already in clinical stages. Synthetic miRNAs are able to restore downregulated levels of intrinsic miRNAs, allowing for parallel regulation of multiple genes involved in a particular disease. In this work, we examined the influence of chemical modifications patterns in miR-200c mimics, assessing the regulation of a selection of target messenger RNAs (mRNA) and, subsequently, of the whole transcriptome in A549 cells. We have probed 37 mimics and provided an initial set of instructions for designing miRNA mimics with potency and selectivity similar to an unmodified miRNA duplex. Additionally, we have examined the stability of selected mimics in serum. Finally, the selected two modification patterns were translated to two other miRNAs, miR-34a and miR-155. To differing degrees, these designs acted on target mRNAs in a similar manner to the unmodified mimic. Here, for the first time, we describe a structured overview of 'miRNA mimics modification templates' that are chemically stabilised and optimised for use in an in vitro set up and highlight the need of further sequence specific optimization when mimics are to be used beyond in vitro tool experiments.
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Affiliation(s)
- Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Russell Hamilton
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Naoko Toki
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Kathrin Stavenhagen
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Clément Paris
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Alessandro Bonetti
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
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5
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Nappi F. Non-Coding RNA-Targeted Therapy: A State-of-the-Art Review. Int J Mol Sci 2024; 25:3630. [PMID: 38612441 PMCID: PMC11011542 DOI: 10.3390/ijms25073630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The use of non-coding RNAs (ncRNAs) as drug targets is being researched due to their discovery and their role in disease. Targeting ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is an attractive approach for treating various diseases, such as cardiovascular disease and cancer. This seminar discusses the current status of ncRNAs as therapeutic targets in different pathological conditions. Regarding miRNA-based drugs, this approach has made significant progress in preclinical and clinical testing for cardiovascular diseases, where the limitations of conventional pharmacotherapy are evident. The challenges of miRNA-based drugs, including specificity, delivery, and tolerability, will be discussed. New approaches to improve their success will be explored. Furthermore, it extensively discusses the potential development of targeted therapies for cardiovascular disease. Finally, this document reports on the recent advances in identifying and characterizing microRNAs, manipulating them, and translating them into clinical applications. It also addresses the challenges and perspectives towards clinical application.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France
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6
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Chen Y, Song Y, Wang X, Tang H, Li C. Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering. Biosens Bioelectron 2024; 247:115943. [PMID: 38141440 DOI: 10.1016/j.bios.2023.115943] [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: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.
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Affiliation(s)
- Yaling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Yongyao Song
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Xiaomei Wang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
| | - Hongwu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chengyu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
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7
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He JW, Sun X, Tang HW, Liu D, Li CY. Photoresponsive CHA-Integrated Self-Propelling 3D DNA Walking Amplifier within the Concentration Localization Effect of DNA Molecular Framework Enables Highly Efficient Fluorescence Bioimaging. Anal Chem 2024; 96:2142-2151. [PMID: 38258616 DOI: 10.1021/acs.analchem.3c04920] [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: 01/24/2024]
Abstract
While three-dimensional (3D) DNA walking amplifiers hold considerable promise in the construction of advanced DNA-based fluorescent biosensors for bioimaging, they encounter certain difficulties such as inadequate sensitivity, premature activation, the need for exogenous propelling forces, and low reaction rates. In this contribution, a variety of profitable solutions have been explored. First, a catalytic hairpin assembly (CHA)-achieved nonenzymatic isothermal nucleic acid amplification is integrated to enhance sensitivity. Subsequently, one DNA component is simply functionalized with a photocleavage-bond to conduct a photoresponsive manner, whereby the target recognition occurs only when the biosensor is exposed to an external ultraviolet light source, overcoming premature activation during biodelivery. Furthermore, a special self-propelling walking mechanism is implemented by reducing biothiols to MnO2 nanosheets, thereby propelling forces that are self-supplied to a Mn2+-reliant DNAzyme. By carrying the biosensing system with a DNA molecular framework to induce a unique concentration localization effect, the nucleic acid contact reaction rate is notably elevated by 6 times. Following these, an ultrasensitive in vitro detection performance with a limit of detection down to 2.89 fM is verified for a cancer-correlated microRNA biomarker (miRNA-21). Of particular importance, our multiple concepts combined 3D DNA walking amplifier that enables highly efficient fluorescence bioimaging in live cells and even bodies, exhibiting a favorable application prospect in disease analysis.
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Affiliation(s)
- Jing-Wei He
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Da Liu
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
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8
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Khan SU, Saeed S, Sheikh AN, Arbi FM, Shahzad A, Faryal U, Lu K. Crafting a Blueprint for MicroRNA in Cardiovascular Diseases (CVDs). Curr Probl Cardiol 2023; 48:102010. [PMID: 37544621 DOI: 10.1016/j.cpcardiol.2023.102010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
Cardiovascular diseases (CVDs) encompass a range of disorders, from congenital heart malformation, cardiac valve, peripheral artery, coronary artery, cardiac muscle diseases, and arrhythmias, ultimately leading to heart failure. Despite therapeutic advancements, CVDs remain the primary cause of global mortality, highlighting the need for a thorough knowledge of CVDs at the level of molecular structure. Gene and microRNA (miRNA) expression variations significantly influence cellular pathways, impacting an organism's physiology. MiRNAs, in particular, serve as regulators of gene expression, playing critical roles in essential cellular pathways and influencing the development of various diseases, including CVD. A wealth of evidence supports the involvement of miRNAs in CVD progression. These findings highlight the potential of miRNAs as valuable diagnostic biomarkers and open new avenues for their therapeutic application in CVDs. This study focuses on the latest advancements in identifying and characterizing microRNAs, exploring their manipulation and clinical application, and discussing future perspectives.
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Affiliation(s)
- Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, 22020, Pakistan
| | - Sumbul Saeed
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ayesha Nazir Sheikh
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro, 76080, Pakistan
| | - Fawad Mueen Arbi
- Quaid-e-Azam Medical College, Bahawalpur, Punjab, 63100, Pakistan
| | - Ali Shahzad
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Uzma Faryal
- Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, 22020, Pakistan
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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9
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Zhang L, Xu S, Zhang Z, Zhang X, Liu X. Transcriptomic profiling and characterization of microRNAs in Macrobrachium rosenbergii potentially involved in immune response to Enterobacter cloacae infection. Microb Pathog 2023; 183:106291. [PMID: 37557932 DOI: 10.1016/j.micpath.2023.106291] [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: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023]
Abstract
Enterobacter cloacae is a member of the Enterobacter family, which could prevent Macrobrachium rosenbergii from growing and cause mass mortality. However, no research has focused on microRNA immunity in M. rosenbergii infected with E. cloacae. To clarify the immune response mechanisms, transcriptomic analysis was performed on the miRNAs of M. rosenbergii infected with E. cloacae YZ3 strain. Following quality screening, 10,616,712 clean reads were obtained from the control group and 12,726,421 from the infected group. Among 899 known miRNAs, 446 differentially expressed miRNAs (DEMs) were identified. Meanwhile, 59 novel miRNAs were predicted, along with 39 DEMs. Target genes of DEMs have been predicted in order to gain a deeper understanding of the immune-related functions. GO and KEGG pathway analysis revealed the biological functions and signaling pathways of target genes. The results indicated that E. cloacae significantly affected the NOD-like receptor, RIG-I-like receptor and Toll-like receptor pathways. Ten DEMs were randomly selected, and their expression level was verified by Quantitative Real-time PCR technology. Overall, this study highlights the influential role of miRNAs in the innate immune system of M. rosenbergii, which has important implications for developing new strategies to prevent and treat related diseases in the future.
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Affiliation(s)
- Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Sunan Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zheling Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
| | - Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China; International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, China.
