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Esmaeilzadeh AA, Yaseen MM, Khudaynazarov U, Al-Gazally ME, Catalan Opulencia MJ, Jalil AT, Mohammed RN. Recent advances on the electrochemical and optical biosensing strategies for monitoring microRNA-21: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4449-4459. [PMID: 36330992 DOI: 10.1039/d2ay01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The small non-coding RNA, microRNA-21 (miR-21), is dysregulated in various cancers and can be considered an appropriate target for therapeutic approaches. Therefore, the detection of miR-21 concentration is important in the diagnosis of diseases. Low specificity and the cost of materials are two necessary limitations in the traditional diagnosis method such as RT-PCR, northern blotting and microarray analysis. Biosensor technology can play an effective role in improving the quality of human life due to its capacity of rapid diagnosis, monitoring different markers, suitable sensitivity, and specificity. Moreover, bioanalytical systems have an essential role in the detection of biomolecules or miRNAs due to their critical features, including easy usage, portability, low cost and real-time analysis. Electrochemical biosensors based on novel nanomaterials and oligonucleotides can hybridize with miR-21 in different ranges. Moreover, optical biosensors and piezoelectric devices have been developed for miR-21 detection. In this study, we have evaluated different materials used in bioanalytical systems for miR-21 detection as well as various nanomaterials that offer improved electrodes for its detection.
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Affiliation(s)
| | - Muna Mohammed Yaseen
- Basic Science Department, Dentistry of College, University of Anbar, Al-Anbar, Iraq
| | - Utkir Khudaynazarov
- Teaching Assistant, MD, Department of Surgical Diseases, Faculty of Pediatrics, Samarkand State Medical Institute, Amir Temur Street 18, Samarkand, Uzbekistan
| | | | | | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, 51001, Iraq.
| | - Rebar N Mohammed
- Medical Laboratory Analysis Department, College of Health Sciences, Cihlan university of Sulaimaniya, Kurdistan Region, Iraq
- College of Veterinary Medicine, University of Sulaimani, Sulaimaniyah, Iraq
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Weng S, Lin D, Lai S, Tao H, Chen T, Peng M, Qiu S, Feng S. Highly sensitive and reliable detection of microRNA for clinically disease surveillance using SERS biosensor integrated with catalytic hairpin assembly amplification technology. Biosens Bioelectron 2022; 208:114236. [DOI: 10.1016/j.bios.2022.114236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
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Kumar D, Downs LP, Embers M, Flynt AS, Karim S. Identification of microRNAs in the Lyme Disease Vector Ixodes scapularis. Int J Mol Sci 2022; 23:5565. [PMID: 35628370 PMCID: PMC9141961 DOI: 10.3390/ijms23105565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in many biological processes, including the immune pathways that control bacterial, parasitic, and viral infections. Pathogens probably modify host miRNAs to facilitate successful infection, so they might be useful targets for vaccination strategies. There are few data on differentially expressed miRNAs in the black-legged tick Ixodes scapularis after infection with Borrelia burgdorferi, the causative agent of Lyme disease in the United States. Small RNA sequencing and qRT-PCR analysis were used to identify and validate differentially expressed I. scapularis salivary miRNAs. Small RNA-seq yielded 133,465,828 (≥18 nucleotides) and 163,852,135 (≥18 nucleotides) small RNA reads from Borrelia-infected and uninfected salivary glands for downstream analysis using the miRDeep2 algorithm. As such, 254 miRNAs were identified across all datasets, 25 of which were high confidence and 51 low confidence known miRNAs. Further, 23 miRNAs were differentially expressed in uninfected and infected salivary glands: 11 were upregulated and 12 were downregulated upon pathogen infection. Gene ontology and network analysis of target genes of differentially expressed miRNAs predicted roles in metabolic, cellular, development, cellular component biogenesis, and biological regulation processes. Several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including sphingolipid metabolism; valine, leucine and isoleucine degradation; lipid transport and metabolism; exosome biogenesis and secretion; and phosphate-containing compound metabolic processes, were predicted as targets of differentially expressed miRNAs. A qRT-PCR assay was utilized to validate the differential expression of miRNAs. This study provides new insights into the miRNAs expressed in I. scapularis salivary glands and paves the way for their functional manipulation to prevent or treat B. burgdorferi infection.
