1
|
Lamprou E, Sotiriou M, Kalligosfyri PM, Kalogianni DP, Christopoulos TK. A universal lateral flow assay for microRNA visual detection in urine samples. Talanta 2023; 262:124682. [PMID: 37244240 DOI: 10.1016/j.talanta.2023.124682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/25/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNAs) have been emerged as novel and significant biomarkers in liquid biopsy that can be found in different body fluids. Several techniques have been developed and applied for miRNAs analysis, including nucleic acid-based amplification methods, next generation sequencing, DNA microarrays and new genome-editing methods. These methods, however, are time-consuming and require expensive instruments and specially trained personnel. Biosensors, on the other hand, are alternative and valuable analytical/diagnostic tools due to their simplicity, cost-effectiveness, rapid analysis and ease of use. Several biosensors, especially nanotechnology-based ones, have been developed for miRNA analysis that are based either on target amplification or signal amplification and target re-cycling for sensitive detection. At this point of view, we have introduced a new and universal lateral flow assay in combination with reverse transcription - polymerase chain reaction (RT-PCR) and gold nanoparticles as reporters for the detection of miR-21 and miR-let-7a in human urine. It is the first time that such a biosensor has been applied to the detection of microRNAs in urine. As low as 102-103 copies of miR-21 and 102--104 copies of miR-let-7a added in urine were detectable by the proposed lateral flow assay with great specificity and repeatability (%CVs <4.5%).
Collapse
Affiliation(s)
- Eleni Lamprou
- Department of Chemistry, University of Patras, GR26504, Rio, Patras, Greece
| | - Markos Sotiriou
- Department of Chemistry, University of Patras, GR26504, Rio, Patras, Greece
| | | | | | - Theodore K Christopoulos
- Department of Chemistry, University of Patras, GR26504, Rio, Patras, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas (FORTH/ICE-HT), Patras, 26504, Greece
| |
Collapse
|
2
|
Lu A. Quantitative Analysis of Extracellular Vesicle Release Using Artificial MicroRNAs. Methods Mol Biol 2023; 2668:191-207. [PMID: 37140798 DOI: 10.1007/978-1-0716-3203-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Despite the widely used concept of extracellular vesicle (EV)-mediated intercellular communication, we are still far from understanding what is the exact role of such nanosized vesicles in human physiology and disease. Thus, development of new methods and tools that enable the study of fundamental EV biology is valuable for advancing the field. Typically, EV production and release are monitored using approaches that rely on either antibody-based FACS assays or genetically encoded fluorescent proteins. We previously devised artificially barcoded exosomal microRNAs (bEXOmiRs) that were used as high-throughput reporters of EV release. In the first part of this protocol, basic steps and considerations for the design and cloning of bEXOmiRs are explained in detail. Next, analysis of bEXOmiR expression and abundance in cells and isolated EVs is described.
Collapse
Affiliation(s)
- Albert Lu
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
3
|
Panwalkar P, Khire A, Shirsat N. Quantification of microRNAs in Cells and Tissues Using Stem-Loop RT PCR and qPCR. Methods Mol Biol 2022; 2423:51-58. [PMID: 34978687 DOI: 10.1007/978-1-0716-1952-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MicroRNA s are small RNA molecules that regulate gene expression by binding to the 3' untranslated region of the mRNA of their target genes. MicroRNA expression is altered in medulloblastoma as compared to the normal brain and this alteration is often associated with the pathogenesis of this tumor. The quantification of microRNA expression is carried out using quantitative/real-time polymerase chain reaction (PCR). In this chapter, we describe the protocol for the quantification of microRNA s in medulloblastoma tissues and cultured cells. This is carried out in three steps: (1) Extraction of total RNA, (2) Stem-loop reverse-transcriptase PCR, and (3) quantitative PCR.
Collapse
Affiliation(s)
- Pooja Panwalkar
- Shirsat Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India.
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA.
| | - Atul Khire
- Shirsat Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Department of Cell biology, Memorial Sloan -Kettering Cancer Centre, New York, NY, USA
| | - Neelam Shirsat
- Shirsat Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| |
Collapse
|
4
|
Mangala LS, Rodriguez-Aguayo C, Bayraktar E, Jennings NB, Lopez-Berestein G, Sood AK. Assessment of In Vivo siRNA Delivery in Cancer Mouse Models. Methods Mol Biol 2021; 2372:157-68. [PMID: 34417750 DOI: 10.1007/978-1-0716-1697-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA interference (RNAi) has rapidly become a powerful tool for target discovery and therapeutics. Small interfering RNAs (siRNAs) are highly effective in mediating sequence-specific gene silencing. However, the major obstacle for using siRNAs for cancer therapeutics is their systemic delivery from the administration site to target cells in vivo. This chapter describes approaches to deliver siRNA effectively for cancer treatment and discusses in detail the current methods to assess pharmacokinetics and biodistribution of siRNAs in vivo.