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10
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Fu J, Imani S, Wu MY, Wu RC. MicroRNA-34 Family in Cancers: Role, Mechanism, and Therapeutic Potential. Cancers (Basel) 2023; 15:4723. [PMID: 37835417 PMCID: PMC10571940 DOI: 10.3390/cancers15194723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
MicroRNA (miRNA) are small noncoding RNAs that play vital roles in post-transcriptional gene regulation by inhibiting mRNA translation or promoting mRNA degradation. The dysregulation of miRNA has been implicated in numerous human diseases, including cancers. miR-34 family members (miR-34s), including miR-34a, miR-34b, and miR-34c, have emerged as the most extensively studied tumor-suppressive miRNAs. In this comprehensive review, we aim to provide an overview of the major signaling pathways and gene networks regulated by miR-34s in various cancers and highlight the critical tumor suppressor role of miR-34s. Furthermore, we will discuss the potential of using miR-34 mimics as a novel therapeutic approach against cancer, while also addressing the challenges associated with their development and delivery. It is anticipated that gaining a deeper understanding of the functions and mechanisms of miR-34s in cancer will greatly contribute to the development of effective miR-34-based cancer therapeutics.
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Affiliation(s)
- Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China
| | - Saber Imani
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310022, China
| | - Mei-Yi Wu
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland Baltimore, Baltimore, MD 21201, USA
| | - Ray-Chang Wu
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20052, USA
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11
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Nappi F, Avtaar Singh SS, Jitendra V, Alzamil A, Schoell T. The Roles of microRNAs in the Cardiovascular System. Int J Mol Sci 2023; 24:14277. [PMID: 37762578 PMCID: PMC10531750 DOI: 10.3390/ijms241814277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The discovery of miRNAs and their role in disease represent a significant breakthrough that has stimulated and propelled research on miRNAs as targets for diagnosis and therapy. Cardiovascular disease is an area where the restrictions of early diagnosis and conventional pharmacotherapy are evident and deserve attention. Therefore, miRNA-based drugs have significant potential for development. Research and its application can make considerable progress, as seen in preclinical and clinical trials. The use of miRNAs is still experimental but has a promising role in diagnosing and predicting a variety of acute coronary syndrome presentations. Its use, either alone or in combination with currently available biomarkers, might be adopted soon, particularly if there is diagnostic ambiguity. In this review, we examine the current understanding of miRNAs as possible targets for diagnosis and treatment in the cardiovascular system. We report on recent advances in recognising and characterising miRNAs with a focus on clinical translation. The latest challenges and perspectives towards clinical application are discussed.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
| | | | - Vikram Jitendra
- Department of Cardiothoracic Surgery, Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK;
| | - Almothana Alzamil
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
| | - Thibaut Schoell
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
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12
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Chen YL, Sun X, He JW, Xin MK, Liu D, Li CY. Light-Driven and Metal-Organic Framework Synergetic Loaded DNA Tetrahedral Amplifier for Exonuclease III-Powered All-in-One Biosensing and Chemotherapy in Live Biosystems. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37410886 DOI: 10.1021/acsami.3c06626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
As a result of inaccurate biosensing and difficult synergetic loading, it is challenging to further impel DNA amplifiers to perform therapeutic application. Herein, we introduce some innovative solutions. First, a smart light-driven biosensing concept based on embedding nucleic acid modules with a simple photocleavage-linker is proposed. In this system, the target identification component is exposed on irradiation with ultraviolet light, thus avoiding an always-on biosensing response during biological delivery. Further, in addition to providing controlled spatiotemporal behavior and precise biosensing information, a metal-organic framework is used for the synergetic loading of doxorubicin in the internal pores, whereafter a rigid DNA tetrahedron-sustained exonuclease III-powered biosensing system is attached to prevent drug leakage and enhance resistance to enzymatic degradation. By selecting a next-generation breast cancer correlative noncoding microRNA biomarker (miRNA-21) as a model low-abundance analyte, a highly sensitive in vitro detection ability even allowing to distinguish single-base mismatching is demonstrated. Moreover, the all-in-one DNA amplifier shows excellent bioimaging competence and good chemotherapy efficacy in live biosystems. These findings will drive research into the use of DNA amplifiers in diagnosis and therapy integrated fields.
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Affiliation(s)
- Ya-Ling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Jing-Wei He
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Meng-Kun Xin
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
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13
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Rybarczyk A, Lehmann T, Iwańczyk-Skalska E, Juzwa W, Pławski A, Kopciuch K, Blazewicz J, Jagodziński PP. In silico and in vitro analysis of the impact of single substitutions within EXO-motifs on Hsa-MiR-1246 intercellular transfer in breast cancer cell. J Appl Genet 2023; 64:105-124. [PMID: 36394782 PMCID: PMC9837009 DOI: 10.1007/s13353-022-00730-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022]
Abstract
MiR-1246 has recently gained much attention and many studies have shown its oncogenic role in colorectal, breast, lung, and ovarian cancers. However, miR-1246 processing, stability, and mechanisms directing miR-1246 into neighbor cells remain still unclear. In this study, we aimed to determine the role of single-nucleotide substitutions within short exosome sorting motifs - so-called EXO-motifs: GGAG and GCAG present in miR-1246 sequence on its intracellular stability and extracellular transfer. We applied in silico methods such as 2D and 3D structure analysis and modeling of protein interactions. We also performed in vitro validation through the transfection of fluorescently labeled miRNA to MDA-MB-231 cells, which we analyzed by flow cytometry and fluorescent microscopy. Our results suggest that nucleotides alterations that disturbed miR-1246 EXO-motifs were able to modulate miRNA-1246 stability and its transfer level to the neighboring cells, suggesting that the molecular mechanism of RNA stability and intercellular transfer can be closely related.
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Affiliation(s)
- Agnieszka Rybarczyk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Tomasz Lehmann
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
| | - Ewa Iwańczyk-Skalska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
| | - Wojciech Juzwa
- Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznan, Poland
| | - Kamil Kopciuch
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paweł P. Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
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14
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Zhao Y, Zhang T, Shen X, Huang A, Li H, Wang L, Liu X, Wang X, Song X, Wang S, Dong J, Shao N. Tumor necrosis factor alpha delivers exogenous inflammation-related microRNAs to recipient cells with functional targeting capabilities. Mol Ther 2022; 30:3052-3065. [PMID: 35791880 PMCID: PMC9481991 DOI: 10.1016/j.ymthe.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/15/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is a critical pro-inflammatory cytokine in a wide range of tumors and infectious diseases. This study showed for the first time that TNF-α could specifically bind to certain intracellular or circulating inflammation-related microRNAs both in vitro and in vivo. The binding sites of TNF-α to microRNAs are located at the N-terminal of TNF-α and the 3'-GGUU motif of microRNAs. TNF-α could deliver exogenous unmodified single-stranded microRNAs into recipient cells through the TNF-α receptors (TNFRs) and stabilize them from being degraded by RNase in cells. Exogenous miR-146a or let-7c delivered into HCT116 cells by TNF-α could escape from lysosomes and specifically downregulate their target genes and then affect cell proliferation and migration in vitro, as well as tumorigenesis in vivo. Based on the above findings, the concept of "non-conjugated ligand-mediated RNA delivery (ncLMRD)" was proposed, which may serve as a promising strategy for therapeutic microRNA delivery in the future.
