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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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Jin J, Yang QQ, Zhou YL. Non-Viral Delivery of Gene Therapy to the Tendon. Polymers (Basel) 2022; 14:polym14163338. [PMID: 36015594 PMCID: PMC9415435 DOI: 10.3390/polym14163338] [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: 06/09/2022] [Revised: 07/07/2022] [Accepted: 07/18/2022] [Indexed: 01/19/2023] Open
Abstract
The tendon, as a compact connective tissue, is difficult to treat after an acute laceration or chronic degeneration. Gene-based therapy is a highly efficient strategy for diverse diseases which has been increasingly applied in tendons in recent years. As technology improves by leaps and bounds, a wide variety of non-viral vectors have been manufactured that attempt to have high biosecurity and transfection efficiency, considered to be a promising treatment modality. In this review, we examine the unwanted biological barriers, the categories of applicable genes, and the introduction and comparison of non-viral vectors. We focus on lipid-based nanoparticles and polymer-based nanoparticles, differentiating between them based on their combination with diverse chemical modifications and scaffolds.
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The Regulatory Effects of MicroRNAs on Tumor Immunity. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2121993. [PMID: 35909469 PMCID: PMC9329000 DOI: 10.1155/2022/2121993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/24/2022] [Indexed: 12/13/2022]
Abstract
MicroRNAs are endogenous noncoding small RNAs that posttranscriptionally regulate the expressions of their target genes. Accumulating research shows that miRNAs are crucial regulators of immune cell growth and antitumor immune response. Studies on miRNAs and tumors primarily focus on the tumor itself. At the same time, relatively few studies on the indirect regulatory effects of miRNAs in the development of tumors are achieved by affecting the immune system of tumor hosts and altering their immune responses. This review discusses the influence of miRNAs on the antitumor immune system.
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Kanoria S, Rennie WA, Carmack CS, Lu J, Ding Y. N 6-methyladenosine enhances post-transcriptional gene regulation by microRNAs. BIOINFORMATICS ADVANCES 2022; 2:vbab046. [PMID: 35098135 PMCID: PMC8792947 DOI: 10.1093/bioadv/vbab046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Indexed: 01/27/2023]
Abstract
MOTIVATION N 6-methyladenosine (m6A) is the most prevalent modification in eukaryotic messenger RNAs. MicroRNAs (miRNAs) are abundant post-transcriptional regulators of gene expression. Correlation between m6A and miRNA-targeting sites has been reported to suggest possible involvement of m6A in miRNA-mediated gene regulation. However, it is unknown what the regulatory effects might be. In this study, we performed comprehensive analyses of high-throughput data on m6A and miRNA target binding and regulation. RESULTS We found that the level of miRNA-mediated target suppression is significantly enhanced when m6A is present on target mRNAs. The evolutionary conservation for miRNA-binding sites with m6A modification is significantly higher than that for miRNA-binding sites without modification. These findings suggest functional significance of m6A modification in post-transcriptional gene regulation by miRNAs. We also found that methylated targets have more stable structure than non-methylated targets, as indicated by significantly higher GC content. Furthermore, miRNA-binding sites that can be potentially methylated are significantly less accessible without methylation than those that do not possess potential methylation sites. Since either RNA-binding proteins or m6A modification by itself can destabilize RNA structure, we propose a model in which m6A alters local target secondary structure to increase accessibility for efficient binding by Argonaute proteins, leading to enhanced miRNA-mediated regulation. AVAILABILITY AND IMPLEMENTATION N/A.
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Affiliation(s)
- Shaveta Kanoria
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, NY 12208, USA
| | - William A Rennie
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, NY 12208, USA
| | - Charles Steven Carmack
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, NY 12208, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA,To whom correspondence should be addressed. or
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, NY 12208, USA,To whom correspondence should be addressed. or
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Sadashiv, Sharma P, Dwivedi S, Tiwari S, Singh PK, Pal A, Kumar S. Micro (mi) RNA and Diabetic Retinopathy. Indian J Clin Biochem 2022; 37:267-274. [DOI: 10.1007/s12291-021-01018-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022]
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Dedeoğlu BG, Noyan S. Experimental MicroRNA Targeting Validation. Methods Mol Biol 2022; 2257:79-90. [PMID: 34432274 DOI: 10.1007/978-1-0716-1170-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
microRNAs (miRNAs) have recently been recognized as a new dimension of posttranscriptional regulation. It is well defined that most human protein-coding genes are regulated by one or more miRNAs. Therefore, it is crucial to identify genes targeted by the miRNAs to better understand their functions. Although bioinformatics tools have the ability to identify target candidates it is still essential to identify physiological targets by experimental approaches. Currently, the majority of miRNA-target experimental validation approaches assess the changes in target expression in mRNA or protein level upon miRNA upregulation or downregulation. Additionally, finding out direct physical interactions between miRNAs and their targets is also among the experimental techniques. In this chapter we reviewed the existing experimental techniques for miRNA target identification by considering their advantages and potential drawbacks.
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Affiliation(s)
| | - Senem Noyan
- Biotechnology Institute, Ankara University, Ankara, Turkey
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Lin Y, Zhao M, Bai L, Li H, Xu Y, Li X, Xie J, Zhang Y, Zheng D. Renal-targeting peptide-microRNA nanocomplex for near IR imaging and therapy of renal ischemia/reperfusion injury. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Dasgupta I, Chatterjee A. Recent Advances in miRNA Delivery Systems. Methods Protoc 2021; 4:mps4010010. [PMID: 33498244 PMCID: PMC7839010 DOI: 10.3390/mps4010010] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation repression or mRNA degradation. Functional studies have demonstrated that miRNAs are engaged in virtually every physiological process and, consequently, miRNA dysregulations have been linked to multiple human pathologies. Thus, miRNA mimics and anti-miRNAs that restore miRNA expression or downregulate aberrantly expressed miRNAs, respectively, are highly sought-after therapeutic strategies for effective manipulation of miRNA levels. In this regard, carrier vehicles that facilitate proficient and safe delivery of miRNA-based therapeutics are fundamental to the clinical success of these pharmaceuticals. Here, we highlight the strengths and weaknesses of current state-of-the-art viral and non-viral miRNA delivery systems and provide perspective on how these tools can be exploited to improve the outcomes of miRNA-based therapeutics.
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Affiliation(s)
- Ishani Dasgupta
- Horae Gene Therapy Center, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA;
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Correspondence:
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Limothai U, Dinhuzen J, Payongsri T, Tachaboon S, Tangkijvanich P, Chuaypen N, Srisawat N. Circulating microtranscriptome profiles reveal distinct expression of microRNAs in severe leptospirosis. PLoS Negl Trop Dis 2020; 14:e0008809. [PMID: 33175842 PMCID: PMC7682886 DOI: 10.1371/journal.pntd.0008809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/23/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
Biomarkers to predict the severity of leptospirosis are still lacking. This study aimed to identify and validate microRNAs in patients with severe leptospirosis, that could potentially be used as biomarkers for predicting an unfavorable outcome. Serum samples were collected from participants with definite diagnosis of leptospirosis. The participants were divided into two groups, non-severe and severe leptospirosis, as defined by the Specific Organ Sequential Organ Failure (SOFA) Score of more than two in any organ. Microtranscriptome analysis was performed using the NanoString miRNA Expression Assay. The expression level of candidate miRNAs was then validated by quantitative RT-PCR. Based on the NanoString, the microtranscriptome profile of the severe group was significantly different from that of the non-severe group. Upregulation of miR155-5p, miR362-3p, miR502-5p, miR601, miR1323, and miR630 in the severe group were identified, and further investigated. A total of 119 participants were enrolled in the validation cohort. Serum miR155-5p and miR630 levels were significantly higher in the severe group compared to the non-severe group. The combined use of miR155-5p or miR-630 with serum bicarbonate levels had an AUC of 0.79 (95%CI; 0.69-0.89, p<0.001) in identifying the severity of the disease. This data provides the first evidence that the microtranscriptome profiles of patients with severe leptospirosis were different from the non-severe group. Serum miR155-5p and miR630 levels might be novel biomarkers for identifying severe leptospirosis.
