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Rahman MM, Nakanishi R, Tsukada F, Takashima S, Wakihara Y, Kamatari YO, Shimizu K, Okada A, Inoshima Y. Identification of Suitable Internal Control miRNAs in Bovine Milk Small Extracellular Vesicles for Normalization in Quantitative Real-Time Polymerase Chain Reaction. MEMBRANES 2023; 13:185. [PMID: 36837688 PMCID: PMC9961204 DOI: 10.3390/membranes13020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
This study aimed to identify a suitable RNA extraction kit and stable internal control microRNA (miRNA) in bovine milk small extracellular vesicles (sEVs) for a quantitative polymerase chain reaction (qPCR) analysis. Two RNA extraction kits, miRNeasy Micro Kit, and Maxwell RSC miRNA Tissue Kit, were compared and evaluated using bovine milk sEVs via qPCR analysis. Five miRNAs, bta-miR-29a, bta-miR-200a, bta-miR-26b, hsa-miR-27b-3p, and hsa-miR-30b-5p, were selected by microarray analyses, and their cycle threshold (Ct) values were further evaluated mathematically using geNorm, NormFinder, BestKeeper, and ∆Ct algorithms. The results revealed that both the miRNeasy Micro Kit and Maxwell RSC miRNA Tissue Kit are useful for the efficient recovery of RNA from bovine milk sEVs. According to the final stability ranking analyzed by RefFinder, hsa-miR-27b-3p and bta-miR-29a can be used as suitable internal control miRNAs in bovine milk sEVs. The study also indicated that using a suitable internal control miRNA may improve the reliability and accuracy of the qPCR analysis for normalization in bovine milk sEVs. To the best of our knowledge, this is the first study to uncover the suitable internal control miRNAs in bovine milk sEVs.
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Affiliation(s)
- Md. Matiur Rahman
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
- Department of Medicine, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Ryoka Nakanishi
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
| | - Fumi Tsukada
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
| | - Shigeo Takashima
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yoshiko Wakihara
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
- Division of Instrumental Analysis, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Kaori Shimizu
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
| | - Ayaka Okada
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu 501-1193, Japan
| | - Yasuo Inoshima
- Laboratory of Food and Environmental Hygiene, Gifu University, Gifu 501-1193, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu 501-1193, Japan
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan
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El-Daly SM, Gouhar SA, Abd Elmageed ZY. Circulating microRNAs as Reliable Tumor Biomarkers: Opportunities and Challenges Facing Clinical Application. J Pharmacol Exp Ther 2023; 384:35-51. [PMID: 35809898 PMCID: PMC9827506 DOI: 10.1124/jpet.121.000896] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs (miRNAs) are involved in the development of human malignancies, and cells have the ability to secrete these molecules into extracellular compartments. Thus, cell-free miRNAs (circulating miRNAs) can potentially be used as biomarkers to evaluate pathophysiological changes. Although circulating miRNAs have been proposed as potential noninvasive tumor biomarkers for diagnosis, prognosis, and response to therapy, their routine application in the clinic is far from being achieved. This review focuses on the recent progress regarding the value of circulating miRNAs as noninvasive biomarkers, with specific consideration of their relevant clinical applications. In addition, we provide an in-depth analysis of the technical challenges that impact the assessment of circulating miRNAs. We also highlight the significance of integrating circulating miRNAs with the standard laboratory biomarkers to boost sensitivity and specificity. The current status of circulating miRNAs in clinical trials as tumor biomarkers is also covered. These insights and general guidelines will assist researchers in experimental practice to ensure quality standards and repeatability, thus improving future studies on circulating miRNAs. SIGNIFICANCE STATEMENT: Our review will boost the knowledge behind the inconsistencies and contradictory results observed among studies investigating circulating miRNAs. It will also provide a solid platform for better-planned strategies and standardized techniques to optimize the assessment of circulating cell-free miRNAs.