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Affiliation(s)
- Yuechao Zhao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Tan Zhang
- Non-commissioned Officer School of Army Medical University, Shijiazhuang 050000, China
| | - Xuelian Shen
- Laibin Maternity and Child Healthcare Hospital, Guangxi 546100, China
| | - Aixue Huang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Lin Wang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xuemei Liu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xuejun Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China
| | - Xiang Song
- Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China
| | - Shengqi Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China
| | - Jie Dong
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
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15
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Kisseljova NP, Fedorova MD, Zaikina AE, Elkina NV, Goldobina EE, Elkin DS, Abramov PM, Pavlova LS, Vinokurova SV. [Identification regulatory noncoding RNAs of human papilloma virus type 16 (Papillomaviridae: Alphapapillomavirus: Human papillomavirus) in cervical tumors]. Vopr Virusol 2022; 67:217-226. [PMID: 35831964 DOI: 10.36233/0507-4088-108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION High carcinogenic-risk human papillomaviruses (hrHPVs) are recognized as etiological agents of cervical cancer. Constant expression of the viral oncoproteins, E6 and E7, is required for maintenance of the malignant phenotype of tumor cells. The exact mechanism of regulation of viral oncogenes expression in tumor cells is not fully elucidated. THE PURPOSE identification of viral noncoding RNAs (ncRNAs) in HPV16-positve cervical cancer. MATERIALS AND METHODS The reverse transcription polymerase chain reactions were used to detect viral ncRNAs in HPV16-positve primary cervical squamous cell carcinomas and SiHa and CasKi cell lines. The knockdown technique with oligonucleotides complementary to ncRNAs was used to elucidate their functions. RESULTS We have identified ncRNAs transcribed in the upstream regulatory region of HPV16 in the cervical carcinoma cell lines and in 32 out 32 cervical squamous cell carcinomas with episomal or integrated forms of HPV16 DNA. Knockdown of sense or antisense strains of ncRNAs by oligonucleotides results in a decrease or increase of the E6 and E7 oncogenes mRNA levels in cells, respectively. These changes of oncogenes mRNA levels are accompanied by the modulation of the levels of the p53 protein, the main target of the E6 oncoprotein. CONCLUSION The presence of regulatory ncRNAs in all examined tumors and cell lines revealed for the first time indicates their necessity for maintenance of constant expression of E6 and E7 oncogenes in them. The findings can be useful for understanding of the fundamental aspects of the viral expression regulation in HPV16-positive tumors.
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Affiliation(s)
- N P Kisseljova
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - M D Fedorova
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - A E Zaikina
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - N V Elkina
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - E E Goldobina
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - D S Elkin
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - P M Abramov
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - L S Pavlova
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
| | - S V Vinokurova
- FSBI «National Medical Research Center of Oncology named after N.N. Blokhin» of the Ministry of Health of Russia
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16
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Abstract
The discovery of microRNAs and their role in diseases was a breakthrough that inspired research into microRNAs as drug targets. Cardiovascular diseases are an area in which limitations of conventional pharmacotherapy are highly apparent and where microRNA-based drugs have appreciably progressed into preclinical and clinical testing. In this Review, we summarize the current state of microRNAs as therapeutic targets in the cardiovascular system. We report recent advances in the identification and characterization of microRNAs, their manipulation and clinical translation, and discuss challenges and perspectives toward clinical application.
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Affiliation(s)
- Bernhard Laggerbauer
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
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17
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Li Z, Wang X, Zhou X, Wang J, Guan Z, Yang Z. Optimization in Chemical Modification of Single-Stranded siRNA Encapsulated by Neutral Cytidinyl/Cationic Lipids. Front Chem 2022; 10:843181. [PMID: 35345539 PMCID: PMC8957067 DOI: 10.3389/fchem.2022.843181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Single-stranded siRNA (ss-siRNA) refers to the antisense strand of siRNA, which plays the role of gene silencing. Since single-stranded RNA is unstable, the present study employed a homemade neutral cytidinyl/cationic lipid delivery system and chemical modifications to improve its stability. The results showed that with the aid of mixed lipids, ss-siRNA could knock down 40% of target mRNA at 25 nM. With 2ʹ-F/2ʹ-OMe, phosphorothioate and 5ʹ-terminal phosphorylation, the optimized ss-siRNA could knock down 80% of target mRNA at 25 nM. Further knocking down AGO2, the ss-siRNAs could not effectively silence target mRNAs. Analysis of the biodistribution in vivo showed that ss-siRNA was less durable than siRNA, but spread more quickly to tissues. This study provides a safe and efficient ss-siRNA delivery and modification strategy, which lays the foundation for future works.
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18
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Lin C, Li Y, Zhang E, Feillet F, Zhang S, Blau N. Importance of the long non-coding RNA (lncRNA) transcript HULC for the regulation of phenylalanine hydroxylase and treatment of phenylketonuria. Mol Genet Metab 2022; 135:171-178. [PMID: 35101330 DOI: 10.1016/j.ymgme.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Eric Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy, France; Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy, France
| | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland.
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19
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Theranostics 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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Affiliation(s)
- Peipei Wang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Yue Zhou
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Arthur M. Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
- Christchurch Heart Institute, Department of Medicine, University of Otago Christchurch, New Zealand
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20
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Gao JL, Liu YH, Zheng B, Liu JX, Fang WK, Liu D, Sun XM, Tang HW, Li CY. Light-Activated and Self-Driven Autonomous DNA Nanomachine Enabling Fluorescence Imaging of MicroRNA in Living Cells with Exceptional Precision and Efficiency. ACS APPLIED MATERIALS & INTERFACES 2021; 13:31485-31494. [PMID: 34184527 DOI: 10.1021/acsami.1c07333] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Owing to their favorable design flexibility and eminent signal amplification ability, DNA nanomachine-supported biosensors have provided an attractive avenue for intracellular fluorescence imaging, especially for DNA walkers. However, this promising option not only suffers from poor controllability but also needs to be supplied with additional driving forces on account of the frequent employment of metal ion-dependent DNAzymes. Aiming at overcoming these obstacles, we introduce some fruitful solutions. On one hand, innovative light-activated walking behavior induced by a photocleavage mode is established on the surfaces of gold nanoparticles, and such a photoselective sensing system can be perfectly prevented from pre-activating during the intracellular delivery process and made to achieve target identification only under irradiation using a moderate ultraviolet light source. On the other hand, this light-switchable sensing frame is encapsulated within a dissociable metal-organic framework (ZIF-8) to facilitate endocytosis and ensure sufficient internal cofactors (Zn2+) to realize a self-driven pattern in the acidic environment of the cell lysosome. Based on the abovementioned efforts, the newly constructed autonomous three-dimensional DNA walkers present satisfactory sensitivity (a limit of detection of down to 19.4 pM) and specificity (even distinguishing single-base changes) toward a model biomarker (microRNA-21). More importantly, the sensing method allows determination of the variations in targets in living cancer cells with exceptional precision and efficiency, offering a powerful assay platform for intracellular imaging.
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Affiliation(s)
- Jia-Ling Gao
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Yu-Heng Liu
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Bei Zheng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
- Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou 310024, People's Republic of China
| | - Jun-Xian Liu
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Wen-Kai Fang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Xiao-Ming Sun
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Human Aantomy, School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
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21
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Kawasaki H, Amano H. Anti‑inflammatory role of microRNA‑429 in human gingival epithelial cells‑inhibition of IL‑8 production through direct binding to IKKβ mRNA. Mol Med Rep 2021; 24:581. [PMID: 34132371 PMCID: PMC8223109 DOI: 10.3892/mmr.2021.12220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs), a family of small non‑coding RNAs, serve a pivotal role in the regulation of the inflammation by modulating the expression of various genes. However, the molecular mechanism by which miRNAs regulate inflammation‑associated molecules in oral epithelial cells remains to be elucidated. The present study examined the biological function of miR‑429 by performing the gain‑/loss‑of‑function studies of miR‑429 in a gingival squamous cell carcinoma line Ca9‑22 cells that either over‑ or under‑expressed miR‑429 through transient transfection with miR‑429 mimic or miR‑429 inhibitor, respectively. The results demonstrated that the over‑expression of miR‑429 suppressed the mRNA level of several interleukins, including IL‑8. In addition, the over‑expression of miR‑429 reduced IL‑8 secretion under the basal and TNF‑α stimulated conditions, whereas the secretion of IL‑8 was enhanced when miR‑429 was under‑expressed. The over‑expression of miR‑429 inhibited the activation of the transcription factor NF‑κB. Furthermore, we found that miR‑429 suppressed both mRNA and protein levels of IKKβ via its direct binding to the 3'‑untranslated region of IKKβ mRNA. In addition, the downregulation of IKKβ by small interfering RNA reduced both NF‑kB activity and IL‑8 production in Ca9‑22 cells. Taken together, the findings revealed the molecular mechanism of miR‑429 to regulate the inflammatory mediator in gingival cells and suggested that it could be useful as a therapeutic target of oral inflammatory diseases.