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Affiliation(s)
- Umaporn Limothai
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Critical Care Nephrology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Janejira Dinhuzen
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Critical Care Nephrology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Titipon Payongsri
- Department of Anesthesiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sasipha Tachaboon
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Critical Care Nephrology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (NC); (NS)
| | - Nattachai Srisawat
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Critical Care Nephrology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, Thailand
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Critical Care Medicine, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- * E-mail: (NC); (NS)
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Gupta M, Chandan K, Sarwat M. Role of microRNA and Long Non-Coding RNA in Hepatocellular Carcinoma. Curr Pharm Des 2020; 26:415-428. [PMID: 31939724 PMCID: PMC7403690 DOI: 10.2174/1381612826666200115093835] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
Hepatocellular carcinoma (HCC) accounts for about 80-90% of all liver cancers and is found to be the third most common cause of cancer mortality in the Asia-Pacific region. Risk factors include hepatitis B and C virus, cirrhosis, aflatoxin-contaminated food, alcohol, and diabetes. Surgically removing the tumor tissue seems effective but a high chance of recurrence has led to an urgent need to develop novel molecules for the treatment of HCC. Clinical management with sorafenib is found to be effective but it is only able to prolong survival for a few months. Various side effects like gastrointestinal and abdominal pain, hypertension, and hemorrhage are also associated with sorafenib, which calls for the unmet need of effective therapies against HCC. Similarly, the genetic mechanisms behind the occurrence of HCC are still unknown and need to be expounded further for developing newer candidates. Since unearthing the concept of these variants, transcriptomics has revealed the role of non-coding RNAs (ncRNAs) in many cellular, physiological and pathobiological processes. They are also found to be widely associated and abundantly expressed in a variety of cancer. Aberrant expression and mutations are closely related to tumorigenesis and metastasis and hence are classified as novel biomarkers and therapeutic targets for the treatment of cancer, including HCC. Herein, this review summarises the relationship between ncRNAs and hepatocellular carcinoma.
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Affiliation(s)
- Meenakshi Gupta
- Amity Institute of Pharmacy, Amity University, Noida-201313, Uttar Pradesh, India
| | - Kumari Chandan
- Amity Institute of Pharmacy, Amity University, Noida-201313, Uttar Pradesh, India
| | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida-201313, Uttar Pradesh, India
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miR-21 Overexpression Promotes Esophageal Squamous Cell Carcinoma Invasion and Migration by Repressing Tropomyosin 1. Gastroenterol Res Pract 2020; 2020:6478653. [PMID: 33193757 PMCID: PMC7641708 DOI: 10.1155/2020/6478653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/22/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
The migration and invasion of esophageal squamous cell carcinoma are associated with clinical outcomes, however, the mechanisms remain poorly understood. Here, we found that miR-21 is significantly overexpressed in ESCC, lung cancer, and bladder cancer compared with the adjacent normal tissue. MiR-21 and TPM1 expressions were analyzed by RT-qPCR and WB in 30 ESCC, 10 lung cancer, and 10 bladder cancer clinical specimens, each with matched adjacent normal tissue. Knockdown and overexpression of miR-21 as well as knockdown of TPM1 in ESCC cell lines were performed using synthetic oligonucleotides. TPM1 3′UTR luciferase reporter constructs were used to investigate targeting of TPM1 by miR-21. ESCC migration and invasion were assessed using transwell migration and invasion assays. Inhibition of miR-21 reduced migration and invasion in two ESCC cell lines, and overexpression of miR-21 promoted migration and invasion in vitro. Interestingly, TPM1 exhibited inverse patterns of expression compared with miR-21 in tissues and cell lines. Luciferase reporter assays demonstrated that TPM1 was directly regulated by miR-21. Moreover, the forced overexpression of miR-21 repressed the TPM1 expression, while silencing of miR-21 restored the TPM1 expression in ESCC cell lines. What is more, simultaneous silencing of miR-21 and TPM1 expressions did not alter the migratory and invasive characteristics demonstrating that the effects of miR-21 were mediated through TPM1. In conclusion, the aberrant overexpression of miR-21 is common in cancer and promotes the migration and invasion of ESCC through inhibiting the TPM1 expression. These results suggest that miR-21 may be a novel predictive marker and therapeutic target for treatment of ESCC.
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Regulatory Mechanisms of Epigenetic miRNA Relationships in Human Cancer and Potential as Therapeutic Targets. Cancers (Basel) 2020; 12:cancers12102922. [PMID: 33050637 PMCID: PMC7600069 DOI: 10.3390/cancers12102922] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary By the virtue of targeting multiple genes, a microRNA (miRNA) can infer variable consequences on tumorigenesis by appearing as both a tumour suppressor and oncogene. miRNAs can regulate gene expression by modulating genome-wide epigenetic status of genes that are involved in various cancers. These miRNAs perform direct inhibition of key mediators of the epigenetic machinery, such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) genes. Along with miRNAs gene expression, similar to other protein-coding genes, miRNAs are also controlled by epigenetic mechanisms. Overall, this reciprocal interaction between the miRNAs and the epigenetic architecture is significantly implicated in the aberrant expression of miRNAs detected in various human cancers. Comprehensive knowledge of the miRNA-epigenetic dynamics in cancer is essential for the discovery of novel anticancer therapeutics. Abstract Initiation and progression of cancer are under both genetic and epigenetic regulation. Epigenetic modifications including alterations in DNA methylation, RNA and histone modifications can lead to microRNA (miRNA) gene dysregulation and malignant cellular transformation and are hereditary and reversible. miRNAs are small non-coding RNAs which regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. miRNAs can target epigenetic modifier enzymes involved in epigenetic modulation, establishing a trilateral regulatory “epi–miR–epi” feedback circuit. The intricate association between miRNAs and the epigenetic architecture is an important feature through which to monitor gene expression profiles in cancer. This review summarises the involvement of epigenetically regulated miRNAs and miRNA-mediated epigenetic modulations in various cancers. In addition, the application of bioinformatics tools to study these networks and the use of therapeutic miRNAs for the treatment of cancer are also reviewed. A comprehensive interpretation of these mechanisms and the interwoven bond between miRNAs and epigenetics is crucial for understanding how the human epigenome is maintained, how aberrant miRNA expression can contribute to tumorigenesis and how knowledge of these factors can be translated into diagnostic and therapeutic tool development.
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Sajid MI, Moazzam M, Kato S, Yeseom Cho K, Tiwari RK. Overcoming Barriers for siRNA Therapeutics: From Bench to Bedside. Pharmaceuticals (Basel) 2020; 13:E294. [PMID: 33036435 PMCID: PMC7600125 DOI: 10.3390/ph13100294] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022] Open
Abstract
The RNA interference (RNAi) pathway possesses immense potential in silencing any gene in human cells. Small interfering RNA (siRNA) can efficiently trigger RNAi silencing of specific genes. FDA Approval of siRNA therapeutics in recent years garnered a new hope in siRNA therapeutics. However, their therapeutic use is limited by several challenges. siRNAs, being negatively charged, are membrane-impermeable and highly unstable in the systemic circulation. In this review, we have comprehensively discussed the extracellular barriers, including enzymatic degradation of siRNAs by serum endonucleases and RNAases, rapid renal clearance, membrane impermeability, and activation of the immune system. Besides, we have thoroughly described the intracellular barriers such as endosomal trap and off-target effects of siRNAs. Moreover, we have reported most of the strategies and techniques in overcoming these barriers, followed by critical comments in translating these molecules from bench to bedside.
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Affiliation(s)
- Muhammad Imran Sajid
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (M.I.S.); (S.K.); (K.Y.C.)
- Faculty of Pharmacy, University of Central Punjab, Lahore 54000, Pakistan;
| | - Muhammad Moazzam
- Faculty of Pharmacy, University of Central Punjab, Lahore 54000, Pakistan;
| | - Shun Kato
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (M.I.S.); (S.K.); (K.Y.C.)
| | - Kayley Yeseom Cho
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (M.I.S.); (S.K.); (K.Y.C.)
| | - Rakesh Kumar Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (M.I.S.); (S.K.); (K.Y.C.)
