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Chen L, Bosmajian C, Woo S. A highly sensitive stem-loop RT-qPCR method to study siRNA intracellular pharmacokinetics and pharmacodynamics. Biol Methods Protoc 2024; 9:bpae029. [PMID: 38783988 PMCID: PMC11112049 DOI: 10.1093/biomethods/bpae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Small interfering RNA (siRNA) is a powerful tool for sequence-specific silencing of disease-related genes. In this study, we established and validated a stem-loop reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method applicable for both chemically unmodified and modified siRNA, aiming to elucidate mechanistic intracellular pharmacokinetic and pharmacodynamic (PK/PD) properties of siRNA. We conducted a comprehensive evaluation of factors affecting intracellular siRNA quantification. Our study revealed that immobilization-based siRNA extraction introduced high variation, making it unsuitable for absolute quantification. Conversely, direct cell lysis followed by stem-loop RT-qPCR demonstrated excellent reproducibility, with a quantification range from 0.0002 to 20 femtomole (fmole) for unmodified siRNA and 0.02 to 20 fmole for modified siRNA. The design of a 6-bp overlapping RT primer facilitated the distinction of full-length antisense from its 3'-metabolites, and pre-annealing of antisense to RT primer enhanced sensitivity and reproducibility. Differences in siRNA loss during storage and sample processing were noted among microcentrifuge tubes from various manufacturers. Endogenous miR-16 served as a reference for normalizing cytoplasmic siRNA, while protein concentration post-immunoprecipitation lysis was used to normalize RNA-induced silencing complex (RISC)-loaded siRNA levels. This method successfully enabled a detailed characterization of the time profiles of cytoplasmic and RISC-loaded siRNA, advancing the in vitro-in vivo translation of siRNA therapeutics.
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Affiliation(s)
- Lin Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Caroline Bosmajian
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Sukyung Woo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
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2
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Monaco F, De Conti L, Vodret S, Zanotta N, Comar M, Manzotti S, Rubini C, Graciotti L, Fulgenzi G, Bovenzi M, Baralle M, Tomasetti M, Santarelli L. Force-feeding malignant mesothelioma stem-cell like with exosome-delivered miR-126 induces tumour cell killing. Transl Oncol 2022; 20:101400. [PMID: 35334283 PMCID: PMC8956928 DOI: 10.1016/j.tranon.2022.101400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
Exosome-enriched miR-126 (exo-miR) induced mass disaggregation of MPM-derived spheroids. Exo-miR plus the inhibitor of exosome release (GW4869) accumulated miR-126 within cells. Exo-miR plus GW4869 induced MPM-stem cell like death and in vivo tumour growth arrest. MiR-126 accumulated in cells induced a protective autophagy which was inhibited by GW4869. Exo-miR plus GW4869 induced a metabolic crisis, thus promoting necroptosis activation.
Malignant pleural mesothelioma (MPM) is an aggressive tumour resistant to treatments. It has been postulated that cancer stem cells (CSCs) persist in tumours causing relapse after multimodality treatment. In the present study, a novel miRNA-based therapy approach is proposed. MPM-derived spheroids have been treated with exosome-delivered miR-126 (exo-miR) and evaluated for their anticancer effect. The exo-miR treatment increased MPM stem-cell like stemness and inhibited cell proliferation. However, at a prolonged time, the up taken miR-126 was released by the cells themselves through exosomes; the inhibition of exosome release by an exosome release inhibitor GW4869 induced miR-126 intracellular accumulation leading to massive cell death and in vivo tumour growth arrest. Autophagy is involved in these processes; miR-126 accumulation induced a protective autophagy and the inhibition of this process by GW4869 generates a metabolic crisis that promotes necroptosis, which was associated with PARP-1 over-expression and cyt-c and AIF release. Here, for the first time, we proposed a therapy against CSCs, a heterogeneous cell population involved in cancer development and relapse.