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Affiliation(s)
- Hiromichi Kawasaki
- Central Research Institute, Wakunaga Pharmaceutical Co. Ltd., Koda‑cho, Akitakata‑shi, Hiroshima 739‑1195, Japan
| | - Hirotaka Amano
- Central Research Institute, Wakunaga Pharmaceutical Co. Ltd., Koda‑cho, Akitakata‑shi, Hiroshima 739‑1195, Japan
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22
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Gandhi G, Abdullah S, Foead AI, Yeo WWY. The potential role of miRNA therapies in spinal muscle atrophy. J Neurol Sci 2021; 427:117485. [PMID: 34015517 DOI: 10.1016/j.jns.2021.117485] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/14/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by low levels of full-length survival motor neuron (SMN) protein due to the loss of the survival motor neuron 1 (SMN1) gene and inefficient splicing of the survival motor neuron 2 (SMN2) gene, which mostly affects alpha motor neurons of the lower spinal cord. Despite the U.S. Food and Drug Administration (FDA) approved SMN-dependent therapies including Nusinersen, Zolgensma® and Evrysdi™, SMA is still a devastating disease as these existing expensive drugs may not be sufficient and thus, remains a need for additional therapies. The involvement of microRNAs (miRNAs) in SMA is expanding because miRNAs are important mediators of gene expression as each miRNA could target a number of genes. Hence, miRNA-based therapy could be utilized in treating this genetic disorder. However, the delivery of miRNAs into the target cells remains an obstacle in SMA, as there is no effective delivery system to date. This review highlights the potential strategies for intracellular miRNA delivery into target cells and current challenges in miRNA delivery. Furthermore, we provide the future prospects of miRNA-based therapeutic strategies in SMA.
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Affiliation(s)
- Gayatri Gandhi
- Perdana University Graduate School of Medicine, Perdana University, Wisma Chase Perdana, Changkat Semantan, Damansara Heights, 50490 Kuala Lumpur, Malaysia
| | - Syahril Abdullah
- Medical Genetics Laboratory, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 UPM, Selangor, Malaysia; Genetics & Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Selangor, Malaysia; UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Selangor, Malaysia
| | - Agus Iwan Foead
- Department of Orthopedics, Perdana University-Royal College of Surgeons in Ireland, Perdana University, Wisma Chase Perdana, Changkat Semantan, Damansara Heights, 50490 Kuala Lumpur, Malaysia
| | - Wendy Wai Yeng Yeo
- Perdana University Graduate School of Medicine, Perdana University, Wisma Chase Perdana, Changkat Semantan, Damansara Heights, 50490 Kuala Lumpur, Malaysia.
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23
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Kratzer K, Getz LJ, Peterlini T, Masson JY, Dellaire G. Addressing the dark matter of gene therapy: technical and ethical barriers to clinical application. Hum Genet 2021; 141:1175-1193. [PMID: 33834266 DOI: 10.1007/s00439-021-02272-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/27/2021] [Indexed: 02/07/2023]
Abstract
Gene therapies for genetic diseases have been sought for decades, and the relatively recent development of the CRISPR/Cas9 gene-editing system has encouraged a new wave of interest in the field. There have nonetheless been significant setbacks to gene therapy, including unintended biological consequences, ethical scandals, and death. The major focus of research has been on technological problems such as delivery, potential immune responses, and both on and off-target effects in an effort to avoid negative clinical outcomes. While the field has concentrated on how we can better achieve gene therapies and gene editing techniques, there has been less focus on when and why we should use such technology. Here we combine discussion of both the technical and ethical barriers to the widespread clinical application of gene therapy and gene editing, providing a resource for gene therapy experts and novices alike. We discuss ethical problems and solutions, using cystic fibrosis and beta-thalassemia as case studies where gene therapy might be suitable, and provide examples of situations where human germline gene editing may be ethically permissible. Using such examples, we propose criteria to guide researchers and clinicians in deciding whether or not to pursue gene therapy as a treatment. Finally, we summarize how current progress in the field adheres to principles of biomedical ethics and highlight how this approach might fall short of ethical rigour using examples in the bioethics literature. Ultimately by addressing both the technical and ethical aspects of gene therapy and editing, new frameworks can be developed for the fair application of these potentially life-saving treatments.
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Affiliation(s)
- Kateryna Kratzer
- Department of Pathology, Faculty of Medicine, Dalhousie University, PO BOX 15000, Halifax, NS, B3H 4R2, Canada
| | - Landon J Getz
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, PO BOX 15000, Halifax, NS, B3H 4R2, Canada
| | - Thibaut Peterlini
- Genome Stability Laboratory, Oncology Division, CHU de Québec Research Centre, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Quebec, G1R 3S3, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Oncology Division, CHU de Québec Research Centre, Quebec, Canada. .,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Quebec, G1R 3S3, Canada.
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, PO BOX 15000, Halifax, NS, B3H 4R2, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, PO BOX 15000, Halifax, NS, B3H 4R2, Canada. .,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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24
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Yoshida K, Yokoi A, Sugiyama M, Oda S, Kitami K, Tamauchi S, Ikeda Y, Yoshikawa N, Nishino K, Niimi K, Suzuki S, Kikkawa F, Yokoi T, Kajiyama H. Expression of the chrXq27.3 miRNA cluster in recurrent ovarian clear cell carcinoma and its impact on cisplatin resistance. Oncogene 2021; 40:1255-1268. [PMID: 33420363 PMCID: PMC7892337 DOI: 10.1038/s41388-020-01595-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Ovarian clear cell carcinoma (OCCC) is a histological subtype of epithelial ovarian cancer and exhibits dismal prognosis due to chemoresistance. Moreover, only few effective therapeutic options exist for patients with recurrent OCCC, and an understanding of its molecular characteristics is essential for the development of novel therapeutic approaches. In the present study, we investigated unique MicroRNAs (miRNA) profiles in recurrent/metastatic OCCC and the role of miRNAs in cisplatin resistance. Comprehensive miRNA sequencing revealed that expression of several miRNAs, including miR-508-3p, miR-509-3p, miR-509-3-5p, and miR-514a-3p was remarkably less in recurrent cancer tissues when compared with that in paired primary cancer tissues. These miRNAs are located in the chrXq27.3 region on the genome. Moreover, its expression was negative in omental metastases in two patients with advanced OCCC. In vitro analyses revealed that overexpression of miR-509-3p and miR-509-3-5p reversed cisplatin resistance and yes-associated protein 1 (YAP1) was partially responsible for the resistance. Immunohistochemistry revealed that YAP1 expression was inversely correlated with the chrXq27.3 miRNA cluster expression. In conclusion, these findings suggest that alteration of the chrXq27.3 miRNA cluster could play a critical role in chemoresistance and miRNAs in the cluster and their target genes can be potential therapeutic targets.
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Affiliation(s)
- Kosuke Yoshida
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Drug Safety Sciences, Division of Clinical Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan. .,Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Mai Sugiyama
- Bell Research Center, Department of Obstetrics and Gynecology Collaborative Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shingo Oda
- Department of Drug Safety Sciences, Division of Clinical Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhisa Kitami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Tamauchi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Ikeda
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhisa Yoshikawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kimihiro Nishino
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kaoru Niimi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shiro Suzuki
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumitaka Kikkawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuyoshi Yokoi
- Department of Drug Safety Sciences, Division of Clinical Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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25
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Moccia M, Mercurio FA, Langella E, Piacenti V, Leone M, Adamo MFA, Saviano M. Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach. Front Chem 2020; 8:568575. [PMID: 33330358 PMCID: PMC7719796 DOI: 10.3389/fchem.2020.568575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
In the present work, structural features of the interaction between peptide nucleic acid (PNA)-based analogs of the tumor-suppressor microRNA-34a with both its binding sites on MYCN mRNA were investigated. In particular, the region from base 1 to 8 ("seed" region) of miR-34a was reproduced in the form of an 8-mer PNA fragment (tiny PNA), and binding to target 3'UTR MYCN mRNA, was studied by a seldom reported and detailed NMR characterization, providing evidence for the formation of anti-parallel duplexes with a well-organized structural core. The formation of PNA-3'UTR duplexes was also confirmed by Circular Dichroism, and their melting curves were measured by UV spectroscopy. Nevertheless, this study offered a valuable comparison between molecular dynamics predictions and experimental evidence, which showed great correlation. Preliminary uptake assays were carried out in Neuroblastoma Kelly cells, using short peptide conjugates as carriers and FITC fluorescent tag for subcellular localization. Moderate internalization was observed without the use of transfecting agents. The reported results corroborate the interest toward the design and development of chimeric PNA/RNA sequences as effective RNA-targeting agents.