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Beylerli OA, Azizova ST, Konovalov NA, Akhmedov AD, Gareev IF, Belogurov AA. [Non-coding RNAs as therapeutic targets in spinal cord injury]. ZHURNAL VOPROSY NEĬROKHIRURGII IMENI N. N. BURDENKO 2020; 84:104-110. [PMID: 32759933 DOI: 10.17116/neiro202084031104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Spinal cord injury (SCI) may be followed by persistent motor dysfunction and somatosensory disturbances that negatively influences the quality of life of patients and creates a significant economic burden. Analysis of secondary biological processes associated with changes in genetic expression is becoming increasingly important every day in understanding the pathophysiology of spinal cord injury. The results of international sequencing of the human genome were analyzed in 2004. These data revealed about 20,000 protein-coding genes covering near 2% of the total genomic sequence. The vast majority of gene transcripts are actually characterized as non-coding RNAs (ncRNAs). These RNA clusters do not encode functional proteins and ensure post-transcriptional regulation of gene expression. The clusters may be small (approximately 20 nucleotides) known as miRNAs or the transcripts can enroll over 200 nucleotides defined as long non-coding RNAs (lncRNAs). Some modern studies describe transient expression of microRNA in case of spinal cord injury. These RNAs are associated with inflammation and apoptosis, functional recovery and regeneration. Large-scale genomic analysis has demonstrated the existence of multiple lncRNAs whose expression is associated with some processes of spinal cord injury. lncRNA can be divided into two categories depending on the position in relation to the coding genes: intergenic and intragenic. Intergenic lncRNAs is currently the most studied class. Intragenic lncRNAs can be subdivided depending on the overlap of the coding genes (antisense, intron, etc.). According to recent studies, long non-coding RNAs are abundantly present in the tissues of central nervous system and may be crucial in the pathogenesis of certain diseases of nervous system. At the cellular level, it has been shown that lncRNAs regulate the expression of protein-coding RNAs. Moreover, these molecules are involved into such processes as neuronal death, demyelination and glia activation. This review is devoted to the role of ncRNAs in the pathogenesis of spinal cord injury and their potential use as targets for the treatment of consequences of spinal cord injury.
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Affiliation(s)
- O A Beylerli
- Bashkir State Medical University of the Ministry of Health of the Russian Federation, Ufa, Russia
| | - Sh T Azizova
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | - I F Gareev
- Bashkir State Medical University of the Ministry of Health of the Russian Federation, Ufa, Russia
| | - A A Belogurov
- Shemyakin-Ovcinnicov Institute of Bioorganic Chemistry, Moscow, Russia
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Khalife H, Skafi N, Fayyad-Kazan M, Badran B. MicroRNAs in breast cancer: New maestros defining the melody. Cancer Genet 2020; 246-247:18-40. [PMID: 32805688 DOI: 10.1016/j.cancergen.2020.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/07/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs, short non-coding single-stranded RNAs, are important regulators and gatekeepers of the coding genes in the human genome. MicroRNAs are highly conserved among species and expressed in different tissues and cell types. They are involved in almost all the biological processes as apoptosis, proliferation, cell cycle arrest and differentiation. Playing all these roles, it is not surprising that the deregulation of the microRNA profile causes a number of diseases including cancer. Breast cancer, the most commonly diagnosed malignancy in women, accounts for the highest cancer-related deaths worldwide. Different microRNAs were shown to be up or down regulated in breast cancer. MicroRNAs can function as oncogenes or tumor suppressors according to their targets. In this review, the most common microRNAs implicated in breast cancer are fully illustrated with their targets. Besides, the review highlights the effect of exosomal microRNA on breast cancer and the effect of microRNAs on drug and therapies resistance as well as the miRNA-based therapeutic strategies used until today.
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Affiliation(s)
- Hoda Khalife
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
| | - Najwa Skafi
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
| | - Mohammad Fayyad-Kazan
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon; Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Bassam Badran
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
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Segal M, Biscans A, Gilles ME, Anastasiadou E, De Luca R, Lim J, Khvorova A, Slack FJ. Hydrophobically Modified let-7b miRNA Enhances Biodistribution to NSCLC and Downregulates HMGA2 In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:267-277. [PMID: 31855835 PMCID: PMC6926262 DOI: 10.1016/j.omtn.2019.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have increasingly been shown to be involved in human cancer, and interest has grown about the potential use of miRNAs for cancer therapy. miRNA levels are known to be altered in cancer cells, including in non-small cell lung cancer (NSCLC), a subtype of lung cancer that is the most prevalent form of cancer worldwide and that lacks effective therapies. The let-7 miRNA is involved in the regulation of oncogene expression in cells and directly represses cancer growth in the lung. let-7 is therefore a potential molecular target for tumor therapy. However, applications of RNA interference for cancer research have been limited by a lack of simple and efficient methods to deliver oligonucleotides (ONs) to cancer cells. In this study, we have used in vitro and in vivo approaches to show that HCC827 cells internalize hydrophobically modified let-7b miRNAs (hmiRNAs) added directly to the culture medium without the need for lipid formulation. We identified functional let-7b hmiRNAs targeting the HMGA2 mRNA, one of the let-7 target genes upregulated in NSCLC, and show that direct uptake in HCC827 cells induced potent and specific gene silencing in vitro and in vivo. Thus, hmiRNAs constitute a novel class of ONs that enable functional studies of genes involved in cancer biology and are potentially therapeutic molecules.
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Affiliation(s)
- Meirav Segal
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maud-Emmanuelle Gilles
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Eleni Anastasiadou
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Roberto De Luca
- HMS Initiative for RNA Medicine, Department of Neurology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Jihoon Lim
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA.
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17
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Kim JO, Ahn EH, Sakong JH, An HJ, Park HS, Kim YR, Lee JR, Lee WS, Kim NK. Association of miR-27aA>G, miR-423C>a, miR-449bA>G, and miR-604A>G Polymorphisms with Risk of Recurrent Implantation Failure. Reprod Sci 2020; 27:29-38. [PMID: 32046408 DOI: 10.1007/s43032-019-00031-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/08/2019] [Indexed: 12/01/2022]
Abstract
Recurrent implantation failure (RIF) is defined when pregnancy failure occurs after two consecutive in vitro fertilization-embryo transfers to the endometrium using at least four high-quality embryos in women. MicroRNAs are well-known function modulators and are involved in many diseases. Recently, studies on microRNA and recurrent pregnancy loss (RPL) have been actively carried out; however, single nucleotide polymorphisms of miRNA in RPL are not well known. Therefore, we set the aim of this study to identify whether polymorphisms in miRNAs that miR-27aA>G, miR-423C>A, miR-449bA>G, and miR-604A>G are risk factors for idiopathic recurrent implantation failure (RIF) in Korean women. Genotyping was assessed with a polymerase chain reaction-restriction fragment length polymorphism assay. We examined polymorphisms in four miRNA genes: miR-27aA>G, miR-423C>A, miR-449bA>G, and miR-604A>G. We found that the miR-27aA>G, miR-449bA>G, and miR-604A>G polymorphisms were significantly associated with a risk of RIF. In addition, the miR-27aA>G and miR-449bA>G polymorphisms were associated with the frequency of implantation failures. Specifically, the miR-449bAG+GG genotype was associated with RIF prevalence (total RIF: adjusted odd ratio [AOR] = 1.584, 95% CI = 1.008-2.490, P = 0.046; IF ≥ 3 group: AOR = 1.747, 95% CI = 1.088-2.803, P = 0.021; IF ≥ 4: AOR = 1.932, 95% CI = 1.122-3.327, P = 0.018). Based on these results, the miR-449b A>G may be a predisposing factor to RIF susceptibility. However, the mechanism underlying the function of miR-449b A>G in RIF remains to be determined and further studies are needed to improve understanding of the roles of miR-449b A>G, using a larger and more heterogeneous cohort.
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Affiliation(s)
- Jung Oh Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, South Korea
| | - Eun Hee Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, 13496, South Korea
| | - Jung Hyun Sakong
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, South Korea
| | - Hui Jeong An
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, South Korea
| | - Han Sung Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, South Korea
| | - Young Ran Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, 13496, South Korea
| | - Jung Ryeol Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Woo Sik Lee
- Fertility Center of CHA Gangnam Medical Center, CHA University, Gangnam, Seoul, 06135, South Korea.
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, South Korea.
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18
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Sabirzhanov B, Matyas J, Coll-Miro M, Yu LL, Faden AI, Stoica BA, Wu J. Inhibition of microRNA-711 limits angiopoietin-1 and Akt changes, tissue damage, and motor dysfunction after contusive spinal cord injury in mice. Cell Death Dis 2019; 10:839. [PMID: 31685802 PMCID: PMC6828685 DOI: 10.1038/s41419-019-2079-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/09/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023]
Abstract
Spinal cord injury (SCI) causes neuronal cell death and vascular damage, which contribute to neurological dysfunction. Given that many biochemical changes contribute to such secondary injury, treatment approaches have increasingly focused on combined therapies or use of multi-functional drugs. MicroRNAs (miRs) are small (20-23 nucleotide), non-protein-coding RNAs and can negatively regulate target gene expression at the post-transcriptional level. As individual miRs can potentially modulate expression of multiple relevant proteins after injury, they are attractive candidates as upstream regulators of the secondary SCI progression. In the present study we examined the role of miR-711 modulation after SCI. Levels of miR-711 were increased in injured spinal cord early after SCI, accompanied by rapid downregulation of its target angiopoietin-1 (Ang-1), an endothelial growth factor. Changes of miR-711 were also associated with downregulation of the pro-survival protein Akt (protein kinase B), another target of miR-711, with sequential activation of glycogen synthase kinase 3 and the pro-apoptotic BH3-only molecule PUMA. Central administration of a miR-711 hairpin inhibitor after SCI limited decreases of Ang-1/Akt expression and attenuated apoptotic pathways. Such treatment also reduced neuronal/axonal damage, protected microvasculature and improved motor dysfunction following SCI. In vitro, miR-711 levels were rapidly elevated by neuronal insults, but not by activated microglia and astrocytes. Together, our data suggest that post-traumatic miR-711 elevation contributes to neuronal cell death after SCI, in part by inhibiting Ang-1 and Akt pathways, and may serve as a novel therapeutic target.