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Affiliation(s)
- Sherien M El-Daly
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
| | - Shaimaa A Gouhar
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
| | - Zakaria Y Abd Elmageed
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
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3
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Skryabin GO, Vinokurova SV, Elkina NV, Denisova DA, Beliaeva AA, Zhordania KI, Bagrov DV, Enikeev AD, Galetsky SA, Komelkov AV, Krasnoshekova GI, Tchevkina EM. Comparison of Methods for MicroRNA Isolation from Extracellular Vesicles Obtained from Ascitic Fluids. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1354-1366. [PMID: 36509726 DOI: 10.1134/s0006297922110141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Secreted extracellular vesicles (EVs) contain active biomolecules, including miRNAs, composition of which reflects epigenetic changes occurring in cells during pathological processes, in particular, malignant transformation. The accumulated pool of data on the role of EVs in carcinogenesis has stimulated investigations of the EV-derived cancer markers. The most important factor limiting development of this scientific direction is lack of "gold standards" both for methods of EV isolation from biological fluids and for analyzing their molecular content, including composition of miRNAs. Here we first examined efficacy of various methods for small RNA isolation from EVs contained in ascitic fluid for subsequent miRNA analysis. Comparison of different commercial kits showed advantages of the methods based on phenol-chloroform extraction: Total Exosome RNA & Protein Isolation Kit and miRNeasy Serum/Plasma Kit. Analysis of the small RNA transcriptome showed presence of various classes of molecules in the EVs, among which proportion of miRNAs averaged 6% and reaching 10% with the Total Exosome RNA & Protein Isolation Kit. The PureLink miRNA Isolation Kit demonstrated the lowest efficiency. The miRNeasy Advanced Serum/Plasma Kit showed the highest concentration of the small RNA fraction, miRNA proportion of which, however, did not exceed that obtained with the miRNeasy Serum/Plasma Kit and Total Exosome RNA & Protein Isolation Kit. Moreover, RT-PCR analysis of the individual molecules showed lower levels of each of investigated miRNAs (miR-1246, miR-200b-5p, miR-200c-3p, and miR-23a-3p) when using the miRNeasy Advanced Serum/Plasma Kit. In conclusion, Total Exosome RNA & Protein Isolation Kit and miRNeasy Serum/Plasma Kit can be considered as optimal kits in terms of performance based on combination of the studied characteristics, including small RNA concentration, percentage of microRNA according to bioanalyzer and sequencing results, and levels of individual miRNAs detected by RT-PCR.
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Affiliation(s)
- Gleb O Skryabin
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Svetlana V Vinokurova
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Nadezhda V Elkina
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Daria A Denisova
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Anastasiya A Beliaeva
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 111234, Russia
| | - Kirill I Zhordania
- Institute of Clinical Oncology, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Dmitry V Bagrov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 111234, Russia
| | - Adel D Enikeev
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Sergey A Galetsky
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Andrey V Komelkov
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.
| | - Galina I Krasnoshekova
- Institute of Clinical Oncology, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Elena M Tchevkina
- Institute of Carcinogenesis, Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
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Nagatake Y, Sato M, Mouri Y, Tomita N. Fully automated microRNA quantification technique based on bioluminescent enzyme immunoassay. Anal Biochem 2022; 656:114880. [PMID: 36063916 DOI: 10.1016/j.ab.2022.114880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
Abstract
MicroRNAs (miRNAs) are potential clinical biomarkers for the detection of various diseases. However, their quantification has not been implemented in clinical practice given the inconsistencies in their variable recovery rate and accuracy of the results. Thus, we utilized a technique based on bioluminescent enzyme immunoassay (BLEIA) to perform fully automated miRNA quantification using magnetic particles conjugated with antibodies targeting DNA-RNA hybrids, biotinylated DNA probes specific to miRNAs, and firefly luciferase-labeled streptavidin. This method enabled direct use of diluted serum and automation of all processes within 1 h. The results revealed a wide linear range between 10 fmol/L and 1 nmol/L, high sensitivity with a detection limit of 6.3 fmol/L or below, high specificity with a false positive rate under 2.4%, and high reproducibility in intra- and inter-experimental observations (under CV 10% and r = 0.9965, respectively). Furthermore, a significant correlation was revealed between quantitative reverse transcription-polymerase chain reaction and BLEIA assay for the quantification of synthetic miRNA (r = 0.9993) and endogenous miRNA in healthy serums (r = 0.8203), respectively. Overall, we developed a fully automated miRNA quantification method based on BLEIA, which can be adopted in a clinical setting. However, further studies are needed to assess its clinical performance.
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Affiliation(s)
- Yuka Nagatake
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
| | - Masaki Sato
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan.
| | - Yuta Mouri
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
| | - Norihiro Tomita
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
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D’Alessandra Y, Valerio V, Moschetta D, Massaiu I, Bozzi M, Conte M, Parisi V, Ciccarelli M, Leosco D, Myasoedova VA, Poggio P. Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR. Biomedicines 2022; 10:biomedicines10061354. [PMID: 35740375 PMCID: PMC9220272 DOI: 10.3390/biomedicines10061354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.