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Affiliation(s)
- Federica Monaco
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy; Department of Excellence SBSP-Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Laura De Conti
- RNA biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Simone Vodret
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Nunzia Zanotta
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Manola Comar
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Sandra Manzotti
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Corrado Rubini
- Department of Excellence SBSP-Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Laura Graciotti
- Department of Excellence SBSP-Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Gianluca Fulgenzi
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimo Bovenzi
- Department of Medical Sciences, Clinical Unit of Occupational Medicine, University of Trieste, Trieste, Italy
| | - Marco Baralle
- RNA biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Marco Tomasetti
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy.
| | - Lory Santarelli
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
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3
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Kubo S, Niimi H, Kitajima I. Rapid detection of blood and semen mRNA markers by reverse transcription-recombinase polymerase amplification. Forensic Sci Int Genet 2022; 58:102665. [DOI: 10.1016/j.fsigen.2022.102665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
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4
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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5
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Eksin E, Torul H, Yarali E, Tamer U, Papakonstantinou P, Erdem A. Paper-based electrode assemble for impedimetric detection of miRNA. Talanta 2020; 225:122043. [PMID: 33592766 DOI: 10.1016/j.talanta.2020.122043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
In the present work, a paper-based electrode assemble was developed and implemented to detect target microRNA 155 (miRNA 155) via electrochemical impedance spectroscopy (EIS) measurements. In this concept, gold nanoparticles (AuNPs) modified paper based electrode assemble system (AuNP-PE) was designed, and characterized by scanning electron microscopy (SEM), cyclic voltammetry (CV) and EIS measurements. The impedimetric detection of miRNA 155 was performed by measuring the fractional change at the charge transfer resistance (Rct). The detection limits were found as 33.8 nM in PBS and 93.4 nM in fetal bovine serum (FBS) medium, respectively. The selectivity of the proposed assay was tested against to non-complementary (NC) and mismatch (MM) miRNA sequences in the presence of mixture sample containing miRNA:NC (1:1) and miRNA:MM (1:1) in PBS (pH 7.40) or FBS. The analytical performance and the selectivity of impedimetric biosensor were also tested in FBS.
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Affiliation(s)
- Ece Eksin
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey
| | - Hilal Torul
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330, Ankara, Turkey
| | - Ece Yarali
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330, Ankara, Turkey.
| | - Pagona Papakonstantinou
- School of Engineering, Engineering Research Institute, Ulster University, Newtownabbey BT37 0QB, United Kingdom
| | - Arzum Erdem
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey.
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6
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Chen J, Futran A, Crithary A, Li S, Wolicki A, Fogarty K, Baldick J, Chase P, Arey BJ, Lippy J. Leveraging Automation toward Development of a High-Throughput Gene Expression Profiling Platform. SLAS DISCOVERY 2020; 26:410-419. [PMID: 32935608 DOI: 10.1177/2472555220956593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We previously developed a panel of one-step real-time quantitative reverse transcription PCR (one-step qRT-PCR; hereafter referred to as qRT-PCR) assays to assess compound efficacy. However, these high-cost, conventional qRT-PCR manual assays are not amenable to high-throughput screen (HTS) analysis in a time-sensitive and complex drug discovery process. Here, we report the establishment of an automated gene expression platform using in-house lysis conditions that allows the study of various cell lines, including primary T cells. This process innovation provides the opportunity to perform genotypic profiling in both immunology and oncology therapeutic areas with quantitative studies as part of routine drug discovery program support. This newly instituted platform also enables a panel screening strategy to efficiently connect HTS, lead identification, and lead optimization in parallel.
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Affiliation(s)
- Jing Chen
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Alan Futran
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Austin Crithary
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Sha Li
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Alex Wolicki
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Kylie Fogarty
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Joe Baldick
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Peter Chase
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Brian J Arey
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jonathan Lippy
- Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
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7
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Direct S-Poly(T) Plus assay in quantification of microRNAs without RNA extraction and its implications in colorectal cancer biomarker studies. J Transl Med 2019; 17:316. [PMID: 31547825 PMCID: PMC6757382 DOI: 10.1186/s12967-019-2061-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Advances in microRNAs (miRNAs) biomarkers have generated disease markers with potential clinical values. However, none of these published results have been applied in clinic until today. The main reason could be the lack of simple but robust miRNA measurements. METHODS We built up a simple but ultrasensitive RT-qPCR protocol, Direct S-Poly(T) Plus assay, for detecting miRNAs without RNA purification. In this study, the method was optimized and compared with other RNA purification-based miRNA assays, and the sensitivity was tested. Using Direct S-Poly(T) Plus method, seven potential miRNA biomarkers of colorectal cancer were validated. RESULTS It is possible to detect approximately 100 miRNAs with minimal plasma inputs (20 μl) and time (~ 140 min) with this approach. The sensitivity of this method was 2.7-343-fold higher than that of the stem-loop method, and comparable with S-Poly(T) plus method. 7 validated miRNA biomarkers of colorectal cancer by Direct S-Poly(T) plus assay could discriminate colorectal cancer stage I from healthy individuals, and promised satisfactory discrimination with the area under receiver operating characteristic (ROC) curve ranging from 0.79 to 0.94 (p value < 0.001). CONCLUSIONS This simple and robust protocol may have strong impact on the development of specific miRNAs as biomarkers in clinic.