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Affiliation(s)
- Maria Moccia
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Emma Langella
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Valerio Piacenti
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Mauro F. A. Adamo
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
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26
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The pHLIP system as a vehicle for microRNAs in the kidney. Nefrologia 2020; 40:491-498. [PMID: 32693933 DOI: 10.1016/j.nefro.2020.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression through post-transcriptional repression of their target messenger RNAs. A study of changes in expression of certain miRNAs in the kidney has supplied evidence on their pathogenic role and therapeutic potential in nephrology. This review proposes a nanotechnology approach based on the binding of analogs or inhibitors of miRNAs formed by peptide nucleic acids (PNAs) to peptides with a transmembrane structure sensitive to a low pH, called pHLIPs (pH [low] insertion peptides). The review draws on the concept that an acidic pH in the microenvironment of the renal tubule may facilitate concentration and distribution of the pHLIP-PNA complex in this organ. In this context, we have demonstrated for the first time that targeted administration of miR-33 inhibitors with the pHLIP system effectively prevents the development of renal fibrosis, thus opening up this technology to new strategies for diagnosis and treatment of kidney diseases.
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27
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Palanikumar L, Al-Hosani S, Kalmouni M, Saleh HO, Magzoub M. Hexokinase II-Derived Cell-Penetrating Peptide Mediates Delivery of MicroRNA Mimic for Cancer-Selective Cytotoxicity. Biochemistry 2020; 59:2259-2273. [PMID: 32491855 DOI: 10.1021/acs.biochem.0c00141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer cells are often characterized by elevated levels of mitochondrion-bound hexokinase II (HKII), which facilitates their survival, proliferation, and metastasis. Here, we have designed a cancer-selective cell-penetrating peptide (CPP) by covalently coupling a short penetration-accelerating sequence (PAS) to the mitochondrial membrane-binding N-terminal 15 amino acids of HKII (pHK). PAS-pHK mediates efficient cellular uptake and cytosolic delivery of a synthetic mimic of miR-126, a tumor suppressor miRNA downregulated in many malignancies. Following uptake by breast cancer MCF-7 cells, the CPP-miRNA conjugate is distributed throughout the cytosol and shows strong colocalization with mitochondria, where PAS-pHK induces depolarization of mitochondrial membrane potential, inhibition of metabolic activities, depletion of intracellular ATP levels, release of cytochrome c, and, finally, apoptosis. Concomitantly, the miR-126 cargo synergistically enhances the anticancer effects of PAS-pHK. Importantly, the PAS-pHK-miR-126 conjugate is not toxic to noncancerous MCF-10A and HEK-93 cells. Our results demonstrate the potential of PAS-pHK-mediated delivery of miRNA mimics as a novel cancer-selective therapeutic strategy.
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Affiliation(s)
- L Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Sumaya Al-Hosani
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Hadi Omar Saleh
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
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28
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Bolz M, Thomas L, Scheffer U, Kalden E, Hartmann RK, Göbel MW. Redirection of miRNA-Argonaute Complexes to Specific Target Sites by Synthetic Adaptor Molecules. Chem Biodivers 2020; 17:e2000272. [PMID: 32428353 DOI: 10.1002/cbdv.202000272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022]
Abstract
Dysregulation of miRNAs is connected with a multitude of diseases for which antagomirs and miRNA replacement are discussed as therapeutic options. Here, we suggest an alternative concept based on the redirection of RISCs to non-native target sites. Metabolically stable DNA-LNA mixmers are used to mediate the binding of RISCs to mRNAs without any direct base complementarity to the presented guide RNA strand. Physical redirection of a dye-labeled miRNA model and of specific miRNA-programmed RISC fractions present in HeLa extracts is demonstrated by pull-down experiments with biotinylated capture oligonucleotides.
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Affiliation(s)
- Mathias Bolz
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Laura Thomas
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Ute Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Elisabeth Kalden
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
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29
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Li CY, Zheng B, Kang YF, Tang HW, Pang DW. Integrating 808 nm Light-Excited Upconversion Luminescence Powering with DNA Tetrahedron Protection: An Exceptionally Precise and Stable Nanomachine for Intracelluar MicroRNA Tracing. ACS Sens 2020; 5:199-207. [PMID: 31833356 DOI: 10.1021/acssensors.9b02043] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although plentiful advanced fluorescence sensors have achieved to analyze microRNAs (miRNAs) in living cells, the prerequisite relating to nucleic acids specific recognition based sensing principle compels them lack favorable accurancy and stability in such complicated biological mediums. Here, we make a double breakthrough for the two challenges by combining a near-infrared (NIR) light powering process with a DNA tetrahedron (DNAT)-based protection concept. In this sensing system, a special nanomachine is first engineered by conjugating a core-shell-structured upconversion nanoparticle capable of highly converting 808 nm NIR photons into ultraviolet ones with self-assembling DNATs. The newly developed nanostructure not only prevents the sensing pathway from triggering during the intracellular delivery as well as reducing the adverse thermal effect for cell viability but also significantly enhances the enzyme resistance to avoid degradation to produce false signals. Furthermore, a fluorescence resonance energy transfer sensing strategy is rationally designed on this nanomachine. Upon using the powering light to excite the upconversion luminescence to activate the nanomachine in living cells, it can stably trace the precise level changes of miRNA-21 sequences at the reaching position with an "off-on" mode of fluorescence outputs.
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Affiliation(s)
- Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People’s Republic of China
| | - Bei Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Ya-Feng Kang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Hong-Wu Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, and College of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
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30
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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31
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Liu Z, Johnson ST, Zhang Z, Corey DR. Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes. Nucleic Acid Ther 2019; 29:323-334. [PMID: 31670606 PMCID: PMC6885777 DOI: 10.1089/nat.2019.0815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The trinucleotide repeat containing 6 (TNRC6) family of proteins are core components of RNA interference (RNAi) and consist of three paralogs (TNRC6A, TNRC6B, and TNRC6C). The TNRC6 paralogs associate with argonaute (AGO) protein, the core RNAi factor, and bridge its interactions with other proteins. We obtained TNRC6A and TNRC6B single and double knockout cell lines to investigate how the TNRC6 paralogs contribute to RNAi. We found that TNRC6 proteins are not required for gene silencing when duplex RNAs are fully complementary. TNRC6 expression was necessary for regulation by a microRNA. TNRC6A, but not TNRC6B, expression was necessary for transcriptional activation by a duplex RNA targeting a gene promoter. By contrast, AGO2 is required for all three gene expression pathways. TNRC6A can affect the Dicer localization in cytoplasm versus the nucleus, but none of the three TNRC6 paralogs was necessary for nuclear localization of AGO2. Our data suggest that the roles of the TNRC6 paralogs differ in some details and that TNRC6 is not required for clinical therapeutic silencing mechanisms that involve fully complementary duplex RNAs.