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Affiliation(s)
- Yuri D’Alessandra
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Vincenza Valerio
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Donato Moschetta
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20122 Milan, Italy
| | - Ilaria Massaiu
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Michele Bozzi
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Maddalena Conte
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
- Casa di Cura San Michele, 81024 Maddaloni, Italy
| | - Valentina Parisi
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84084 Fisciano, Italy;
| | - Dario Leosco
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
| | - Veronika A. Myasoedova
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Paolo Poggio
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
- Correspondence: ; Tel.: +39-02-5800-2853
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6
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Radojičić O, Dobrijević Z, Robajac D, Gligorijević N, Mandić Marković V, Miković Ž, Nedić O. Gestational Diabetes is Associated with an Increased Expression of miR-27a in Peripheral Blood Mononuclear Cells. Mol Diagn Ther 2022; 26:421-435. [PMID: 35578107 DOI: 10.1007/s40291-022-00591-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Dysregulation of microRNA-based mechanisms is associated with various human pathologies, including gestational diabetes mellitus (GDM), suggesting they may be potential diagnostic and/or prognostic biomarkers of GDM. METHODS The expression of miR-340-5p, miR-27a-3p and miR-222-3p in peripheral blood mononuclear cells (PBMCs) obtained from patients with GDM (n = 42) and healthy controls (n = 34) were evaluated, together with their correlation to the clinical parameters of participants and their newborns. Expression of the selected microRNAs was quantified by quantitative real-time polymerase chain reaction (qPCR), after reverse transcription with microRNA-specific stem-loop primers. RESULTS The expression of miR-27a-3p was significantly higher in patients with GDM than in controls (p = 0.036), whereas no significant difference between groups was found for the other two tested microRNAs. The expression level of miR-27a-3p in GDM patients was found to negatively correlate with the number of erythrocytes, concentration of haemoglobin, haematocrit, and low- and high-density lipoprotein (LDL/HDL) ratio, and positively with the concentration of glycated haemoglobin (HbA1c). In the case of miR-222-3p, a negative correlation between its expression and the concentration of cholesterol, LDL and LDL/HDL ratio was found only in healthy pregnant women. The expression level of miR-340-5p negatively correlated with erythrocyte count, haemoglobin concentration and haematocrit in GDM patients, as well as with the concentration of cholesterol, LDL and LDL/HDL ratio in healthy women. CONCLUSIONS The results obtained illustrate the potential of PBMC-derived microRNA miR-27a-3p to serve as a diagnostic biomarker of GDM. On the other hand, MiR-27a and miR-340 may help in assessing the metabolic status relevant for pregnancy.
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Affiliation(s)
- Ognjen Radojičić
- University Clinic for Gynecology and Obstetrics "Narodni Front", Belgrade, Serbia
| | - Zorana Dobrijević
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia.
| | - Dragana Robajac
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Nikola Gligorijević
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Vesna Mandić Marković
- University Clinic for Gynecology and Obstetrics "Narodni Front", Belgrade, Serbia
- Medical School, University of Belgrade, Belgrade, Serbia
| | - Željko Miković
- University Clinic for Gynecology and Obstetrics "Narodni Front", Belgrade, Serbia
- Medical School, University of Belgrade, Belgrade, Serbia
| | - Olgica Nedić
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
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7
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Schönberg J, Borlak J. Reliable miRNA biomarker quantification in clinical practice - are we there yet? Anal Biochem 2021; 634:114431. [PMID: 34695390 DOI: 10.1016/j.ab.2021.114431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022]
Abstract
Blood-borne miRNAs serve as disease diagnostic biomarkers and await clinical validation. Here, we evaluated Cel-miR-39-3p and miRNA16-5p as calibrator for the quantification of 15 miRNAs linked to hepatic impairment. We added defined copy numbers of Cel-miR-39-3p to plasma of healthy controls (N = 5) and patient samples undergoing liver resection (N = 51). The miRNAs were isolated according to SOPs and quantified by RT-qPCR using the 2-(ΔΔ-CT)-method. Although miRNA16-5p and the spike-in control behaved similar in qPCR assays (R2 = 0.8591) the spike-in control suffered from high inter-patient variability (median 7.6-fold) and low recoveries (median 5.6%, 95% CI 1.5-11.8%). Adding Cel-miR-39-3p to blood samples prior to RNA-isolation improved the recoveries (median 105.7%; 95% CI 29.9-219.9%), yet the inter-patient variability remained high (median 7.2-fold). Alike, we observed significant variability in CT-values for miRNA16-5p (range 14.7-fold) thus rendering this internal, blood-borne reference gene unacceptable as comparator. Specifically, 10 out of 15 diagnostic miRNAs failed the criteria R2 ≥ 0.8 even though we added a defined copy number of Cel-miR-39-3p. This suggests interference of the spike-in control with individual miRNAs in the assay. Our study highlights current limitations in the quantification of blood-borne miRNAs that is of particularly importance when used for disease diagnostic and therapeutic interventions.