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8
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Ma X, Zhang Y, Qiao F, Wang M, Zuo Z, Zhang Y, Wang Y. Comparison of RNA extraction and microRNA detection protocols for a small amount of germinal vesicle oocytes in bovine. Anim Reprod Sci 2018; 195:112-120. [PMID: 29859700 DOI: 10.1016/j.anireprosci.2018.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 11/17/2022]
Abstract
RT-qPCR is a widely used method to detect miRNA expression. Compared with mRNA, miRNA has a shorter length and lower abundance which hinders the acquisition of reliable results. Thus, miRNA detection requires a method with high sensitivity and accuracy. Collecting large amounts of material is particularly difficult for oocytes and pre-implantation embryos of domestic animals. Establishing a set of miRNA detection methods that are suitable to detect trace amounts of such materials is urgently needed. In this study, the total RNA in 50 germinal vesicle (GV) oocytes was isolated through direct lysis and by using mirVana miRNA Isolation Kit and miRNeasy Micro Kit. The OD260/280 values and concentrations of the RNA in these three groups were compared to identify a superior RNA isolation method. In addition, the specificity and sensitivity of common DNA and LNA primers were compared by real-time quantitative polymerase chain reaction for miRNA detection. Results show that the RNA concentration of in the direct lysis group was significantly higher than that in the other two groups. The specificity between the DNA primers and LNA primers was identical, whereas the sensitivity of LNA primers was superior to that of DNA primers. These results suggest that direct lysis combined with LNA primers might be a suitable protocol for the miRNA detection of a small amounts of GV oocytes and pre-implantation embryos in cattle.
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Affiliation(s)
- Xiaonan Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Ying Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Fang Qiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Mengyun Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Zhenzi Zuo
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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9
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Nikas I, Hapfelmeier A, Mollenhauer M, Angermeier D, Bettstetter M, Götz R, Schmidmayr M, Seifert-Klauss V, Muckenhuber A, Schenck U, Weirich G. Integrated morphologic and molecular analysis of Trichomonas vaginalis, Mycoplasma hominis, and human papillomavirus using cytologic smear preparations. Parasitol Res 2018; 117:1443-1451. [PMID: 29549429 DOI: 10.1007/s00436-018-5829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/06/2018] [Indexed: 01/03/2023]
Abstract
Pathogenic microbes may colonize the female genital tract via sexual transmission and cause health issues like inflammation or malignancy, summarized as sexually transmitted disease (STD). A major representative of such pathogens is Trichomonas vaginalis (T.v.), whose role in the etiology of cervical cancer remains elusive. Traditional morphologic screening of cervical smears is able to detect T.v., although its identification may be complicated by look-alikes such as degenerated granulocytes and basal cells. In addition, the parasite's endosymbiont Mycoplasma hominis (M.h.) cannot be detected in the Pap test. This investigation was aimed at designing a PCR-based method to detect specific pathogenic germs by using cervical cytology slides to overcome morphologic uncertainty and increase diagnostic accuracy. To test our molecular screening method on T.v., M.h., and HPV in archival smears, we elaborated a multiplex PCR approach based on microdissection. This assay was applied to a minute quantity of starting material which harbored or was suspected to harbor T.v.; the resulting isolated DNA was used for subsequent molecular analyses of T.v., M.h., and HPV. We clarified the diagnosis of genital T.v. infection in 88 and 1.8% of morphologically suspicious and T.v.-negative cases, respectively. We also revealed a tendency of M.h. co-infection in high-risk HPV cases. In conclusion, a microdissection-based approach to detect pathogenic microbes such as T.v., HPV, and M.h. is a molecular tool easy to implement and may help to better understand the interactivity of these germs with respect to pathogenesis.