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Affiliation(s)
- Boris Sabirzhanov
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA
| | - Jessica Matyas
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA
| | - Marina Coll-Miro
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA
| | - Laina Lijia Yu
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA
| | - Alan I Faden
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA.,University of Maryland Center to Advance Chronic Pain Research, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Bogdan A Stoica
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA
| | - Junfang Wu
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), School of Medicine, Baltimore, MD, USA. .,University of Maryland Center to Advance Chronic Pain Research, University of Maryland Baltimore, Baltimore, MD, 21201, USA.
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19
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Kaban K, Salva E, Akbuga J. Modulation of the dual-faced effects of miR-141 with chitosan/miR-141 nanoplexes in breast cancer cells. J Gene Med 2019; 21:e3116. [PMID: 31389101 DOI: 10.1002/jgm.3116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND miR-141, known as a tumor suppressive microRNA, is downregulated in breast cancer. However, recent contrasting studies report that it also acts as oncogene when it is upregulated. The present study aimed to investigate whether miR-141 is a tumor suppressor or oncogenic when it reaches normal levels in chitosan/miR-141 nanoplexes. METHODS Chitosan nanoplexes were prepared using simple complexation method. Nanoplexes were characterized by a gel retardation assay and zeta potential and particle size measurements. To determine the expression level of miR-141, a quantitative real-time polymerase chain reaction was performed. The effects of miR-141 mimics were investigated with respect to angiogenesis by vascular endothelial growth factor (VEGF), epithelial-mesenchymal transition (EMT) by E-cadherin, metastasis by Igfbp-4 and Tinagl1 enzyme-linked immunosorbent assays, invasion by an invasion chamber, and apoptosis by Annexin V. RESULTS The miR-141 expression levels of MDA-MB-231 and MDA-MB-435 cells by administration of chitosan/mimic miR-141 nanoplexes reached endogenous miR-141 levels of a non-tumorigenic epithelial breast cell line, MCF-10A. According to our results, metastasis, VEGF, EMT and invasion in breast cancer cells were diminished, whereas apoptosis increased by 1.5- and 2.4-fold in breast cancer cell lines as a result of the miR-141 mimics. CONCLUSIONS In conclusion, we have demonstrated that administration of miR-141 mimics at the determined doses to breast cancer cells revealed a tumor suppressor effect, and not the oncogenic face. The delivery of miR-141 by chitosan nanoplexes presents a promising approach for the suppression of breast cancer.
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Affiliation(s)
- Kubra Kaban
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Emine Salva
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Inonu University, Malatya, Turkey
| | - Julide Akbuga
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
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20
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Chan C, Guo N, Duan X, Han W, Xue L, Bryan D, Wightman SC, Khodarev NN, Weichselbaum RR, Lin W. Systemic miRNA delivery by nontoxic nanoscale coordination polymers limits epithelial-to-mesenchymal transition and suppresses liver metastases of colorectal cancer. Biomaterials 2019; 210:94-104. [PMID: 31060867 PMCID: PMC6579118 DOI: 10.1016/j.biomaterials.2019.04.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022]
Abstract
Though early detection and treatment of primary tumors has significantly improved in recent years, metastatic disease remains among the most significant challenges in cancer therapy. Cancer cells can disseminate before the primary tumor is detected to form micro or gross metastases, requiring toxic systemic therapies. To prevent and suppress metastases, we have developed a nontoxic, long-circulating nanoscale coordination polymer (NCP) protecting microRNA (miRNA) in circulation and releasing it in tumors. PtIV(en)2 [en = ethylenediamine] containing NCPs (PtEN) can release a nontoxic, kinetically inert PtII(en)2 compound and carbon dioxide which aids the endosomal escape of its miRNA cargo, miR-655-3p. Without the presence of the PtEN core, the miRNA showed cellular uptake but no effect. When transfected into human colorectal HCT116 cells by NCPs, this oligometastatic miRNA limited proliferation and epithelial-to-mesenchymal transition by preventing β-catenin nuclear translocation and tumor cell invasion. Systemic administrations of PtEN/miR-655-3p sustained effective transfection to reduce liver colonization and tumor burden in a xenogenic hepatic metastatic model of HCT116 without any observable toxicity.
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Affiliation(s)
- Christina Chan
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Nining Guo
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Radiation and Cellular Oncology and the Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaopin Duan
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Wenbo Han
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Lai Xue
- Department of Surgery, The University of Chicago, Chicago, IL, 60637, USA
| | - Darren Bryan
- Department of Surgery, The University of Chicago, Chicago, IL, 60637, USA
| | - Sean C Wightman
- Department of Surgery, The University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai N Khodarev
- Department of Radiation and Cellular Oncology and the Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology and the Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA.
| | - Wenbin Lin
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Radiation and Cellular Oncology and the Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA.
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21
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Dong J, Dong H, Dai W, Meng X, Zhang K, Cao Y, Yang F, Zhang X. Functional DNA hexahedron for real-time detection of multiple microRNAs in living cells. Anal Chim Acta 2019; 1078:176-181. [PMID: 31358217 DOI: 10.1016/j.aca.2019.06.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/20/2019] [Accepted: 06/13/2019] [Indexed: 01/08/2023]
Abstract
Intracellular microRNA (miRNA) analysis in single cell is highly informative and offers valuable insights to its physiological and pathological state, but it must confront the pivotal challenge of gene probe delivery and conditional release. Herein, we report an assembled DNA mini-hexahedron (DMH) that can selectively package and protect miRNA probe, target-cell-specific delivery and release it based on the target sequence recognition for intracellular miRNA detection. In brief, the DMH is self-assembled from six single-stranded oligonucleotide strands through rational design, one of which containing AS1411 sequence for specific uptake. Two fluorescent dye labeled recognition strands are inserted into two DMH edges with quencher groups through partially complementary hybridization. We find that this DMH possesses great biocompatibility, good trans-membrane ability and are able to protect the gene cargo against enzymatic degradation and protein binding. Fluorescence restoration caused by the target-mediated competitive chain replacement reaction allows to simultaneous detection of two cancer-related intracellular miRNAs with little false-positive signal, providing a powerful tool to discriminate healthy normal cell and cancerous cell. Thus, the construct opens a new avenue to circumvent the challenges in gene delivery, specific delivery and intrinsic interferences resistance.