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Affiliation(s)
- Juliette Schönberg
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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8
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Roest HP, IJzermans JNM, van der Laan LJW. Evaluation of RNA isolation methods for microRNA quantification in a range of clinical biofluids. BMC Biotechnol 2021; 21:48. [PMID: 34362351 PMCID: PMC8344161 DOI: 10.1186/s12896-021-00706-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/12/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Extracellular microRNAs (miRNAs), released from cells into biofluids, have emerged as promising biomarkers for diagnostic and prognostic purposes. Several RNA isolation methods are available for the analysis of these cell-free miRNAs by RT-qPCR. Not all methods, however, are equally suitable for different biofluids. Here, we extracted total RNA from four very diverse biofluids: serum, urine, bile, and graft preservation fluid (perfusate). Four different protocols were used: a phenol-chloroform extraction and alcohol precipitation in combination with a precipitation carrier (QP) and three different column-based isolation methods, one with phenol-chloroform extraction (RN) and two without (NG and CU). For this range of clinical biofluid samples, we evaluated the potential of these different RNA isolation methods assessing recovery efficiency and the co-purification of RT-qPCR inhibiting compounds. RESULTS Differences were observed between each of the RNA isolation methods in the recovery of cel-miR-39, a synthetic miRNA spiked in during the workup procedure, and for endogenous miRNAs. Co-purification of heparin, a known RT-qPCR inhibitor, was assessed using heparinase I during cDNA synthesis. RT-qPCR detection of synthetic miRNAs cel-miR-39, spiked in during RNA workup, cel-miR-54, spiked in during cDNA synthesis, and endogenous miRNAs was strongly improved in the presence of heparinase I for some, but not all, isolation methods. Other, co-isolated RT-qPCR inhibitors were not identified, except for biliverdin, which co-isolated from some bile samples with one of the methods. In addition, we observed that serum and urine contain compounds that enhance the binding of heparin to certain solid-phase columns. CONCLUSIONS For reliable measurements of miRNA-based biomarkers in biofluids, optimization of RNA isolation procedures is recommended as methods can differ in miRNA detection and in co-purification of RT-qPCR inhibitory compounds. Heparinase I treatment confirmed that heparin appeared to be the major RT-qPCR inhibiting compound, but also biliverdin, co-isolated from bile, could interfere with detection.
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Affiliation(s)
- Henk P Roest
- Department of Surgery, Laboratory of Experimental Transplantation and Intestinal Surgery (LETIS), Erasmus MC - University Medical Center, P.O. Box 2040, Room Na-1005, 3000, CA, Rotterdam, the Netherlands.
| | - Jan N M IJzermans
- Department of Surgery, Laboratory of Experimental Transplantation and Intestinal Surgery (LETIS), Erasmus MC - University Medical Center, P.O. Box 2040, Room Na-1005, 3000, CA, Rotterdam, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Laboratory of Experimental Transplantation and Intestinal Surgery (LETIS), Erasmus MC - University Medical Center, P.O. Box 2040, Room Na-1005, 3000, CA, Rotterdam, the Netherlands
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9
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Ahlberg E, Jenmalm MC, Tingö L. Evaluation of five column-based isolation kits and their ability to extract miRNA from human milk. J Cell Mol Med 2021; 25:7973-7979. [PMID: 34180134 PMCID: PMC8358847 DOI: 10.1111/jcmm.16726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNA can be found in various body fluids, including breast milk. MicroRNA may be transferred from mother to infant via breast milk and potentially regulate the development of the infant's immune system on a post‐transcriptional level. This study aimed to determine the microRNA extraction efficiency of five RNA extraction kits from human skim milk samples. Their efficiency was determined by comparing microRNA concentrations, total RNA yield and purity. Furthermore, hsa‐miR‐148a‐3p expression and the recovery of an exogenous control, cel‐miR‐39‐3p, were quantified using qPCR. Each kit extracted different amounts of microRNA and total RNA, with one kit tending to isolate the highest amount of both RNA species. Based on these results, the extraction kit ReliaPrep™ miRNA Cell and Tissue Miniprep System from Promega was found to be the most appropriate kit for microRNA extraction from human skim milk. Moreover, further research is needed to establish a standardized protocol for microRNA extraction from breast milk.
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Affiliation(s)
- Emelie Ahlberg
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria C Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lina Tingö
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Örebro University Food and Health Programme, School of Medical Sciences, Örebro University, Örebro, Sweden
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Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
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Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
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11
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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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12
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Dole NS, Yee CS, Schurman CA, Dallas SL, Alliston T. Assessment of Osteocytes: Techniques for Studying Morphological and Molecular Changes Associated with Perilacunar/Canalicular Remodeling of the Bone Matrix. Methods Mol Biol 2021; 2230:303-323. [PMID: 33197021 PMCID: PMC9165628 DOI: 10.1007/978-1-0716-1028-2_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent advances have revived interest in the concept of osteocyte perilacunar/canalicular remodeling (PLR) and have motivated efforts to identify the mechanisms regulating this process in bone in the context of normal physiology and pathological conditions. Here, we describe several methods that are evaluating morphological changes associated with PLR function of osteocytes.
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Affiliation(s)
- Neha S Dole
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Cristal S Yee
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Charles A Schurman
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Sarah L Dallas
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, USA.
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, USA.
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13
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Gessner I, Fries JWU, Brune V, Mathur S. Magnetic nanoparticle-based amplification of microRNA detection in body fluids for early disease diagnosis. J Mater Chem B 2020; 9:9-22. [PMID: 33179710 DOI: 10.1039/d0tb02165b] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Circulating biomarkers such as microRNAs (miRNAs), short noncoding RNA strands, represent prognostic and diagnostic indicators for a variety of physiological disorders making their detection and quantification an attractive approach for minimally invasive early disease diagnosis. However, highly sensitive and selective detection methods are required given the generally low abundance of miRNAs in body fluids together with the presence of large amounts of other potentially interfering biomolecules. Although a variety of miRNA isolation and detection methods have been established in clinics, they usually require trained personnel and often constitute labor-, time- and cost-intensive approaches. During the last years, nanoparticle-based biosensors have received increasing attention due to their superior detection efficiency even in very low concentration regimes. This is based on their unique physicochemical properties in combination with their high surface area that allows for the immobilization of multiple recognition sites resulting in fast and effective recognition of analytes. Among various materials, magnetic nanoparticles have been identified as useful tools for the separation, concentration, and detection of miRNAs. Here, we review state-of-the-art technology with regard to magnetic particle-based miRNA detection from body fluids, critically discussing challenges and future perspective of such biosensors while comparing their handling, sensitivity as well as selectivity against the established miRNA isolation and detection methods.