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Affiliation(s)
- I Nikas
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany.,School of Medicine, European University Cyprus, Nicosia, Cyprus
| | - A Hapfelmeier
- Institute of Medical Informatics, Statistics and Epidemiology, Technische Universität München, Munich, Germany
| | - M Mollenhauer
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany
| | - D Angermeier
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany
| | | | - R Götz
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany
| | - M Schmidmayr
- Frauenklinik und Poliklinik, Technische Universität München, Munich, Germany
| | - V Seifert-Klauss
- Frauenklinik und Poliklinik, Technische Universität München, Munich, Germany
| | - A Muckenhuber
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany
| | - U Schenck
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany.,MVZ Gynäkologie & Pathologie, Munich, Germany
| | - Gregor Weirich
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675, Munich, Germany.
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10
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Hakimian F, Ghourchian H, Hashemi AS, Arastoo MR, Behnam Rad M. Ultrasensitive optical biosensor for detection of miRNA-155 using positively charged Au nanoparticles. Sci Rep 2018; 8:2943. [PMID: 29440644 PMCID: PMC5811613 DOI: 10.1038/s41598-018-20229-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/11/2018] [Indexed: 01/10/2023] Open
Abstract
An ultrasensitive optical biosensor for microRNA-155 (miR-155) was developed to diagnose breast cancer at early stages. At first, the probe DNA covalently bind to the negatively charged gold nanoparticles (citrate-capped AuNPs). Then, the target miR-155 electrostatically adsorb onto the positively charged gold nanoparticles (polyethylenimine-capped AuNP) surface. Finally, by mixing citrate-capped AuNP/probe and polyethylenimine-capped AuNP/miR-155, hybridization occurs and the optical signal of the mixture give a measure to quantify the miR-155 content. The proposed biosensor is able to specify 3-base-pair mismatches and genomic DNA from target miR-155. The novelty of this biosensor is in its ability to trap the label-free target by its branched positively charged polyethylenimine. This method increases loading the target on the polyethylenimine-capped AuNPs' surface. So, proposed sensor enables miR-155 detection at very low concentrations with the detection limit of 100 aM and a wide linear range from 100 aM to 100 fM.
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Affiliation(s)
- Fatemeh Hakimian
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azam Sadat Hashemi
- Hematology, Oncology & Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Reza Arastoo
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Mohammad Behnam Rad
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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11
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Attri KS, Mehla K, Shukla SK, Singh PK. Microscale Gene Expression Analysis of Tumor-Associated Macrophages. Sci Rep 2018; 8:2408. [PMID: 29402936 PMCID: PMC5799305 DOI: 10.1038/s41598-018-20820-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/19/2018] [Indexed: 12/17/2022] Open
Abstract
Macrophages, apart from being the key effector cells of the innate immune system, also play critical roles during the development and progression of various complex diseases, including cancer. Tumor-associated macrophages, infiltrate tumors during different stages of cancer progression to regulate motility, invasion, and intravasation to metastatic sites. Macrophages can exist in different polarization states associated with unique function in tumors. Since tumor-associated macrophages constitute a very small proportion of tumor cells, analysis of gene expression pattern using normal extraction buffer-based methods remains a challenging task. Therefore, it is imperative to develop low-throughput strategies to investigate transcriptional regulations from a small number of immune cells. Here, we describe an efficient, sensitive, and cost-effective approach for gene expression analysis of a small number of fluorescence-activated sorted tumor-associated macrophages. Our analyses from the different number of stable, primary, and sorted macrophages suggest 5,000 cells is an optimal number for performing quantitative, real-time PCR analysis of multiple genes. Our studies could detect expression of macrophage-specific genes from cultured primary macrophages, and FACS-sorted macrophages from different biological tissues without introducing biases in comparative gene expression ratios. In conclusion, our kit-based method for quantitative gene expression analysis from a small number of cells found in biological tissues will provide an opportunity to study cell-specific, transcriptional changes.
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Affiliation(s)
- Kuldeep S Attri
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kamiya Mehla
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Surendra K Shukla
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Pankaj K Singh
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.
- Department of Biochemistry and Molecular biology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA.