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Affiliation(s)
- Jinhong Dong
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Haifeng Dong
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
| | - Wenhao Dai
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Xiangdan Meng
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Kai Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Yu Cao
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Fan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Xueji Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
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22
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Basu A, Suresh Kumar G. Interaction of proflavine with the RNA polynucleotide polyriboadenylic acid-polyribouridylic acid: photophysical and calorimetric studies. J Biomol Struct Dyn 2019; 38:1590-1597. [PMID: 31057051 DOI: 10.1080/07391102.2019.1615001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid-polyuridylic acid is investigated here to understand the structural and thermodynamic basis of the binding process. Such binding data are crucial for designing viable theraperutic agents. Spectroscopic studies clearly suggest a strong binding interaction between proflavine and polyadenylic acid-polyuridylic acid leading to efficient energy transfer between the poly AU base pairs and proflavine. The stoichiometry of proflavine polyadenylic acid-polyuridylic acid binding was independently estimated by continuous variation analysis of Job. An intercalative binding model is envisaged for the binding from hydrodynamic studies. Circular dichroism experiments revealed that the binding induced conformational changes in the RNA, and also led to induction of optical activity in the bound dye molecules. The binding affinity of the complex was deduced to be (6.57 ± 0.75) 105 M-1 at (298.15 ± 0.10) K from isothermal titration calorimetry experiment. Positive entropy and negative enthalpy changes characterized the complexation. The binding was observed to be weaker both at higher temperatures and increased [Na+]. The affinity of binding decreased with increasing [Na+]. When the Gibbs energy was parsed between polyelectrolytic and nonpolyelectropytic components, it surprisingly revealed a higher role for the non-polyelectrolytic forces. These results present new data for developing RNA targeted ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anirban Basu
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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23
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Hande M, Saher O, Lundin KE, Smith CIE, Zain R, Lönnberg T. Oligonucleotide⁻Palladacycle Conjugates as Splice-Correcting Agents. Molecules 2019; 24:E1180. [PMID: 30917503 PMCID: PMC6470670 DOI: 10.3390/molecules24061180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
2'-O-Methylribo phosphorothioate oligonucleotides incorporating cyclopalladated benzylamine conjugate groups at their 5'-termini have been prepared and their ability to hybridize with a designated target sequence was assessed by conventional UV melting experiments. The oligonucleotides were further examined in splice-switching experiments in human cervical cancer (HeLa Luc/705), human liver (HuH7_705), and human osteosarcoma (U-2 OS_705) reporter cell lines. Melting temperatures of duplexes formed by the modified oligonucleotides were approximately 5 °C lower than melting temperatures of the respective unmodified duplexes. The cyclopalladated oligonucleotides functioned as splice-correcting agents in the HeLa Luc/705 cell line somewhat more efficiently than their unmodified counterparts. Furthermore, the introduction of this chemical modification did not induce toxicity in cells. These results demonstrate the feasibility of using covalently metalated oligonucleotides as therapeutic agents.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Osama Saher
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Pharmaceutics and Industrial Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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24
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Rennie W, Kanoria S, Liu C, Carmack CS, Lu J, Ding Y. Sfold Tools for MicroRNA Target Prediction. Methods Mol Biol 2019; 1970:31-42. [PMID: 30963486 DOI: 10.1007/978-1-4939-9207-2_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. In this chapter, we describe STarMir and STarMirDB, two application modules of the Sfold RNA package. STarMir is a Web server for performing miRNA binding site predictions for mRNA and target sequences submitted by users. STarMirDB is a database of precomputed transcriptome-scale predictions. Both STarMir and STarMirDB provide comprehensive sequence, thermodynamic, and target structure features, a logistic probability as a measure of confidence for each predicted site, and a publication-quality diagram of the predicted miRNA-target hybrid. In addition, STarMir now offers a new quantitative score to address combined regulatory effects of multiple seed and seedless sites. This score provides a quantitative measure of the overall regulatory effects of both seed and seedless sites on the target. STarMir and STarMirDB are freely available to all through the Sfold Web application server at http://sfold.wadsworth.org .
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Affiliation(s)
- William Rennie
- New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA
| | - Shaveta Kanoria
- New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA
| | - Chaochun Liu
- New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA
| | - C Steven Carmack
- New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA
| | - Jun Lu
- Department of Genetics, Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Ye Ding
- New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA.
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25
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Characterization of the microtranscriptome of macrophages infected with virulent, attenuated and saprophyte strains of Leptospira spp. PLoS Negl Trop Dis 2018; 12:e0006621. [PMID: 29979677 PMCID: PMC6051669 DOI: 10.1371/journal.pntd.0006621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/18/2018] [Accepted: 06/19/2018] [Indexed: 01/18/2023] Open
Abstract
Leptospirosis is a bacterial zoonosis, caused by Leptospira spp., that leads to significant morbidity and mortality worldwide. Despite considerable advances, much is yet to be discovered about disease pathogenicity. The influence of epigenetic mechanisms, particularly RNA-mediated post-transcriptional regulation of host immune response has been described following a variety of bacterial infections. The current study examined the microtranscriptome of macrophages J774A.1 following an 8h infection with virulent, attenuated and saprophyte strains of Leptospira. Microarray analysis revealed that 29 miRNAs were misregulated following leptospiral infection compared to control macrophages in a strain and virulence-specific manner. Pathway analysis for targets of these differentially expressed miRNAs suggests that several processes involved in immune response could be regulated by miRNAs. Our data provides the first evidence that host miRNAs are regulated by Leptospira infection in macrophages. A number of the identified miRNA targets participate in key immune response processes. We suggest that post-transcriptional regulation by miRNAs may play a role in host response to infection in leptospirosis. Leptospirosis is a zoonotic disease, distributed worldwide, affecting millions of people each year, and leading to sixty thousand deaths per year. These bacteria are found in soil and water and are eliminated by the urine of rodents, their natural reservoir. Through skin contact, bacteria can be acquired, infecting the host. Infection process in leptospirosis is not completely understood and here we add another layer of disease regulation. Recent studies have shown that pathogens can modulate host response. Our current study examined the expression of microRNAs in murine macrophages following an 8h infection with virulent, attenuated and saprophyte strains of Leptospira. This study provides the first evidence that these post-transcriptional regulatory molecules, microRNAs, are modulated in macrophages in a species and virulence-specific manner, following infection with different strains of Leptospira spp. These microRNAs are involved in the regulation of inflammatory and antimicrobial responses in the host and could lead to the identification of biomarkers or therapeutic targets for this disease.
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26
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Hosseinahli N, Aghapour M, Duijf PHG, Baradaran B. Treating cancer with microRNA replacement therapy: A literature review. J Cell Physiol 2018. [PMID: 29521426 DOI: 10.1002/jcp.26514] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally by interfering with the translation of one or more target mRNAs. The unique miRNA sequences are involved in many physiological and pathological processes. Dysregulation of miRNAs contributes to the pathogenesis of all types of cancer. Notably, the diminished expression of tumor suppressor miRNAs, such as members of the Let-7 and miR-34 family, promotes tumor progression, invasion and metastasis. The past lustrum in particular, has witnessed substantial improvement of miRNA replacement therapy. This approach aims to restore tumor suppressor miRNA function in tumor cells using synthetic miRNA mimics or miRNA expression plasmids. Here, we provide a comprehensive review of recent advances in miRNA replacement therapy for treatment of cancer and its advantages over conventional gene therapy. We discuss a wide variety of delivery methods and vectors, as well as obstacles that remain to be overcome. Lastly, we review efforts to reverse epigenetic alterations, which affect miRNA expression in cancer cells, and the promising observation that restoring miRNA function re-sensitizes resistant tumor cells to chemotherapeutic drugs. The fact that various miRNA replacement therapies are currently in clinical trial demonstrates the great potential of this approach to treat cancer.
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Affiliation(s)
- Nayer Hosseinahli
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahyar Aghapour
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Ou M, Huang J, Yang X, He X, Quan K, Yang Y, Xie N, Li J, Wang K. Live-Cell MicroRNA Imaging through MnO2
Nanosheet-Mediated DD-A Hybridization Chain Reaction. Chembiochem 2017; 19:147-152. [DOI: 10.1002/cbic.201700573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Min Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Yanjing Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
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28
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Schmieder S, Weißpflog J, Danz N, Hübner M, Kreth S, Klotzbach U, Sonntag F. Ultrasensitive SPR detection of miRNA-93 using antibody-enhanced and enzymatic signal amplification. Eng Life Sci 2017; 17:1264-1270. [PMID: 32624754 DOI: 10.1002/elsc.201700104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023] Open
Abstract
MiRNAs are endogenous noncoding RNA molecules. They play important gene-regulatory roles by binding to the mRNA of target genes thereby leading to either transcript degradation or translational repression. In virtually all diseases, distinct alterations of miRNA expression profiles have been found thus suggesting miRNAs as interesting biomarkers. Here, we present an SPR biosensor that utilizes disposable, injection-molded sensor chip/microfluidic hybrids combined with a lateral imaging optical system for parallel analysis of three one-dimensional spot arrays to detect miRNA-93. To increase the sensitivity of the biosensor we used two different amplification strategies. By adding an RNA-DNA-hybrid antibody for primary signal amplification, a limit of detection of 10 pmol/L was achieved. Based on that method we demonstrate the detection of miRNA-93 in total RNA lysate from HEK-293 cells. Utilizing an enzymatic signal amplification with Poly(A) polymerase, the sensitivity could be increased even further leading to a limit of detection of 1 fmol/L.