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Affiliation(s)
- Isabel Gessner
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
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14
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Browne DJ, Brady JL, Waardenberg AJ, Loiseau C, Doolan DL. An Analytically and Diagnostically Sensitive RNA Extraction and RT-qPCR Protocol for Peripheral Blood Mononuclear Cells. Front Immunol 2020; 11:402. [PMID: 32265908 PMCID: PMC7098950 DOI: 10.3389/fimmu.2020.00402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Reliable extraction and sensitive detection of RNA from human peripheral blood mononuclear cells (PBMCs) is critical for a broad spectrum of immunology research and clinical diagnostics. RNA analysis platforms are dependent upon high-quality and high-quantity RNA; however, sensitive detection of specific responses associated with high-quality RNA extractions from human samples with limited PBMCs can be challenging. Furthermore, the comparative sensitivity between RNA quantification and best-practice protein quantification is poorly defined. Therefore, we provide herein a critical evaluation of the wide variety of current generation of RNA-based kits for PBMCs, representative of several strategies designed to maximize sensitivity. We assess these kits with a reverse transcription quantitative PCR (RT-qPCR) assay optimized for both analytically and diagnostically sensitive cell-based RNA-based applications. Specifically, three RNA extraction kits, one post-extraction RNA purification/concentration kit, four SYBR master-mix kits, and four reverse transcription kits were tested. RNA extraction and RT-qPCR reaction efficiency were evaluated with commonly used reference and cytokine genes. Significant variation in RNA expression of reference genes was apparent, and absolute quantification based on cell number was established as an effective RT-qPCR normalization strategy. We defined an optimized RNA extraction and RT-qPCR protocol with an analytical sensitivity capable of single cell RNA detection. The diagnostic sensitivity of this assay was sufficient to show a CD8+ T cell peptide epitope hierarchy with as few as 1 × 104 cells. Finally, we compared our optimized RNA extraction and RT-qPCR protocol with current best-practice immune assays and demonstrated that our assay is a sensitive alternative to protein-based assays for peptide-specific responses, especially with limited PBMCs number. This protocol with high analytical and diagnostic sensitivity has broad applicability for both primary research and clinical practice.
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Affiliation(s)
- Daniel J Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Jamie L Brady
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Ashley J Waardenberg
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
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15
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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16
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Rodríguez A, Duyvejonck H, Van Belleghem JD, Gryp T, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS One 2020; 15:e0229423. [PMID: 32084228 PMCID: PMC7034890 DOI: 10.1371/journal.pone.0229423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
RNA quality and quantity are important factors for ensuring the accuracy of gene expression analysis and other RNA-based downstream applications. Thus far, only a limited number of methodological studies have compared sample storage and RNA extraction procedures for human cells. We compared three commercially available RNA extraction kits, i.e., (NucliSENS) easyMAG, RNeasy (Mini Kit) and RiboPure (RNA Purification Kit–blood). In addition, additional conditions, such as storage medium and storage temperature of human peripheral blood mononuclear cells were evaluated, i.e., 4 °C for RNAlater or -80 °C for QIAzol and for the respective cognate lysis buffers; easyMAG, RNeasy or RiboPure. RNA was extracted from aliquots that had been stored for one day (Run 1) or 83 days (Run 2). After DNase treatment, quantity and quality of RNA were assessed by means of a NanoDrop spectrophotometer, 2100 Bioanalyzer and RT-qPCR for the ACTB reference gene. We observed that high-quality RNA can be obtained using RNeasy and RiboPure, regardless of the storage medium, whereas samples stored in RNAlater resulted in the least amount of RNA extracted. In addition, RiboPure combined with storage of samples in its cognate lysis buffer yielded twice as much RNA as all other procedures. These results were supported by RT-qPCR and by the reproducibility observed for two independent extraction runs.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Jonas D. Van Belleghem
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tessa Gryp
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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17
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Ramaswamy P, Yadav R, Pal PK, Christopher R. Clinical Application of Circulating MicroRNAs in Parkinson's Disease: The Challenges and Opportunities as Diagnostic Biomarker. Ann Indian Acad Neurol 2020; 23:84-97. [PMID: 32055127 PMCID: PMC7001448 DOI: 10.4103/aian.aian_440_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Discovery of evolutionarily conserved, nonprotein-coding, endogenous microRNAs has induced a paradigm shift in the overall understanding of gene regulation. Now, microRNAs are considered and classified as master regulators of gene expression as they regulate a wide range of processes – gene regulation, splicing, translation and posttranscriptional modifications. Besides, dysregulated microRNAs have been related to many diseases, including Parkinson's and related disorders. Several studies proposed that differentially expressed microRNAs as a potential biomarker. So far, there is no accepted clinical diagnostic test for Parkinson's disease based on biochemical analysis of biological fluids. However, circulating microRNAs possess many vital features typical of reliable biomarkers and discriminates Parkinson's patients from healthy control with much higher sensitivity and specificity. Though they show tremendous promise as a putative biomarker, translating these research findings to clinical application is often met with many obstacles. Most of the candidate microRNAs reported as a diagnostic biomarker is not organ-specific, and their overlap is low between studies. Therefore this review aimed to highlight the challenges in the application of microRNA in guiding disease discrimination decisions and its future prospects as a diagnostic biomarker in Parkinson's Disease.