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12
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Chiba M, Monzen S, Iwaya C, Kashiwagi Y, Yamada S, Hosokawa Y, Mariya Y, Nakamura T, Wojcik A. Serum miR-375-3p increase in mice exposed to a high dose of ionizing radiation. Sci Rep 2018; 8:1302. [PMID: 29358747 PMCID: PMC5778023 DOI: 10.1038/s41598-018-19763-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022] Open
Abstract
Exposure to high-doses of ionizing radiation (IR) leads to development of a strong acute radiation syndrome (ARS) in mammals. ARS manifests after a latency period and it is important to develop fast prognostic biomarkers for its early detection and assessment. Analysis of chromosomal aberrations in peripheral blood lymphocytes is the gold standard of biological dosimetry, but it fails after high doses of IR. Therefore, it is important to establish novel biomarkers of exposure that are fast and reliable also in the high dose range. Here, we investigated the applicability of miRNA levels in mouse serum. We found significantly increased levels of miR-375-3p following whole body exposure to 7 Gy of X-rays. In addition, we analyzed their levels in various organs of control mice and found them to be especially abundant in the pancreas and the intestine. Following a dose of 7 Gy, extensive cell death occurred in these tissues and this correlated negatively with the levels of miR-375-3p in the organs. We conclude that high expressing tissues of miR-375-3p may secrete this miRNA in serum following exposure to 7 Gy. Therefore, elevated miR-375-3p in serum may be a predictor of tissue damage induced by exposure to a high radiation dose.
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Affiliation(s)
- Mitsuru Chiba
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan.
| | - Satoru Monzen
- Department of Radiation Sciences, Graduate School of Health Sciences, Hirosaki University, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Chihiro Iwaya
- Department of Medical Technology, Hirosaki University School of Health Sciences, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Yuri Kashiwagi
- Department of Medical Technology, Hirosaki University School of Health Sciences, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Sunao Yamada
- Department of Medical Technology, Hirosaki University School of Health Sciences, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Yoichiro Hosokawa
- Department of Radiation Sciences, Graduate School of Health Sciences, Hirosaki University, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Yasushi Mariya
- Department of Radiology and Radiation Oncology, Mutsu General Hospital, 1-2-8, Kogawa-machi, Mutsu, Aomori, 035-0071, Japan
| | - Toshiya Nakamura
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, 66-1, Hon-cho, Hirosaki, Aomori, 036-8564, Japan
| | - Andrzej Wojcik
- Department of Molecular Biosciences, The Wenner Gren Instititute, Stockholm University, Svante Arrhenius väg 20 C, 10691, Stockholm, Sweden.,Department of Radiobiology and Immunology, Institute of Biology, Jan Kochanowski University, ul. Swietokrzyska 15, 25-406, Kielce, Poland
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13
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Budzinska M, Owczarz M, Pawlik-Pachucka E, Roszkowska-Gancarz M, Slusarczyk P, Puzianowska-Kuznicka M. miR-96, miR-145 and miR-9 expression increases, and IGF-1R and FOXO1 expression decreases in peripheral blood mononuclear cells of aging humans. BMC Geriatr 2016; 16:200. [PMID: 27903254 PMCID: PMC5131432 DOI: 10.1186/s12877-016-0379-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/25/2016] [Indexed: 02/08/2023] Open
Abstract
Background In mammals, the IGF-1 pathway affects the phenotype of aging. Since the function of the immune system is modulated by IGF-1, it is plausible that immunosenescence might in part result from altered control by this pathway. We therefore examined whether the expression of IGF-1R, FOXO1, and FOXO3a in peripheral blood mononuclear cells (PBMC) changes with age and if this might be due to changes in the expression of select miRNAs. Methods The expression of IGF-1R, FOXO1, FOXO3a, as well as of miR-9, miR-96, miR-99a, miR-132, miR-145, and miR-182 was examined in PBMC of young (27.8 ± 3.7 years), elderly (65.6 ± 3.4 years), and long-lived (94.0 ± 3.7 years) Polish Caucasians using real-time PCR. mRNA/miRNA interactions were studied in HEK 293 cells using luciferase-expressing pmirGLO reporter vector. Results The median expression of IGF-1R decreased with age (p < 0.000001), as did the expression of FOXO1 (p < 0.000001), while the expression of FOXO3a remained stable. We also found an age-associated increase of the median expression of miR-96 (p = 0.002), miR-145 (p = 0.024) and miR-9 (p = 0.026), decrease of the expression of miR-99a (p = 0.037), and no changes regarding miR-132 and miR-182. Functional studies revealed that miR-96 and miR-182 interacted with human IGF-1R mRNA, and that miR-145 and miR-132 interacted with human FOXO1 mRNA. Conclusions The age-associated higher expression of miR-96 and miR-145 might contribute to the lower expression of IGF-1R while the higher expression of miR-96, miR-145 and miR-9 might contribute to the lower expression of FOXO1 in peripheral blood mononuclear cells of aging humans. Sustained expression/function of FOXO3a but not of the other two genes might be important for the maintenance of the immune system function in these individuals.