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Affiliation(s)
- Stefan Schmieder
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Janek Weißpflog
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Norbert Danz
- Microoptical Systems Fraunhofer Institute for Applied Optics and Precision Engineering IOF Jena Germany
| | - Max Hübner
- Walter-Brendel-Centre for Experimental Medicine Ludwig-Maximilians-University Munich Germany.,Department of Anesthesiology Hospital of the Ludwig-Maximilians-University Munich Germany
| | - Simone Kreth
- Walter-Brendel-Centre for Experimental Medicine Ludwig-Maximilians-University Munich Germany.,Department of Anesthesiology Hospital of the Ludwig-Maximilians-University Munich Germany
| | - Udo Klotzbach
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Frank Sonntag
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
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29
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Basu P, Suresh Kumar G. Small molecule-RNA recognition: Binding of the benzophenanthridine alkaloids sanguinarine and chelerythrine to single stranded polyribonucleotides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:173-181. [PMID: 28779690 DOI: 10.1016/j.jphotobiol.2017.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 01/18/2023]
Abstract
Single stranded RNAs are biologically potent as they participate in various key cellular processes. The binding efficacy of two potent anticancer alkaloids, sanguinarine (here after SANG) and chelerythrine (here after CHEL), with single-stranded ribonucleic acids poly(rI), poly(rG), and poly(rC) were studied using spectroscopic and thermodynamic tools. Results reveal that both SANG and CHEL binds well with single stranded RNAs with affinity in the order poly(rI)>poly(rG)>poly(rC). CHEL showed slightly higher affinity compared to SANG with all the single stranded RNAs. Both SANG and CHEL showed association affinity of the lower 106 order with poly(rI), higher 105 order binding with poly(rG) and lower 105 order with poly(rC). The binding mode was partial intercalation due to the staking interaction between the bases and the alkaloids. The complexation of both the SANG and CHEL to the RNAs were mainly enthalpy driven and also favoured by entropy changes. Perturbation was observed in the RNA conformation due to binding of the alkaloids. In this present study we have deciphered the fundamental structural and calorimetric aspects of the interaction of the natural benzophenanthridine alkaloids with single stranded RNAs and these results may help to develop new generation alkaloid based therapeutics targeting single stranded RNAs.
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Affiliation(s)
- Pritha Basu
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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30
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Yang J, Zhou Y, Ng SK, Huang KC, Ni X, Choi PW, Hasselblatt K, Muto MG, Welch WR, Berkowitz RS, Ng SW. Characterization of MicroRNA-200 pathway in ovarian cancer and serous intraepithelial carcinoma of fallopian tube. BMC Cancer 2017. [PMID: 28623900 PMCID: PMC5473983 DOI: 10.1186/s12885-017-3417-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Ovarian cancer is the leading cause of death among gynecologic diseases in Western countries. We have previously identified a miR-200-E-cadherin axis that plays an important role in ovarian inclusion cyst formation and tumor invasion. The purpose of this study was to determine if the miR-200 pathway is involved in the early stages of ovarian cancer pathogenesis by studying the expression levels of the pathway components in a panel of clinical ovarian tissues, and fallopian tube tissues harboring serous tubal intraepithelial carcinomas (STICs), a suggested precursor lesion for high-grade serous tumors. METHODS RNA prepared from ovarian and fallopian tube epithelial and stromal fibroblasts was subjected to quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) to determine the expression of miR-200 families, target and effector genes and analyzed for clinical association. The effects of exogenous miR-200 on marker expression in normal cells were determined by qRT-PCR and fluorescence imaging after transfection of miR-200 precursors. RESULTS Ovarian epithelial tumor cells showed concurrent up-regulation of miR-200, down-regulation of the four target genes (ZEB1, ZEB2, TGFβ1 and TGFβ2), and up-regulation of effector genes that were negatively regulated by the target genes. STIC tumor cells showed a similar trend of expression patterns, although the effects did not reach significance because of small sample sizes. Transfection of synthetic miR-200 precursors into normal ovarian surface epithelial (OSE) and fallopian tube epithelial (FTE) cells confirmed reduced expression of the target genes and elevated levels of the effector genes CDH1, CRB3 and EpCAM in both normal OSE and FTE cells. However, only FTE cells had a specific induction of CA125 after miR-200 precursor transfection. CONCLUSIONS The activation of the miR-200 pathway may be an early event that renders the OSE and FTE cells more susceptible to oncogenic mutations and histologic differentiation. As high-grade serous ovarian carcinomas (HGSOC) usually express high levels of CA125, the induction of CA125 expression in FTE cells by miR-200 precursor transfection is consistent with the notion that HGSOC has an origin in the distal fallopian tube.
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Affiliation(s)
- Junzheng Yang
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Yilan Zhou
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Shu-Kay Ng
- School of Medicine and Menzies Health Institute Queensland, Griffith University, QLD, Nathan, 4111, Australia
| | - Kuan-Chun Huang
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Xiaoyan Ni
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Pui-Wah Choi
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kathleen Hasselblatt
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michael G Muto
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - William R Welch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Ross S Berkowitz
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Shu-Wing Ng
- Department of Obstetrics/Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA. .,Laboratory of Gynecologic Oncology, Brigham and Women's Hospital, 221 Longwood Avenue, Boston, MA, 02115, USA.
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31
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Su J, Li C, Zhang Y, Yan T, Zhu X, Zhao M, Xing D, Dong Y, Guo X, Zhao T. Identification of microRNAs expressed in the midgut of Aedes albopictus during dengue infection. Parasit Vectors 2017; 10:63. [PMID: 28159012 PMCID: PMC5292000 DOI: 10.1186/s13071-017-1966-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 01/02/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The midgut is the first barrier to dengue virus (DENV) infections of mosquitoes and therefore is a major bottleneck for the subsequent development of vector competence. However, the molecular mechanisms responsible for this barrier are unknown. RESULTS We constructed three small RNA libraries from the midguts of adult Aedes albopictus females that had been fed on either sugar solution, an uninfected blood meal, or a blood meal infected with DENV-2, and112 conserved microRNAs represented by 173 miRNA sequences were identified, with 34 novel microRNAs predicted by Mireap, RNAfold and Sfold software. In addition, the expression of aal-miR-1174, aal-miR-2951 and aal-miR-956 was confirmed via stem-loop quantitative real-time PCR (qRT-PCR). Compared with microRNA expression profiles of mosquitoes that had ingested a regular blood meal, 43 microRNAs were upregulated and 4were downregulated in mosquitoes that had ingested a DENV-2-infected blood meal. Among the differentially expressed microRNAs, miR-1767, miR-276-3p, miR-4448 and miR-4728-5p were verified via stem-loop qRT-PCR. CONCLUSIONS Analyses indicated that the changing patterns in miRNA expression during DENV-2 infection were significant and varied at different time points post infection. Most miRNA were upregulated at 24 h but were downregulated at 48 h post DENV-2 intake. The aal-miR-4728-5p was chosen for an in vitro transient transfection assay, and the results show that this miRNA enhances DENV replication in C6/36 cells. This study provides the first information on microRNAs expressed in the midgut of Ae. albopictus and describes species-specific changes in their expression levels following infection by DENV-2.
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Affiliation(s)
- Jianxin Su
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
- Center for Disease Control and Prevention of Guangzhou Military Region, Guangzhou, 510507 People’s Republic of China
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Yingmei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Ting Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Xiaojuan Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Minghui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Yande Dong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Xiaoxia Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 People’s Republic of China
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Sharma S, Mathew AB, Chugh J. miRNAs: Nanomachines That Micromanage the Pathophysiology of Diabetes Mellitus. Adv Clin Chem 2017; 82:199-264. [PMID: 28939211 DOI: 10.1016/bs.acc.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Diabetes mellitus (DM) refers to a combination of heterogeneous complex metabolic disorders that are associated with episodes of hyperglycemia and glucose intolerance occurring as a result of defects in insulin secretion, action, or both. The prevalence of DM is increasing at an alarming rate, and there exists a need to develop better therapeutics and prognostic markers for earlier detection and diagnosis. In this review, after giving a brief introduction of diabetes mellitus and microRNA (miRNA) biogenesis pathway, we first describe various in vitro and animal model systems that have been developed to study diabetes. Further, we elaborate on the significant roles played by miRNAs as regulators of gene expression in the context of development of diabetes and its secondary complications. The different approaches to quantify miRNAs and their potential to be used as therapeutic targets for alleviation of diabetes have also been discussed.