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Affiliation(s)
- Palaniswamy Ramaswamy
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
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18
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Felekkis K, Papaneophytou C. Challenges in Using Circulating Micro-RNAs as Biomarkers for Cardiovascular Diseases. Int J Mol Sci 2020; 21:ijms21020561. [PMID: 31952319 PMCID: PMC7013987 DOI: 10.3390/ijms21020561] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Micro-RNAs (miRNAs) play a pivotal role in the development and physiology of the cardiovascular system while they have been associated with multiple cardiovascular diseases (CVDs). Several cardiac miRNAs are detectable in circulation (circulating miRNAs; c-miRNAs) and are emerging as diagnostic and therapeutic biomarkers for CVDs. c-miRNAs exhibit numerous essential characteristics of biomarkers while they are extremely stable in circulation, their expression is tissue-/disease-specific, and they can be easily detected using sequence-specific amplification methods. These features of c-miRNAs are helpful in the development of non-invasive assays to monitor the progress of CVDs. Despite significant progress in the detection of c-miRNAs in serum and plasma, there are many contradictory publications on the alterations of cardiac c-miRNAs concentration in circulation. The aim of this review is to examine the pre-analytical and analytical factors affecting the quantification of c-miRNAs and provide general guidelines to increase the accuracy of the diagnostic tests in order to improve future research on cardiac c-miRNAs.
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19
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Synovial-Fluid miRNA Signature for Diagnosis of Juvenile Idiopathic Arthritis. Cells 2019; 8:cells8121521. [PMID: 31779271 PMCID: PMC6952798 DOI: 10.3390/cells8121521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) is the most common chronic inflammatory rheumatism in childhood; microRNAs (miRNAs) have been proposed as diagnostic biomarkers. Although joints are the primary targets for JIA, a synovial fluid-based miRNA signature has never been studied. We aim to identify miRNA biomarkers in JIA by comparing synovial fluid and serum samples from children with JIA and K. kingae septic arthritis (SA). With next-generation high-throughput sequencing, we measured the absolute levels of 2083 miRNAs in synovial fluid and serum from an exploratory cohort of children and validated differentially expressed miRNAs in a replication study by using RT-qPCR. We identified a 19-miRNA signature only in synovial fluid samples that was significantly deregulated, with at least 2-fold change in expression, in JIA versus SA (p < 0.01). The combination of miR-6764-5p, miR-155, and miR-146a-5p expression in synovial fluid yielded an area under the receiver operating characteristic curve of 1 (95% CI 0.978 to 1), thereby perfectly differentiating JIA from SA in children. We propose, for the first time, a synovial fluid-specific miRNA signature for JIA and associated signaling pathways that may indicate potential biomarkers to assist in the classification and differential diagnosis of JIA and help in understanding JIA pathogenesis.
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20
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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21
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Khnouf R, Han CM, Munro SA. Isolation of enriched small RNA from cell-lysate using on-chip isotachophoresis. Electrophoresis 2019; 40:3140-3147. [PMID: 31675123 DOI: 10.1002/elps.201900215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 11/08/2022]
Abstract
In spite of the growing interest in the roles and applications of small RNAs (sRNAs), sRNA isolation methods are inconsistent, tedious, and dependent on the starting number of cells. In this work, we employ ITP to isolate sRNAs from the cell-lysate of K562 (chronic myelogenous leukemia) cells in a polydimethylsiloxane (PDMS) mesofluidic device. Our method specifically purifies sRNA of <60 nucleotides from lysate of a wide range of cell number spanning from 100 to 1 000 000 cells. We measured the amount of sRNA using the Agilent Bioanalyzer and further verified the extraction efficiency by reverse transcription quantitative PCR. Our method was shown to be more efficient in sRNA extraction than commercial sRNA isolation kits, especially when using smaller numbers of starting cells. Our assay presents a simple and rapid sRNA extraction method with 20 min assay time and no intermediate transfer steps.