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Affiliation(s)
- Monika Budzinska
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Magdalena Owczarz
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland.,Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Eliza Pawlik-Pachucka
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland.,Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Malgorzata Roszkowska-Gancarz
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Przemyslaw Slusarczyk
- PolSenior Project, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Monika Puzianowska-Kuznicka
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland. .,Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, Pawinskiego 5, 02-106, Warsaw, Poland.
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14
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Wang X, Teferedegne B, Shatzkes K, Tu W, Murata H. Endogenous RNase inhibitor contributes to stability of RNA in crude cell lysates: Applicability to RT-qPCR. Anal Biochem 2016; 513:21-27. [PMID: 27544650 DOI: 10.1016/j.ab.2016.08.011] [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] [Received: 07/06/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 10/21/2022]
Abstract
Crude cell lysates are increasingly used as input for direct analysis by reverse transcription quantitative PCR (RT-qPCR), particularly for high-throughput applications. We previously demonstrated that a simple buffer containing a non-ionic detergent can serve as an inexpensive alternative to commercial cell-lysis reagents for the preparation of RT-qPCR-ready cell lysates; addition of an exogenous RNase inhibitor (RI) to the lysis buffer was found to be unnecessary to maintain RNA stability in cell lysates either freshly prepared or previously stored frozen at -80 °C. In the present study, we have demonstrated that the stability of RNA observed in our cell lysates is due to the presence of the endogenous RI. Furthermore, we have established the generalizability and applicability of this phenomenon by evaluating lysates prepared from cell lines commonly used in virology (A549, HeLa, MDCK, and Vero). Awareness of the mechanism underlying RNA stability may engender greater confidence in generating cell lysates for RT-qPCR without relying on addition of exogenous RI (a substantial cost-saving benefit) and encourage appropriate practices for handling and storage of samples.
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Affiliation(s)
- Xiao Wang
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Silver Spring, MD 20993, USA
| | - Belete Teferedegne
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Silver Spring, MD 20993, USA
| | - Kenneth Shatzkes
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Silver Spring, MD 20993, USA
| | - Wei Tu
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Silver Spring, MD 20993, USA
| | - Haruhiko Murata
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Silver Spring, MD 20993, USA.
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15
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Zhao Q, Deng S, Wang G, Liu C, Meng L, Qiao S, Shen L, Zhang Y, Lü J, Li W, Zhang Y, Wang M, Pestell RG, Liang C, Yu Z. A direct quantification method for measuring plasma MicroRNAs identified potential biomarkers for detecting metastatic breast cancer. Oncotarget 2016; 7:21865-74. [PMID: 26967564 PMCID: PMC5008329 DOI: 10.18632/oncotarget.7990] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/21/2016] [Indexed: 02/06/2023] Open
Abstract
Circulating miRNAs are protected from ribonuclease degradation by assembly into microvesicles and exosomes. Releasing miRNAs completely from these particles is the key step to quantify the circulating miRNAs. Currently purified RNA-based quantitative analysis is widely used while it is time and cost consuming with high risk for those circulating miRNAs with low abundance due to partial loss of RNA during the steps of total RNA extraction and small RNA enrichment. Herein, we optimized a simple, effective and time-saving method to directly measure plasma miRNAs without RNA isolation. It is based on complete miRNA release from the protein complexes, followed by miRNA-specific reverse transcription and quantitative real-time PCR amplification. By comparison to the RNA-based approach, the direct quantification method showed more efficiency for circulating miRNA analysis, higher accuracy and specificity. By application of the direct quantification method to clinical samples combined with the RNA-based miRNA screening analysis, upregulation of miR-106a in blood was validated in metastatic breast cancer patients, indicating miR-106a are a potential biomarker for metastatic breast cancer.