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Zhou W, Bi X, Gao G, Sun L. miRNA-133b and miRNA-135a induce apoptosis via the JAK2/STAT3 signaling pathway in human renal carcinoma cells. Biomed Pharmacother 2016; 84:722-729. [DOI: 10.1016/j.biopha.2016.09.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 01/15/2023] Open
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34
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Arzel L, Dubreuil D, Dénès F, Silvestre V, Mathé-Allainmat M, Lebreton J. Synthesis of Ribonucleosidic Dimers with an Amide Linkage from d-Xylose. J Org Chem 2016; 81:10742-10758. [DOI: 10.1021/acs.joc.6b01822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laurence Arzel
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Didier Dubreuil
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Fabrice Dénès
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Virginie Silvestre
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Monique Mathé-Allainmat
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Jacques Lebreton
- Université de Nantes, CEISAM-UMR CNRS 6230, Faculté des Sciences et
des Techniques, 2 rue
de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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Tahamtan A, Inchley CS, Marzban M, Tavakoli‐Yaraki M, Teymoori‐Rad M, Nakstad B, Salimi V. The role of microRNAs in respiratory viral infection: friend or foe? Rev Med Virol 2016; 26:389-407. [PMID: 27373545 PMCID: PMC7169129 DOI: 10.1002/rmv.1894] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) have emerged as a class of regulatory RNAs in host-pathogen interactions. Aberrant miRNA expression seems to play a central role in the pathology of several respiratory viruses, promoting development and progression of infection. miRNAs may thus serve as therapeutic and prognostic factors for respiratory viral infectious disease caused by a variety of agents. We present a comprehensive review of recent findings related to the role of miRNAs in different respiratory viral infections and discuss possible therapeutic opportunities aiming to attenuate the burden of viral infections. Our review supports the emerging concept that cellular and viral-encoded miRNAs might be broadly implicated in human respiratory viral infections, with either positive or negative effects on virus life cycle. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alireza Tahamtan
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Christopher S. Inchley
- Department of Pediatric and Adolescent MedicineAkershus University HospitalLørenskogNorway
| | - Mona Marzban
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Majid Teymoori‐Rad
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Britt Nakstad
- Department of Pediatric and Adolescent MedicineAkershus University HospitalLørenskogNorway
- Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Vahid Salimi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
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Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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Zhou W, Li D, Xiong C, Yuan R, Xiang Y. Multicolor-Encoded Reconfigurable DNA Nanostructures Enable Multiplexed Sensing of Intracellular MicroRNAs in Living Cells. ACS APPLIED MATERIALS & INTERFACES 2016; 8:13303-8. [PMID: 27195747 DOI: 10.1021/acsami.6b03165] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Despite the widespread utilization of gold nanoparticles and graphene for in vivo applications, complex steps for the preparation and functionalization of these nanomaterials are commonly required. In addition, the cytotoxicity of such materials is currently still under debate. In this work, by taking the significant advantages of DNA in terms of biocompatibility, nontoxicity, and controllability as building blocks for DNA nanostructures, we describe the construction of a reconfigurable, multicolor-encoded DNA nanostructure for multiplexed monitoring of intracellular microRNAs (miRNAs) in living cells. The DNA nanostructure nanoprobes containing two fluorescently quenched hairpins can be obtained by simple thermal annealing of four ssDNA oligonucleotides. The presence of the target miRNAs can unfold the hairpin structures and recover fluorescent emissions at distinct wavelengths to achieve multiplexed detection of miRNAs. Importantly, the DNA nanostructure nanoprobes exhibit significantly improved stability over conventional DNA molecular beacon probes in cell lysates and can steadily enter cells to realize simultaneous detection of two types of intracellular miRNAs. The demonstration of the self-assembled DNA nanostructures for intracellular sensing thus offers great potential application of these nanoprobes for imaging, drug delivery and cancer therapy in vivo.
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Affiliation(s)
- Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P.R. China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P.R. China
| | - Chengyi Xiong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P.R. China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P.R. China
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Mehrotra N, Tripathi RM. Short interfering RNA therapeutics: nanocarriers, prospects and limitations. IET Nanobiotechnol 2016; 9:386-95. [PMID: 26647816 DOI: 10.1049/iet-nbt.2015.0018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the first experiment depicting gene inhibition using RNA interference mechanism, extensive research has been carried out to design targeted delivery systems that use short interfering RNAs (siRNAs) for gene expression regulation. Although several siRNAs loaded nanoparticle systems have reached clinical trial stage, cellular uptake, reticuloendothelial entrapment and endosomal escape still limit the efficacy of these drugs considerably. This review discusses about the RNA interference mechanism, nanostructures being used as non-viral vectors for targeted delivery, limitations of the common delivery systems and the current siRNA-loaded nanoparticle formulations undergoing clinical testing.
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Affiliation(s)
- Neha Mehrotra
- Amity Institute of Nanotechnology, Amity University, Sector 125, Noida 201303, India
| | - Ravi Mani Tripathi
- Amity Institute of Nanotechnology, Amity University, Sector 125, Noida 201303, India.
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39
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Pan D. Next generation gene delivery approaches: recent progress and hurdles. Mol Pharm 2016; 12:299-300. [PMID: 25639168 DOI: 10.1021/mp5008635] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dipanjan Pan
- Department of Materials Science and Engineering, Department of Bioengineering and Beckman Institute, University of Illinois at Urbana-Champaign and Carle Foundation Hospital , 502 North Busey, Urbana, Illinois 61801, United States
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40
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miR-133 regulates Evi1 expression in AML cells as a potential therapeutic target. Sci Rep 2016; 6:19204. [PMID: 26754824 PMCID: PMC4709720 DOI: 10.1038/srep19204] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/08/2015] [Indexed: 01/18/2023] Open
Abstract
The Ecotropic viral integration site 1 (Evi1) is a zinc finger transcription factor, which is located on chromosome 3q26, over-expression in some acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Elevated Evi1 expression in AML is associated with unfavorable prognosis. Therefore, Evi1 is one of the strong candidate in molecular target therapy for the leukemia. MicroRNAs (miRNAs) are small non-coding RNAs, vital to many cell functions that negatively regulate gene expression by translation or inducing sequence-specific degradation of target mRNAs. As a novel biologics, miRNAs is a promising therapeutic target due to its low toxicity and low cost. We screened miRNAs which down-regulate Evi1. miR-133 was identified to directly bind to Evi1 to regulate it. miR-133 increases drug sensitivity specifically in Evi1 expressing leukemic cells, but not in Evi1-non-expressing cells The results suggest that miR-133 can be promising therapeutic target for the Evi1 dysregulated poor prognostic leukemia.
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Khan AY, Suresh Kumar G. Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:417-425. [PMID: 26241827 DOI: 10.1016/j.saa.2015.07.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/08/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Abstract
Epigenetic regulation refers to heritable changes in gene expression that do not involve any alteration of the DNA sequence. DNA methylation, histone modification, and gene regulation by microRNAs are well-known epigenetic modulations that are closely associated with several cellular processes and diverse disease states, such as cancers, even under precancerous conditions. More recently, several studies have indicated that epigenetic changes may be associated with renal cystic diseases, including autosomal dominant polycystic kidney disease, and the restoration of altered epigenetic factors may become a therapeutic target of renal cystic disease and would be expected to have minimal side effects. This review focuses on recently reported findings on epigenetic and considers the potential of targeting epigenetic regulation as a novel therapeutic approach to control cystogenesis.
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Rubio AR, Busto N, Leal JM, García B. Doxorubicin binds to duplex RNA with higher affinity than ctDNA and favours the isothermal denaturation of triplex RNA. RSC Adv 2016. [DOI: 10.1039/c6ra21387a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The higher affinity of DOX with AU to give the intercalated complex AU/DOX is responsible for the disproportionation of the groove binding complex, UAU/DOX, to give rise to the AU/DOX and the U/DOX complexes at 25 °C
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Affiliation(s)
- Ana R. Rubio
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - Natalia Busto
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - José M. Leal
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - Begoña García
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
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Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods Mol Biol 2016; 1490:73-82. [PMID: 27665594 DOI: 10.1007/978-1-4939-6433-8_6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous short noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. As regulatory molecules, miRNAs are involved in many mammalian biological processes and also in the manifestation of certain human diseases. As miRNAs play central role in the regulation of gene expression, understanding miRNA-binding patterns is essential to gain an insight of miRNA mediated gene regulation and also holds promise for therapeutic applications. Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. This chapter provides protocols for using the STarMir web server for improved predictions of miRNA binding sites on a target mRNA. As an application module of the Sfold RNA package, the current version of STarMir is an implementation of logistic prediction models developed with high-throughput miRNA binding data from cross-linking immunoprecipitation (CLIP) studies. The models incorporated comprehensive thermodynamic, structural, and sequence features, and were found to make improved predictions of both seed and seedless sites, in comparison to the established algorithms (Liu et al., Nucleic Acids Res 41:e138, 2013). Their broad applicability was indicated by their good performance in cross-species validation. STarMir is freely available at http://sfold.wadsworth.org/starmir.html .
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Affiliation(s)
- Shaveta Kanoria
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA
| | - William Rennie
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA
| | - Chaochun Liu
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA
| | - C Steven Carmack
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT, 06520, USA
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA.