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Affiliation(s)
- Ruba Khnouf
- Department of Mechanical Engineering, Stanford University, Stanford, CA, United States.,Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Crystal M Han
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, United States.,Department of Mechanical Engineering, San Jose State University, San Jose, CA, United States
| | - Sarah A Munro
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, United States.,Minnesota Supercomputing Institute, University of Minnesota, MN, United States
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22
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Chu CP, Nabity MB. Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids. Vet Clin Pathol 2019; 48:310-319. [PMID: 31077418 DOI: 10.1111/vcp.12743] [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] [Received: 09/02/2018] [Revised: 12/17/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Small RNA sequencing (RNA-seq) of biofluids is challenging due to the relative scarcity of microRNAs (miRNAs), limited sample volumes, and the lack of a gold standard isolation method. Additionally, few comparisons exist for the RNA isolation and sequencing methods of biofluids. OBJECTIVES We aimed to compare the performance of six commercial RNA isolation kits and two library preparation methods for small RNA-seq using canine serum and urine. METHODS Serum and urine were collected from seven dogs with protein-losing nephropathy, and the samples were pooled. Total RNA from serum (2 mL) and urine (10 mL) was isolated in triplicate using three methods each for serum (Zymo Direct-zol, mirVana PARIS, miRCURY Biofluids) and urine (Qiagen exoRNeasy, Norgen Urine Exosome, miRCURY Exosome). For each sample type, the two kits yielding the highest RNA concentration were selected, and small RNA-seq was performed using TruSeq and NEXTflex library preparations. Data were analyzed by CPSS 2.0 and DESeq2. RESULTS For serum, Zymo Direct-zol combined with NEXTflex was the only combination that enabled successful library preparation, while for urine, Qiagen exoRNeasy combined with NEXTflex outperformed other combinations for detecting miRNAs. The total number of miRNAs detected in serum and urine was 198 and up to 115, respectively. miRNA expression in serum was distinct from urine. Furthermore, the library preparation method introduced a higher variation of urine results than the RNA isolation method. CONCLUSIONS Different isolation and library preparation methods show significant differences in miRNA results that could affect biomarker discovery. Small RNA-seq provides an unbiased, global assessment to compare these methods in canine biofluids.
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Affiliation(s)
- Candice P Chu
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas
| | - Mary B Nabity
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas
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23
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Ford KL, Anwar M, Heys R, Ahmed EM, Caputo M, Game L, Reeves BC, Punjabi PP, Angelini GD, Petretto E, Emanueli C. Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance. PLoS One 2019; 14:e0213685. [PMID: 30870483 PMCID: PMC6417664 DOI: 10.1371/journal.pone.0213685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/18/2019] [Indexed: 01/08/2023] Open
Abstract
This study aimed to optimise techniques for whole transcriptome and small RNA analyses on clinical tissue samples from patients with cardiovascular disease. Clinical samples often represent a particular challenge to extracting RNA of sufficient quality for robust RNA sequencing analysis, and due to availability, it is rarely possible to optimise techniques on the samples themselves. Therefore, we have used equivalent samples from pigs undergoing cardiopulmonary bypass surgery to test different protocols for optimal RNA extraction, and then validated the protocols in human samples. Here we present an assessment of the quality and quantity of RNA obtained using a variety of commercially-available RNA extraction kits on both left ventricular biopsies and blood plasma. RNA extraction from these samples presents different difficulties; left ventricular biopsies are small and fibrous, while blood plasma has a low RNA content. We have validated our optimised extraction techniques on human clinical samples collected as part of the ARCADIA (Association of non-coding RNAs with Coronary Artery Disease and type 2 Diabetes) cohort study, resulting in successful whole transcriptome and small RNA sequencing of human left ventricular tissue.
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Affiliation(s)
- Kerrie L. Ford
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Maryam Anwar
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Rachael Heys
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Eltayeb Mohamed Ahmed
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Massimo Caputo
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Laurence Game
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Barnaby C. Reeves
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Prakash P. Punjabi
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Gianni D. Angelini
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Costanza Emanueli
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
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24
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Cao H, Zhou X, Zeng Y. Microfluidic Exponential Rolling Circle Amplification for Sensitive microRNA Detection Directly from Biological Samples. SENSORS AND ACTUATORS. B, CHEMICAL 2019; 279:447-457. [PMID: 30533973 PMCID: PMC6284813 DOI: 10.1016/j.snb.2018.09.121] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
There is an urgent need of sensitive bioanalytical platforms for sensitive and precise quantification of low-abundance microRNA targets in complex biological samples, including liquid biopsies of tumors. Many of current miRNA biosensing methods require laborious sample pretreatment procedures, including extraction of total RNA, which largely limits their biomedical and clinical applications. Herein we developed an integrated Microfluidic Exponential Rolling Circle Amplification (MERCA) platform for sensitive and specific detection of microRNAs directly in minimally processed samples. The MERCA system integrates and streamlines solid-phase miRNA isolation, miRNA-adapter ligation, and a dualphase exponential rolling circle amplification (eRCA) assay in one analytical workflow. By marrying the advantages of microfluidics in leveraging bioassay performance with the high sensitivity of eRCA, our method affords a remarkably low limit of detection at <10 zeptomole levels, with the ability to discriminate single-nucleotide difference. Using the MERCA chip, we demonstrated quantitative detection of miRNAs in total RNA, raw cell lysate, and cellderived exosomes. Comparing with the parallel TaqMan RT-qPCR measurements verified the adaptability of the MERCA system for detection of miRNA biomarkers in complex biological materials. In particular, high sensitivity of our method enables direct detection of low-level exosomal miRNAs in as few as 2 × 106 exosomes. Such analytical capability immediately addresses the unmet challenge in sample consumption, a key setback in clinical development of exosome-based liquid biopsies. Therefore, the MERCA would provide a useful platform to facilitate miRNA analysis in broad biological and clinical applications.