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Affiliation(s)
- Qian Zhao
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shengqiong Deng
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guangxue Wang
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Cuicui Liu
- Shanghai East Hospital, Dalian Medical University, Dalian, China
| | - Lingyu Meng
- Shanghai East Hospital, Dalian Medical University, Dalian, China
| | - Shanshan Qiao
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Shen
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yue Zhang
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinhui Lü
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wenshu Li
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuzhen Zhang
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Min Wang
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Richard G. Pestell
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Chunli Liang
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zuoren Yu
- Research Center for Translational Medicine, Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai East Hospital, Dalian Medical University, Dalian, China
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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16
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Dellett M, Simpson DA. Considerations for optimization of microRNA PCR assays for molecular diagnosis. Expert Rev Mol Diagn 2016; 16:407-14. [PMID: 26854938 DOI: 10.1586/14737159.2016.1152184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The heterogeneity of microRNAs, with each one comprising a series of variants or 'isomiRs', adds additional complexity. Presented here are the key considerations for use of RT-qPCR to measure microRNAs and their isomiRs, with a focus on plasma. Modified nucleotides can be incorporated into primer sequences to enhance affinity and provide increased specificity and sensitivity for RT-qPCR assays. Approaches based upon polyA tailing and use of a common oligo(dT)-based reverse transcription oligonucleotide will detect most isomiRs. Conversely, stem-loop RT oligonucleotides and sequence specific probes can enable detection of specific isomiRs of interest. Next generation sequencing of all the products of a microRNA RT-PCR reaction is a promising new approach for both microRNA quantification and characterization.
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Affiliation(s)
- Margaret Dellett
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
| | - David Arthur Simpson
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
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17
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Lee H, Shapiro SJ, Chapin SC, Doyle PS. Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates. Anal Chem 2016; 88:3075-81. [DOI: 10.1021/acs.analchem.5b03902] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hyewon Lee
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Sarah J. Shapiro
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen C. Chapin
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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18
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Wang X, Peden K, Murata H. RT-qPCR-based microneutralization assay for human cytomegalovirus using fibroblasts and epithelial cells. Vaccine 2015; 33:7254-7261. [DOI: 10.1016/j.vaccine.2015.10.110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 08/28/2015] [Accepted: 10/28/2015] [Indexed: 01/03/2023]
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19
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Zhang H, Zhu G. Quantitative RT-PCR assay for high-throughput screening (HTS) of drugs against the growth of Cryptosporidium parvum in vitro. Front Microbiol 2015; 6:991. [PMID: 26441920 PMCID: PMC4585199 DOI: 10.3389/fmicb.2015.00991] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 09/04/2015] [Indexed: 12/20/2022] Open
Abstract
Our laboratory has previously developed a qRT-PCR assay to assess drug efficacy on the growth of Cryptosporidium parvum in vitro by detecting the levels of parasite 18S rRNA. This approach displayed up to four orders of magnitude of linear dynamic range and was much less labor-intensive than the traditional microscopic methods. However, conventional qRT-PCR protocol is not very amendable to high-throughput analysis when total RNA needs to be purified by lengthy, multi-step procedures. Recently, several commercial reagents are available for preparing cell lysates that could be directly used in downstream qRT-PCR analysis (e.g., Ambion Cell-to-cDNA kit and Bio-Rad iScript sample preparation reagent). Using these reagents, we are able to adapt the qRT-PCR assay into high-throughput screening of drugs in vitro (i.e., 96-well and 384-well formats for the cultivation of parasites and qRT-PCR detection, respectively). This qRT-PCR protocol is able to give a >150-fold linear dynamic range using samples isolated from cells infected with various numbers of parasites. The new assay is also validated by the NIH-recommended intra-plate, inter-plate, and inter-day uniformity tests. The robustness and effectiveness of the assay are also confirmed by evaluating the anti-cryptosporidial efficacy of paromomycin and by a small scale screening of compounds.