Collapse
|
5
|
Verma S, Gautam V, Sarkar AK. Improved laser capture microdissection (LCM)-based method for isolation of RNA, including miRNA and expression analysis in woody apple bud meristem. Planta 2019; 249:2015-2020. [PMID: 30976910 DOI: 10.1007/s00425-019-03127-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Isolation of high-quality RNA, including miRNA, from microscopic woody apple bud meristem using laser capture microdissection-based method. It is often challenging to study the expression of microRNAs (miRNAs) or genes in less accessible inner tissues of tree species rich in polyphenols or polysaccharides. Here, we report a laser capture microdissection (LCM)-based method for efficient and cost-effective isolation and expression analysis of miRNAs and genes in the meristem tissue of woody apple bud. The tissue fixation, processing, infiltration, and sectioning steps were optimized for LCM-based excision and subsequent RNA isolation. Further, we have confirmed that RNA isolated from LCM-derived apple bud meristem contained miRNAs and was of good quantity and quality, sufficient for downstream expression analysis.
Collapse
Affiliation(s)
- Swati Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
6
|
Abstract
RNA interference (RNAi) has rapidly become a powerful tool for target discovery and therapeutics. Small interfering RNAs (siRNAs) are highly effective in mediating sequence-specific gene silencing. However, the major obstacle for using siRNAs as cancer therapeutics is their systemic delivery from the administration site to target cells in vivo. This chapter describes approaches to deliver siRNA effectively for cancer treatment and discusses in detail the current methods to assess pharmacokinetics and biodistribution of siRNAs in vivo.
Collapse
Affiliation(s)
- Hiroto Hatakeyama
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA
| | - Sherry Y Wu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA
| | - Gabriel Lopez-Berestein
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA.,Department of Experimental Therapeutics, The University of Texas MDAnderson Cancer Center (MDACC), Houston, TX, 77054, USA.,Department of Cancer Biology, The University of Texas MDAnderson Cancer Center (MDACC), Houston, TX, 77054, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA. .,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, 77054, USA. .,Department of Cancer Biology, The University of Texas MDAnderson Cancer Center (MDACC), Houston, TX, 77054, USA.
| |
Collapse
|
7
|
Chaves SS, Fernandes-Brum CN, Silva GFF, Ferrara-Barbosa BC, Paiva LV, Nogueira FTS, Cardoso TCS, Amaral LR, de Souza Gomes M, Chalfun-Junior A. New Insights on Coffea miRNAs: Features and Evolutionary Conservation. Appl Biochem Biotechnol 2015; 177:879-908. [PMID: 26277190 DOI: 10.1007/s12010-015-1785-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/27/2015] [Indexed: 12/31/2022]
Abstract
Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.
Collapse
Affiliation(s)
- S S Chaves
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - C N Fernandes-Brum
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - G F F Silva
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - B C Ferrara-Barbosa
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - L V Paiva
- Central Laboratory of Molecular Biology (LCBM), Chemistry Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - F T S Nogueira
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - T C S Cardoso
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - L R Amaral
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - M de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - A Chalfun-Junior
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
| |
Collapse
|
8
|
Fallah P, Amirizadeh N, Poopak B, Toogeh G, Arefian E, Kohram F, Hosseini Rad SMA, Kohram M, Teimori Naghadeh H, Soleimani M. Expression pattern of key microRNAs in patients with newly diagnosed chronic myeloid leukemia in chronic phase. Int J Lab Hematol 2015; 37:560-8. [PMID: 25833191 DOI: 10.1111/ijlh.12351] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/09/2015] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Chronic myeloid leukemia (CML) is caused by reciprocal translocation in hematopoietic stem cells (HSCs). This translocation forms the BCR-ABL1 oncogene, which alters several signaling pathways that control malignancy. CML has three phases: chronic, accelerated, and blast crisis. The microRNAs (miRNAs or miRs) are noncoding RNAs that downregulate their target gene by targeting 3' UTR of mRNA or through translational inhibition. It has been shown that miRNAs regulate many biological processes, and dysregulation of these regulatory RNAs is involved in disease development, particularly in cancer. The important role of miRNAs as therapeutic agents and biomarkers has been demonstrated in CML patients at different phases of the disease. METHODS Stem-loop reverse transcription polymerase chain reaction was used to characterize differentially expressed miRNAs of leukocytes in the peripheral blood of 50 newly diagnosed CML patients in chronic phase. RESULTS Some onco-miRNAs were found to be downregulated (miR-155 and miR-106), and some tumor suppressor miRs (miR-16-1, miR-15a, miR-101, miR-568) were upregulated. CONCLUSION These results show that very few miRNAs alone would be good candidates for CML diagnosis independently of conflicting results, but together could be an additional tool for CML diagnosis. Moreover, miRNAs might be good candidates for prognosis prediction and CML therapy.
Collapse
Affiliation(s)
- P Fallah
- Blood Transfusion Research center, High institute for Research and Education in Transfusion Medicine, Tehran, Iran.,Alborz University of Medical Science, Karaj, Iran
| | - N Amirizadeh
- Blood Transfusion Research center, High institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - B Poopak
- Medical science branch, Islamic Azad University of Tehran, Tehran, Iran
| | - G Toogeh
- Thrombosis and Homeostasis Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - E Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - F Kohram
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - S M A Hosseini Rad
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - M Kohram
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - H Teimori Naghadeh
- Blood Transfusion Research center, High institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - M Soleimani
- Department of Hematology, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|