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Affiliation(s)
- Zhongtian Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.,Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
| | - Samantha T Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
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32
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Jiang S, Fang X, Liu M, Ni Y, Ma W, Zhao R. MiR-20b Down-Regulates Intestinal Ferroportin Expression In Vitro and In Vivo. Cells 2019; 8:cells8101135. [PMID: 31554201 PMCID: PMC6829237 DOI: 10.3390/cells8101135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/16/2019] [Accepted: 09/21/2019] [Indexed: 12/11/2022] Open
Abstract
Ferroportin (FPN) is the only known cellular iron exporter in mammalian. However, post-transcriptional regulation of intestinal FPN has not yet been completely understood. In this study, bioinformatics algorithms (TargetScan, PicTar, PITA, and miRanda) were applied to predict, screen and obtain microRNA-17 family members (miR-17, miR-20a, miR-20b, and miR-106a) targeting FPN, ‘seed sequence’ and responding binding sites on the 3′untranslated region (3′UTR) region of FPN. Dual-luciferase reporter assays revealed miRNA-17 family members’ mimics decreased the luciferase activity, whereas their inhibitors increased the luciferase activity. Compared with the FPN 3′UTR wild type reporter, co-transfection of a miRNA-17 family members’ over-expression plasmids and FPN 3′UTR mutant reporters enhanced the luciferase activity in HCT116 cells. Transfection with miR-20b overexpression plasmid significantly enhanced its expression, and it inhibited endogenous FPN protein expression in Caco-2 cells. Additionally, tail-vein injection of miR-20b resulted in increasing duodenal miR-20b expression, decreasing duodenal FPN protein expression, which was closely related to lower plasma iron level in mice. Taken together, these data suggest that the miR-20b is identified to regulate intestinal FPN expression in vitro and in vivo, which will provide a potential target for intestinal iron exportation.
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Affiliation(s)
- Shuxia Jiang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Xi Fang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Mingni Liu
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Yingdong Ni
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Wenqiang Ma
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Ruqian Zhao
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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33
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Aquilano K, Ceci V, Gismondi A, De Stefano S, Iacovelli F, Faraonio R, Di Marco G, Poerio N, Minutolo A, Minopoli G, Marcone A, Fraziano M, Tortolici F, Sennato S, Casciardi S, Potestà M, Bernardini R, Mattei M, Falconi M, Montesano C, Rufini S, Canini A, Lettieri-Barbato D. Adipocyte metabolism is improved by TNF receptor-targeting small RNAs identified from dried nuts. Commun Biol 2019; 2:317. [PMID: 31453381 PMCID: PMC6704100 DOI: 10.1038/s42003-019-0563-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/30/2019] [Indexed: 01/22/2023] Open
Abstract
There is a growing interest in therapeutically targeting the inflammatory response that underlies age-related chronic diseases including obesity and type 2 diabetes. Through integrative small RNA sequencing, we show the presence of conserved plant miR159a and miR156c in dried nuts having high complementarity with the mammalian TNF receptor superfamily member 1a (Tnfrsf1a) transcript. We detected both miR159a and miR156c in exosome-like nut nanovesicles (NVs) and demonstrated that such NVs reduce Tnfrsf1a protein and dampen TNF-α signaling pathway in adipocytes. Synthetic single-stranded microRNAs (ss-miRs) modified with 2'-O-methyl group function as miR mimics. In plants, this modification naturally occurs on nearly all small RNAs. 2'-O-methylated ss-miR mimics for miR156c and miR159a decreased Tnfrsf1a protein and inflammatory markers in hypertrophic as well as TNF-α-treated adipocytes and macrophages. miR156c and miR159a mimics effectively suppress inflammation in mice, highlighting a potential role of plant miR-based, single-stranded oligonucleotides in treating inflammatory-associated metabolic diseases.
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Affiliation(s)
- Katia Aquilano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Veronica Ceci
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Angelo Gismondi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Susanna De Stefano
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | | | - Raffaella Faraonio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Noemi Poerio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Giuseppina Minopoli
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Antonia Marcone
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Flavia Tortolici
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Simona Sennato
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
| | - Stefano Casciardi
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, National Institute for Insurance against Accidents at Work (INAIL) Research, Rome, Italy
| | - Marina Potestà
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Roberta Bernardini
- Interdepartmental Service Center-Station for Anima Technology (STA), University of Rome Tor Vergata, Rome, Italy
| | - Maurizio Mattei
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Interdepartmental Service Center-Station for Anima Technology (STA), University of Rome Tor Vergata, Rome, Italy
| | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Carla Montesano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Rufini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Canini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Daniele Lettieri-Barbato
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
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Piacenti V, Langella E, Autiero I, Nolan JC, Piskareva O, Adamo MFA, Saviano M, Moccia M. A combined experimental and computational study on peptide nucleic acid (PNA) analogues of tumor suppressive miRNA-34a. Bioorg Chem 2019; 91:103165. [PMID: 31419642 DOI: 10.1016/j.bioorg.2019.103165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/19/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022]
Abstract
MicroRNAs are a ubiquitous class of non-coding RNAs able to regulate gene expression in diverse biological processes. Widespread miRNAs deregulation was reported in numerous diseases including cancer, with several miRNAs playing oncogenic and/or tumor suppressive role by targeting multiple mRNAs simultaneously. Based on these findings, miRNAs have emerged as promising therapeutic tools for cancer treatment. Herein, for the first time, peptide nucleic acids (PNAs) were studied to develop a new class of molecules able to target 3'UTR on MYCN mRNA without a fully complementary base pairing sequence (as miRNAs). For our proof of concept study we have selected as a model the miRNA-34a, which acts as a tumor suppressor in a number of cancers including neuroblastoma. In particular, miRNA-34a is a direct regulator of MYCN oncogene, whose overexpression is a prominent biomarker for the highly aggressive neuroblastoma phenotype. The design and synthesis of three PNA-based oligomers of different length was described, and their interaction with two binding sites on the target MYCN mRNA was investigated by molecular dynamics simulation, and spectroscopic techniques (CD, UV). Intake assay and confocal microscopy of PNA sequences were also carried out in vitro on neuroblastoma Kelly cells. Despite the presence of multiple mismatches, the PNA/RNA hetero duplexes retain very interesting features in terms of stability, affinity as well as of cellular uptake.
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Affiliation(s)
- Valerio Piacenti
- RCSI, Dept. of Pharmaceutical & Medicinal Chemistry, 123 St Stephen's Green, Dublin 2, Ireland
| | - Emma Langella
- National Research Council (CNR)-IBB, via Mezzocannone 16, 80134 Naples, Italy
| | - Ida Autiero
- National Research Council (CNR)-IBB, via Mezzocannone 16, 80134 Naples, Italy
| | - John C Nolan
- RCSI, Dept. of Cancer Genetics, York Street, Dublin 2, Ireland
| | - Olga Piskareva
- RCSI, Dept. of Cancer Genetics, York Street, Dublin 2, Ireland
| | - Mauro F A Adamo
- RCSI, Dept. of Pharmaceutical & Medicinal Chemistry, 123 St Stephen's Green, Dublin 2, Ireland
| | - Michele Saviano
- National Research Council (CNR)-IC, via G. Amendola 122/O, 70126 Bari, Italy
| | - Maria Moccia
- National Research Council (CNR)-IC, via G. Amendola 122/O, 70126 Bari, Italy.
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Ramchandran R, Chaluvally-Raghavan P. miRNA-Mediated RNA Activation in Mammalian Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639193 DOI: 10.1007/978-981-10-4310-9_6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNA (miRNA or miR) is a small noncoding RNA molecule ~22 nucleotides in size, which is found in plants, animals, and some viruses. miRNAs are thought to primarily down regulate gene expression by binding to 3' untranslated regions of target transcripts, thereby triggering mRNA cleavage or repression of translation. Recently, evidence has emerged that miRNAs can interact with the promoter and activate gene expression. This mechanism, called RNA activation (RNAa), is a process of transcriptional activation where the direct interaction of miRNA on the promoter triggers the recruitment of transcription factors and RNA-Polymerase-II on the promoter to activate gene transcription. To date, very little is known about the mechanism by which miRNA regulates RNA activation (RNAa) and their role in tumor progression. This is an emerging field in RNA biology. In this chapter, we describe the mechanisms utilized by miRNAs to activate transcription.