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Affiliation(s)
- Deepak Kumar
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Latoyia P. Downs
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Monica Embers
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Alex Sutton Flynt
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Shahid Karim
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
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Salim U, Kumar A, Kulshreshtha R, Vivekanandan P. Biogenesis, characterization, and functions of mirtrons. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1680. [PMID: 34155810 DOI: 10.1002/wrna.1680] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023]
Abstract
MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression. They base pair with the complementary target mRNA at the 3'UTR and modulate cellular processes by repressing the mRNA translation or degrading the mRNA. There are well-documented mechanisms of biogenesis of miRNA; however, a sizeable number of miRNAs are also produced by non-canonical pathways. Mirtrons represent a predominant class of non-canonical miRNAs. Mirtrons originate from intronic regions and are produced in a splicing-dependent and Drosha-independent manner. Mirtrons constitute about 15% of all miRNAs produced in a human body and have caught attention of researchers worldwide due to their unconventional origin, sequence characteristics, evolutionary dynamics, ability to regulate variety of cellular processes and their immense potential in disease therapeutics. In this comprehensive review we collate the research done in the past decade including biogenesis, sequence characteristics, regulation, and emerging therapeutic roles of mirtrons. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Uzma Salim
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
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Ning Y, Chen S, Hu J, Li L, Cheng L, Lu F. Fluorometric determination of agrA gene transcription in methicillin-resistant Staphylococcus aureus with a graphene oxide-based assay using strand-displacement polymerization recycling and hybridization chain reaction. Mikrochim Acta 2020; 187:372. [PMID: 32504215 DOI: 10.1007/s00604-020-04347-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/18/2020] [Indexed: 01/22/2023]
Abstract
A graphene oxide (GO)-based fluorescent bioassay was developed to quantify agrA gene transcription (its mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). This method is based on the use of Klenow fragment (KF)-assisted target recycling amplification and hybridization chain reaction (HCR). A triple complex was designed that contained a capture probe (CP), a trigger probe (TP), and a help probe (HP), which were partially complementary to one another. In the absence of the target, all the oligonucleotides labeled with carboxyfluorescein (FAM) are adsorbed onto the surface of GO by π-stacking interactions. This adsorption quenches the FAM signal. On the contrary, the target RNA causes the triple complex to disintegrate and initiates strand-displacement polymerization reaction (SDPR) and HCR in the presence of the appropriate raw materials, including the primer, KF, dNTPs, hairpin 1 (H1), and hairpin 2 (H2), generating double-stranded DNA (dsDNA) products. These dsDNA products are repelled by GO and produce strong fluorescence, measured at excitation/emission wavelengths of 480/514 nm. The fluorescent signal is greatly amplified by SYBR Green I (SGI) due to the synergistic effect of dsDNA-SGI. The target was assayed with this method at concentrations in the range 10 fM to 100 pM, and the detection limit (LOD) was 10 fM. This method also displayed good applicability in the analysis of real samples. It provides a new way of monitoring biofilm formation and studying the mechanisms of drug actions. Graphical abstract Schematic representation of the graphene oxide-based fluorescent bioassay for agrA gene transcription in methicillin-resistant Staphylococcus aureus by using strand-displacement polymerization recycling and hybridization chain reaction.
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Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, People's Republic of China
| | - Shanquan Chen
- Department of General Education, The School of Humanities and Social Science, The Chinese University of Hong Kong (Shenzhen campus), Shenzhen, 518172, Guangdong, People's Republic of China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, People's Republic of China
| | - Ling Li
- Experimental Center of molecular biology, The Chinese Medicine School of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, People's Republic of China
| | - Lijuan Cheng
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, People's Republic of China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, People's Republic of China.
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