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Affiliation(s)
- Haili Zhang
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University College Station, TX, USA
| | - Guan Zhu
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University College Station, TX, USA
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20
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Ginsberg SD, Che S. Methods and compositions for amplification and detection of microRNAs (miRNAs) and noncoding RNAs (ncRNAs) using the signature sequence amplification method (SSAM). ACTA ACUST UNITED AC 2015; 8:2-9. [PMID: 25564022 DOI: 10.2174/2352092208666141001154206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/17/2022]
Abstract
The signature sequence amplification method (SSAM) described herein is an approach for amplifying noncoding RNA (ncRNA), microRNA (miRNA), and small polynucleotide sequences. A key point of the SSAM technology is the generation of signature sequences. The signature sequences include target sequences (miRNA, ncRNA, and/or any small polynucleotide sequence) flanked by two DNA fragments. Target sequences can be amplified through DNA synthesis, RNA synthesis, or the combination of DNA and RNA synthesis. The amplification of signature sequences provides an efficient and reproducible mechanism to determine the presence or absence of the target miRNAs/ncRNAs, to analyze the quantities of the miRNAs in biological samples, and for miRNA/ncRNA profiling.
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Affiliation(s)
| | - Shaoli Che
- Center for Dementia Research, Nathan Kline Institute, NYU Langone Medical Center, 140 Old Orangeburg Road, Orangeburg, NY 10962, 845-398-2170, USA.
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21
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Nano-topology guided neurite outgrowth in PC12 cells is mediated by miRNAs. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2014; 10:1871-5. [PMID: 25101881 DOI: 10.1016/j.nano.2014.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/20/2014] [Accepted: 07/27/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED MicroRNAs (miRNAs) are master regulators of gene expression at post-transcriptional level. The present study investigated the involvement of miRNAs in topological guidance of neurite outgrowth in an NGF treated PC12 cell model cultured on nano-patterned polyethylene terephthalate (PET) substrates fabricated with interference lithography. The expressions of 38 neuronal miRNAs were measured and 3 were found to be differentially regulated during topological guidance of neurite outgrowth. Altering the intracellular levels of these miRNAs disrupted the orderly growth of neurite along nano-patterned substrate. Our results showed miRNAs to be versatile regulators and their involvement should be thoroughly investigated for better understanding of biological processes. FROM THE CLINICAL EDITOR In this basic science study, strong evidence was found that topological guidance is only one factor, and miRNA-s regulate axonal outgrowth from neurites. Nano-patterned polyethylene terephthalate substrates were used for the study, fabricated using interference lithography. Further studies of this biologically relevant process may pave the way to clinically useful axonal regrowth and axonal guidance methods.
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22
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Shatzkes K, Teferedegne B, Murata H. A simple, inexpensive method for preparing cell lysates suitable for downstream reverse transcription quantitative PCR. Sci Rep 2014; 4:4659. [PMID: 24722424 PMCID: PMC3983595 DOI: 10.1038/srep04659] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/24/2014] [Indexed: 11/30/2022] Open
Abstract
Sample nucleic acid purification can often be rate-limiting for conventional quantitative PCR (qPCR) workflows. We recently developed high-throughput virus microneutralization assays using an endpoint assessment approach based on reverse transcription qPCR (RT-qPCR). The need for cumbersome RNA purification is circumvented in our assays by making use of a commercial reagent that can easily generate crude cell lysates amenable to direct analysis by one-step RT-qPCR. In the present study, we demonstrate that a simple buffer containing a non-ionic detergent can serve as an inexpensive alternative to commercially available reagents for the purpose of generating RT-qPCR-ready cell lysates from MDCK cells infected with influenza virus. We have found that addition of exogenous RNase inhibitor as a buffer component is not essential in order to maintain RNA integrity, even following stress at 37 °C incubation for 1-2 hours, in cell-lysate samples either freshly prepared or previously stored frozen at -80 °C.
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Affiliation(s)
- Kenneth Shatzkes
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Bethesda, MD 20892, USA
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, OVRR, CBER, FDA, Bethesda, MD 20892, USA
- These authors contributed equally to this work
- Current address: Graduate School of Biomedical Sciences, New Jersey Medical School and Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Belete Teferedegne
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Bethesda, MD 20892, USA
- These authors contributed equally to this work
| | - Haruhiko Murata
- Laboratory of DNA Viruses, Division of Viral Products, OVRR, CBER, FDA, Bethesda, MD 20892, USA
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