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Affiliation(s)
- Ramani Ramchandran
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Pradeep Chaluvally-Raghavan
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA. .,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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36
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Nogimori T, Furutachi K, Ogami K, Hosoda N, Hoshino SI. A novel method for stabilizing microRNA mimics. Biochem Biophys Res Commun 2019; 511:422-426. [PMID: 30799083 DOI: 10.1016/j.bbrc.2019.02.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate gene expression at post-transcriptional level via translational repression and/or mRNA degradation. miRNAs are associated with many cellular processes, and down-regulation of miRNAs causes numerous diseases including cancer, neurological disorders, inflammation, and cardiovascular diseases, for which miRNA replacement therapy has emerged as a promising approach. This approach aims to restore down-regulated miRNAs using synthetic miRNA mimics. However, it remains a critical issue that miRNA mimics are unstable and transient in cells. Here, we first show that miRNA mimics are rapidly degraded by a mechanism different from Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay, which degrades endogenous miRNAs, and newly identified 2'-5'-oligoadenylate synthetase (OAS)/RNase L as key factors responsible for the degradation of miRNA mimics in human cells. Our results suggest that the OAS1 recognizes miRNA mimics and produces 2'-5'-oligoadenylates (2-5A), which leads to the activation of latent endoribonuclease RNase L to degrade miRNA mimics. A small-molecule inhibitor that blocks RNase L can stabilize miRNA mimics. These findings provide a promising method for the stabilization of miRNA mimics, as well as for the efficient miRNA replacement therapy.
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Affiliation(s)
- Takuto Nogimori
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Kazuya Furutachi
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Koichi Ogami
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
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37
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miR-181b regulates ER stress induced neuron death through targeting Heat Shock Protein A5 following intracerebral haemorrhage. Immunol Lett 2018; 206:1-10. [PMID: 30503822 DOI: 10.1016/j.imlet.2018.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/01/2018] [Accepted: 11/28/2018] [Indexed: 11/22/2022]
Abstract
Endoplasmic reticulum (ER) stress acts as a protein folding and contributes to neuronal damage and neurological deterioration following intracerebral hemorrhage (ICH). Heat Shock Protein A5 (HSPA5) serves as an essential regulator of the endoplasmic reticulum (ER) stress response. However, the specific mechanism has not been will identified. Primary cortical neurons from C57BL/6 mice were subjected to erythrocyte lysates. Cell viability, microRNA and HSPA5 levels, and ER stress was detected. The interaction between microRNA and the target HSPA5 was identified by dual luciferase reporter gene assay. In addition, inflammatory cytokines, brain edema, and neurological functions in ICH mice were also assessed. Erythrocyte lysates induced ER stress and neuron damage, downregulated miR-181b and upregulated HSPA5 levels. MiR-181b suppressed HSPA5 expression by directly binding its 3'-untranslated region. Correspondingly, our data demonstrated that overexpression of miR-181b attenuated erythrocyte lysates induced neuronal necrosis and apoptosis. In vivo, downregulated miR-181b increased the HSPA5 level, along with significant elevations of pro-inflammatory cytokines, brain edema, and neurological injury following ICH. HSPA5 pathway plays an important role in ER stress induced brain damage following ICH. In addition, miR-181b has neuroprotective effects that alleviates neurological injury and represents a promising therapeutic strategy in ICH.
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38
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Ferino A, Miglietta G, Picco R, Vogel S, Wengel J, Xodo LE. MicroRNA therapeutics: design of single-stranded miR-216b mimics to target KRAS in pancreatic cancer cells. RNA Biol 2018; 15:1273-1285. [PMID: 30306823 PMCID: PMC6284578 DOI: 10.1080/15476286.2018.1526536] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Datasets reporting microRNA expression profiles in normal and cancer cells show that miR-216b is aberrantly downregulated in pancreatic ductal adenocarcinoma (PDAC). We found that KRAS, whose mutant G12D allele drives the pathogenesis of PDAC, is a target of miR-216b. To suppress oncogenic KRAS in PDAC cells, we designed single-stranded (ss) miR-216b mimics with unlocked nucleic acid (UNA) modifications to enhance their nuclease resistance. We prepared variants of ss-miR-216b mimics with and without a 5ʹ phosphate group. Both variants strongly suppressed oncogenic KRAS in PDAC cells and inhibited colony formation in pancreatic cancer cells. We observed that the designed ss-miR-216b mimics engaged AGO2 to promote the silencing of KRAS. We also tested a new delivery strategy based on the use of palmityl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with ss-miR-216b conjugated with two palmityl chains and a lipid-modified cell penetrating peptide (TAT). These versatile nanoparticles suppressed oncogenic KRAS in PDAC cells.
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Affiliation(s)
- Annalisa Ferino
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Giulia Miglietta
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Raffaella Picco
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Stefan Vogel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Jesper Wengel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Luigi E Xodo
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
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39
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Liu J, Liu Z, Corey DR. The Requirement for GW182 Scaffolding Protein Depends on Whether Argonaute Is Mediating Translation, Transcription, or Splicing. Biochemistry 2018; 57:5247-5256. [PMID: 30086238 DOI: 10.1021/acs.biochem.8b00602] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
GW182 and argonaute 2 (AGO2) are core proteins of the RNA interference complex. GW182 is a scaffolding protein that physically associates with AGO2 and bridges its interactions with other proteins. A fundamental problem in biology is how scaffolding proteins adapt or contribute to differing functional demands within cells. Here we test the necessity for human GW182 proteins (paralogs TNRC6A, TNRC6B, and TNRC6C) for several mechanisms of small duplex RNA-mediated control of gene expression, including translational silencing by miRNAs, translational silencing by siRNAs, transcriptional silencing, transcriptional activation, and splicing. We find that GW182 is required for transcriptional activation and for the activity of miRNAs but is dispensable for the regulation of splicing, transcriptional silencing, and the action of siRNAs. AGO2, by contrast, is necessary for each of these processes. Our data suggest that GW182 does not alter AGO2 to make it active. Instead, GW182 organizes protein complexes around AGO2. Sometimes this higher level of organization is necessary, and sometimes it is not. AGO2 and GW182 offer an example for how a partnership between a scaffolding protein and a functional protein can be powerful but not obligatory.
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Affiliation(s)
- Jing Liu
- Departments of Pharmacology and Biochemistry , The University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Zhongtian Liu
- Departments of Pharmacology and Biochemistry , The University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States.,College of Animal Science and Technology , Northwest A&F University , Shaanxi , China 712100
| | - David R Corey
- Departments of Pharmacology and Biochemistry , The University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
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40
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Das A, Samidurai A, Salloum FN. Deciphering Non-coding RNAs in Cardiovascular Health and Disease. Front Cardiovasc Med 2018; 5:73. [PMID: 30013975 PMCID: PMC6036139 DOI: 10.3389/fcvm.2018.00073] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
After being long considered as “junk” in the human genome, non-coding RNAs (ncRNAs) currently represent one of the newest frontiers in cardiovascular disease (CVD) since they have emerged in recent years as potential therapeutic targets. Different types of ncRNAs exist, including small ncRNAs that have fewer than 200 nucleotides, which are mostly known as microRNAs (miRNAs), and long ncRNAs that have more than 200 nucleotides. Recent discoveries on the role of ncRNAs in epigenetic and transcriptional regulation, atherosclerosis, myocardial ischemia/reperfusion (I/R) injury and infarction (MI), adverse cardiac remodeling and hypertrophy, insulin resistance, and diabetic cardiomyopathy prompted vast interest in exploring candidate ncRNAs for utilization as potential therapeutic targets and/or diagnostic/prognostic biomarkers in CVDs. This review will discuss our current knowledge concerning the roles of different types of ncRNAs in cardiovascular health and disease and provide some insight on the cardioprotective signaling pathways elicited by the non-coding genome. We will highlight important basic and clinical breakthroughs that support employing ncRNAs for treatment or early diagnosis of a variety of CVDs, and also depict the most relevant limitations that challenge this novel therapeutic approach.