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Gómez de Cedrón M, Ramírez de Molina A. Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism. J Lipid Res 2015; 57:193-206. [PMID: 26630911 DOI: 10.1194/jlr.r061812] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Indexed: 01/04/2023] Open
Abstract
Metabolic reprogramming has emerged as a hallmark of cancer. MicroRNAs are noncoding RNAs that posttranscriptionally repress the expression of target mRNAs implicated in multiple physiological processes, including apoptosis, differentiation, and cancer. MicroRNAs can affect entire biological pathways, making them good candidates for therapeutic intervention compared with classical single target approaches. Moreover, microRNAs may become more relevant in the fine-tuning adaptation to stress situations, such as oncogenic events, hypoxia, nutrient deprivation, and oxidative stress. Furthermore, artificial microRNAs can be designed to modulate the expression of multiple targets of a specific pathway. In this review, we describe the metabolic reprogramming associated to cancer, with a special interest in the altered lipid metabolism. Next, we describe specific features of microRNAs that make them relevant to target cancer cell metabolism. Finally, in an attempt to open new therapeutic windows, we emphasize two exciting scenarios for microRNA-mediated intervention that need to be further explored: 1) the cooperation between FA biosynthesis (lipogenesis) and FA oxidation as complementary partners for the survival of cancer cells; and 2) the regulation of the intracellular lipid content modulating both lipid storage into lipid droplets, and lipid mobilization through lipolysis and/or lipophagy.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology and Nutritional Genomics of Cancer Group, IMDEA (Madrid Institute of Advanced Studies)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Ana Ramírez de Molina
- Molecular Oncology and Nutritional Genomics of Cancer Group, IMDEA (Madrid Institute of Advanced Studies)-Food, CEI UAM + CSIC, Madrid, Spain
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Kumar GS, Basu A. The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures. Biochim Biophys Acta Gen Subj 2015; 1860:930-944. [PMID: 26522497 DOI: 10.1016/j.bbagen.2015.10.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/06/2015] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND RNA has now emerged as a potential target for therapeutic intervention. RNA targeted drug design requires detailed thermodynamic characterization that provides new insights into the interactions and this together with structural data, may be used in rational drug design. The use of calorimetry to characterize small molecule-RNA interactions has emerged as a reliable and sensitive tool after the recent advancements in biocalorimetry. SCOPE OF THE REVIEW This review summarizes the recent advancements in thermodynamic characterization of small molecules, particularly some natural alkaloids binding to various RNA structures. Thermodynamic characterization provides information that can supplement structural data leading to more effective drug development protocols. MAJOR CONCLUSIONS This review provides a concise report on the use of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques in characterizing small molecules, mostly alkaloids-RNA interactions with particular reference to binding of tRNA, single stranded RNA, double stranded RNA, poly(A), triplex RNA. GENERAL SIGNIFICANCE It is now apparent that a combination of structural and thermodynamic data is essential for rational design of specific RNA targeted drugs. Recent advancements in biocalorimetry instrumentation have led to detailed understanding of the thermodynamics of small molecules binding to various RNA structures paving the path for the development of many new natural and synthetic molecules as specific binders to various RNA structures. RNA targeted drug design, that remained unexplored, will immensely benefit from the calorimetric studies leading to the development of effective drugs for many diseases.
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Affiliation(s)
- Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| | - Anirban Basu
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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Khilari R, Thakur Y, Pardhi M, Pande R. RNA-Binding Efficacy of N-Phenylbenzohydroxamic Acid: An Invitro and Insilico Approach. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:332-47. [PMID: 25874942 DOI: 10.1080/15257770.2014.1001073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RNA has attracted recent attention for its key role in gene expression and hence targeting by small molecules for therapeutic intervention. This study is aimed to elucidate the specificity of RNA binding affinity of parent compound of N-arylhydroxamic acids series, N-phenylbenzohydroxamic acid trivially named as PBHA,C6H5NOH.C6H5C˭O. The binding behavior was examined by various biophysical methods such as absorption, fluorescence, and viscosity measurements. Molecular docking was also done. The value of affinity constant and overall binding constant was calculated 5.79±0.03×10(4) M(-1) and K'=1.09±0.03×10(5) M(-1), respectively. The Stern-Volmer constant Ksv obtained was 2.28±0.04×10(4) M(-1). The compound (PBHA) shows a concentration-based enhancement of fluorescence intensity with increasing RNA concentration. Fluorescence quenching of PBHA-RNA complex in presence of K4 [Fe(CN)6] was also observed. Viscometric studies complimented the UV results where a continuous increase in relative viscosity of the RNA solution was observed with added optimal PBHA concentration. All the experimental evidences indicate that PBHA can strongly bind to RNA through an intercalative mode.
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Affiliation(s)
- Rubi Khilari
- a School of Studies in Chemistry, Pt. Ravishankar Shukla University , Raipur , Chhattisgarh , India
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Lin CW, Jan MS, Kuo JHS. Exploring MicroRNA Expression Profiles Related to the mTOR Signaling Pathway in Mouse Embryonic Fibroblast Cells Treated with Polyethylenimine. Mol Pharm 2015; 12:2858-68. [PMID: 26158199 DOI: 10.1021/acs.molpharmaceut.5b00329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although the toxicology of poly(ethylenimine) (PEI) in gene expression levels has been previously investigated, little is known about the effects of PEI on the expression of microRNAs (miRNAs) that regulate gene expression at the post-transcriptional level. In this study, we explored miRNA expression profiles related to cell death mechanisms in mouse embryonic fibroblast (MEF) cells treated with PEI by applying microarray analysis. Based on the analysis of the mTOR signaling pathway, three upregulated miRNAs (mmu-miR-3090-5p, mmu-miR-346-3p, and mmu-miR-494-3p) were verified in MEF cells treated with PEI at 24 h using real-time quantitative reverse transcriptase-polymerase chain reaction. We further demonstrated that these three upregulated miRNAs resulted in the decrease of gene and protein expressions of the target gene growth factor Igf1 in MEF cells treated with PEI or transfected with three upregulated miRNA mimics. However, these three upregulated miRNAs are not all cell-specific. Finally, we demonstrated that the mTOR signaling pathway is inhibited by autophagy induction and that the cell viability decreases in MEF cells treated with PEI or transfected with these three miRNA mimics. Collectively, our data suggested that PEI may affect the regulation of miRNAs in target cells.
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Affiliation(s)
| | | | - Jung-Hua Steven Kuo
- §Department of Pharmacy, Chia Nan University of Pharmacy and Science, 60 Erh-Jen Road, Section 1, Jen-Te, Tainan 717, Taiwan
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Quinzaños-Fresnedo J, Sahagún-Olmos RC. [Micro RNA and its role in the pathophysiology of spinal cord injury - a further step towards neuroregenerative medicine]. CIR CIR 2015; 83:442-7. [PMID: 26162489 DOI: 10.1016/j.circir.2015.05.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 10/06/2014] [Indexed: 12/28/2022]
Abstract
In the pathophysiology of spinal cord injury, the secondary biological processes involving changes in gene expression become more important day a day. Within these changes, the expression of different microRNAs has been involved in some of the pathophysiological processes of spinal cord injury. There are several studies that describe the transient expression of microRNA in spinal cord injury, some of them related to inflammation and apoptosis and others to functional recovery and regeneration. MicroRNA may be a potential target for the treatment of spinal cord injury, modifying the processes of inflammation, oxidation, apoptosis, functional recovery and regeneration. It is necessary to continue the study of microRNAs in spinal cord injury, as well as the identification of their target genes and signaling mechanisms involved in its neurological effects. With this, the ultimate goal is the development of effective and safe therapeutic and diagnostic strategies for patients with spinal cord injury.
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50
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Ong SM, Biswas SK, Wong SC. MicroRNA-mediated immune modulation as a therapeutic strategy in host-implant integration. Adv Drug Deliv Rev 2015; 88:92-107. [PMID: 26024977 DOI: 10.1016/j.addr.2015.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 05/05/2015] [Accepted: 05/21/2015] [Indexed: 12/29/2022]
Abstract
The concept of implanting an artificial device into the human body was once the preserve of science fiction, yet this approach is now often used to replace lost or damaged biological structures in human patients. However, assimilation of medical devices into host tissues is a complex process, and successful implant integration into patients is far from certain. The body's immediate response to a foreign object is immune-mediated reaction, hence there has been extensive research into biomaterials that can reduce or even ablate anti-implant immune responses. There have also been attempts to embed or coat anti-inflammatory drugs and pro-regulatory molecules onto medical devices with the aim of preventing implant rejection by the host. In this review, we summarize the key immune mediators of medical implant reaction, and we evaluate the potential of microRNAs to regulate these processes to promote wound healing, and prolong host-implant integration.
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Affiliation(s)
- Siew-Min Ong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos Building, Level 4, Biopolis, Singapore 138648, Singapore
| | - Subhra K Biswas
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos Building, Level 4, Biopolis, Singapore 138648, Singapore
| | - Siew-Cheng Wong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos Building, Level 4, Biopolis, Singapore 138648, Singapore.
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