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Affiliation(s)
- Anindita Das
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Arun Samidurai
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Fadi N Salloum
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
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41
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Ji Q, Xu X, Song Q, Xu Y, Tai Y, Goodman SB, Bi W, Xu M, Jiao S, Maloney WJ, Wang Y. miR-223-3p Inhibits Human Osteosarcoma Metastasis and Progression by Directly Targeting CDH6. Mol Ther 2018; 26:1299-1312. [PMID: 29628305 PMCID: PMC5993963 DOI: 10.1016/j.ymthe.2018.03.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/26/2018] [Accepted: 03/10/2018] [Indexed: 01/08/2023] Open
Abstract
Cadherin-6 (CDH6) is aberrantly expressed in cancer and closely associated with tumor progression. However, the functions of CDH6 in human osteosarcoma and the molecular mechanisms underlying CDH6 in osteosarcoma oncogenesis remain poorly understood. In this work, we assessed the role of CDH6 in human osteosarcoma and identified that the expression of CDH6 was closely related with the overall survival and poor prognosis of osteosarcoma patients. MicroRNAs (miRNAs) have been implicated as important epigenetic regulators during the progression of osteosarcoma. Using dual-luciferase reporter assays, we showed that miR-223-3p suppresses CDH6 expression by directly binding to the 3' UTR of CDH6. miR-223-3p overexpression significantly inhibited cell invasion, migration, growth, and proliferation by suppressing the CDH6 expression in vivo and in vitro. Besides, CDH6 overexpression in the miR-223-3p-transfected osteosarcoma cells effectively rescued the inhibition of cell invasion, migration, growth, and proliferation mediated by miR-223-3p. Additionally, Kaplan-Meier analysis suggests that the expression of miR-223-3p predicts favorable clinical outcomes for osteosarcoma patients. Moreover, the expression of miR-223-3p was downregulated in osteosarcoma patients and was negatively associated with the expression of CDH6. Collectively, these data highlight that miR-223-3p/CDH6 axis is an important novel pleiotropic regulator and could early predict the metastatic potential in human osteosarcoma treatments.
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Affiliation(s)
- Quanbo Ji
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing, China; Department of Orthopaedic Surgery, Stanford University, Stanford, CA, USA
| | - Xiaojie Xu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Qi Song
- Department of Oncology, General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Yameng Xu
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanhong Tai
- Department of Pathology, the 307 Hospital of Chinese People's Liberation Army, Beijing, China
| | - Stuart B Goodman
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA, USA
| | - Wenzhi Bi
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Meng Xu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Shunchang Jiao
- Department of Oncology, General Hospital of Chinese People's Liberation Army, Beijing, China
| | - William J Maloney
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA, USA.
| | - Yan Wang
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing, China.
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42
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Tang L, Chen HY, Hao NB, Tang B, Guo H, Yong X, Dong H, Yang SM. microRNA inhibitors: Natural and artificial sequestration of microRNA. Cancer Lett 2017; 407:139-147. [PMID: 28602827 DOI: 10.1016/j.canlet.2017.05.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNAs) is post-transcriptional regulator of mRNA. However, the prevalence and activity of miRNA are regulated by other regulators. miRNA inhibitors are natural or artificial RNA transcripts that sequestrate miRNAs and decrease or even eliminate miRNA activity. Competing endogenous RNAs (ceRNAs) are natural and intracellular miRNA inhibitors that compete to bind to shared miRNA recognition elements (MREs) to decrease microRNA availability and relieve the repression of target RNAs. In recent years, studies have revealed that ceRNA crosstalk is involved in many pathophysiological processes and adds a new dimension to miRNA regulation. Artificial miRNA inhibitors are RNA transcripts that are synthesized via chemical and genetic methods. Artificial miRNA inhibitors can be used in miRNA loss-of-function research and gene therapies for certain diseases. In this review, we summarize the recent advances in the two different types of miRNA inhibitors.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong-Yan Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Ning-Bo Hao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong Guo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xin Yong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hui Dong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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43
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Hu J, Rigo F, Prakash TP, Corey DR. Recognition of c9orf72 Mutant RNA by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2017; 27:87-94. [PMID: 28005462 PMCID: PMC5372765 DOI: 10.1089/nat.2016.0655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023] Open
Abstract
Mutations within the chromosome 9 open reading frame 72 (c9orf72) gene are associated with both familial amyotrophic lateral sclerosis and frontotemporal dementia. The mutation leads to an expanded GGGGCC hexanucleotide repeat within the first intron of c9orf72 and an expanded CCCCGG repeat within a corresponding antisense transcript. Both the mutant intronic and antisense RNAs have been implicated in disease. We have previously reported that duplex RNAs complementary to the repeats can recognize disease-causing RNA and block detection of nuclear foci formed by the mutant transcripts. Here, we test the hypothesis that inhibition can also be achieved by single-stranded silencing RNAs (ss-siRNAs). ss-siRNAs are single-stranded antisense oligonucleotides (ASOs) that function through RNAi interference (RNAi) to silence gene expression. ss-siRNAs can block the expanded repeats within both intronic RNA and the antisense transcripts. Inhibition is more potent than by analogous duplex RNAs. Our data suggest that the potent effects on foci are caused by a combination of mechanisms including RNAi and direct binding of the ss-siRNA to the target transcripts. These findings reinforce the suggestion that ss-siRNAs combine the favorable properties of duplex RNA and single-stranded ASOs.
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Affiliation(s)
- Jiaxin Hu
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Frank Rigo
- 3 Ionis Pharmaceuticals , Carlsbad, California
| | | | - David R Corey
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
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44
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Ajami M, Pazoki-Toroudi H, Amani H, Nabavi SF, Braidy N, Vacca RA, Atanasov AG, Mocan A, Nabavi SM. Therapeutic role of sirtuins in neurodegenerative disease and their modulation by polyphenols. Neurosci Biobehav Rev 2016; 73:39-47. [PMID: 27914941 DOI: 10.1016/j.neubiorev.2016.11.022] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/26/2016] [Accepted: 11/26/2016] [Indexed: 12/15/2022]
Abstract
Searching for effective therapeutic agents to prevent neurodegeneration is a challenging task due to the growing list of neurodegenerative disorders associated with a multitude of inter-related pathways. The induction and inhibition of several different signaling pathways has been shown to slow down and/or attenuate neurodegeneration and decline in cognition and locomotor function. Among these signaling pathways, a new class of enzymes known as sirtuins or silent information regulators of gene transcription has been shown to play important regulatory roles in the ageing process. SIRT1, a nuclear sirtuin, has received particular interest due to its role as a deacetylase for several metabolic and signaling proteins involved in stress response, apoptosis, mitochondrial function, self-renewal, and neuroprotection. A new strategy to treat neurodegenerative diseases is targeted therapy. In this paper, we reviewed up-to-date findings regarding the targeting of SIRT1 by polyphenolic compounds, as a new approach in the search for novel, safe and effective treatments for neurodegenerative diseases. .
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Affiliation(s)
- Marjan Ajami
- National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center and Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Amani
- Physiology Research Center and Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Australia.
| | - Rosa Anna Vacca
- Institute of Biomembranes and Bioenergetics, National Council of Research, Bari, Italy.
| | - Atanas Georgiev Atanasov
- Department of Pharmacognosy, University of Vienna, 1090 Vienna, Austria; Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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45
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Abstract
MicroRNAs (miRNAs) provide a unique mechanism of gene regulation and play a key role in different pathologies ranging from metabolic diseases to cancer. miRNAs can impact biological function as either suppressors of gene expression when their expression levels are enhanced in a disease state or they can cause upregulation of gene expression when their expression levels are reduced. Therefore both gain- and loss-of- function strategies are needed to fully exploit their therapeutic potential. miRNA research first focused on inhibition of single miRNAs using oligonucleotide inhibitors. However, more recent approaches explore the potential to deliver oligonucleotides to mimic miRNA expression or to employ small molecules to increase or inhibit miRNA function. Although we need to know more about the potential side effects and tissue specific delivery systems, these studies provide grounds to further exploit miRNAs as novel therapeutic targets in the clinic.
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Affiliation(s)
- Jan Krützfeldt
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Zurich and University Hospital Zurich, Switzerland; Competence Center Personalized Medicine, ETH Zurich and University of Zurich, Switzerland; Zurich Center for Integrative Human Physiology, University of Zurich, Switzerland.
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