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Affiliation(s)
- Hongmei Cao
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Xin Zhou
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
- University of Kansas Cancer Center, Kansas City, KS 66160
- Corresponding authors: , Fax: 785-864-5396
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25
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First field evaluation of the optimized CE marked Abbott protocol for HIV RNA testing on dried blood spot in a routine clinical setting in Vietnam. PLoS One 2018; 13:e0191920. [PMID: 29425216 PMCID: PMC5806875 DOI: 10.1371/journal.pone.0191920] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/12/2018] [Indexed: 11/19/2022] Open
Abstract
Background Viral load (VL) monitoring of HIV-infected patients in decentralized areas is limited due to logistic constraints. Dried Blood Spots (DBS) offer the opportunity to collect samples in remote area which can be easily transferred and tested at a central laboratory. The MOVIDA (Monitoring Of Viral load In Decentralized Area) project evaluated the performance of VL measurements on DBS using the new CE marked optimized Abbott protocol. Methods HIV-1 infected adults from three outpatient clinics in Hanoi (Vietnam) were enrolled into the study between 1 March and 13 April 2017. VL was measured on DBS using the optimized protocol provided by the manufacturer and compared to plasma VL as reference method on the Abbott m2000rt RealTime HIV-1 platform. Sensitivity was defined as the ability for DBS samples to correctly identify VL failure at the threshold of 1000 copies/mL of plasma, while specificity represented the ability to identify patients with a plasma HIV-RNA VL of <1000 copies/mL. Results A total of 203 patients were enrolled in the study, of which 152 (75%) were male. Median age was 38 [inter quartile range: 34–43] years. Of these patients, 37 were untreated, 38 on ART for <6 months and 117 were on ART for ≥6 months. A strong correlation between VL results in plasma and from DBS was observed (ρ = 0.95; p<0.001). Plasma VL was ≥1000 copies/mL in 71 patients. The sensitivity of DBS was 90.1% (95% confidence interval [CI]: 80.7–95.9) and the specificity was 96.2% (95% CI: 91.4–98.8). Conclusions The new optimized Abbott DBS protocol performed well in this study, meeting the WHO performance criteria for the use of DBS for HIV VL monitoring. Scaling up VL monitoring using DBS can be used to reach the last 90 in the UNAIDS targets of 90-90-90 to help end the AIDS epidemics. However, sensitivity remains the main challenge for manufacturers to prevent maintaining patients in virological failure on inefficient ART.
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26
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Neo SH, Chung KY, Quek JM, Too HP. Trehalose significantly enhances the recovery of serum and serum exosomal miRNA from a paper-based matrix. Sci Rep 2017; 7:16686. [PMID: 29192155 PMCID: PMC5709463 DOI: 10.1038/s41598-017-16960-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/19/2017] [Indexed: 12/27/2022] Open
Abstract
The preservation of nucleic acids from clinical samples is critical to facilitate accurate molecular diagnosis. The use of a paper matrix, Flinders Technology Associates (FTA) Elute cards, to archive DNA and viral RNA is well-documented. However, the feasibility of FTA Elute cards for archiving serum and serum exosomal microRNAs (miRNAs) remains unclear. Here, we performed a comprehensive evaluation of FTA Elute cards for miRNA storage and recovery in different pre-analytical conditions. The recovery of serum miRNA dry-spotted on FTA Elute cards by direct elution with water at high temperature was poor. However, serum miRNAs dry-spotted on the cards were isolated with about 40% yield when using QIAzol lysis reagent and recovery was improved remarkably (>80%) upon extraction from cards pre-treated with trehalose. miRNAs stored on the cards remained stable at room temperature and can be kept for prolonged periods. Furthermore, miRNAs could be similarly recovered from serum exosomes dry-spotted on the cards. Importantly, when using sera from gastric cancer (GC) patients, the miRNAs were efficiently recovered from trehalose pre-treated cards without affecting their representation. Collectively, we have demonstrated the potential of FTA Elute cards to archive serum and serum exosomal miRNAs, making it useful for biomarker discovery and diagnostics.
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Affiliation(s)
- Shu Hui Neo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
| | - Ka Yan Chung
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Jia Min Quek
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Heng-Phon Too
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Block MD7, 8 Medical Drive, Singapore, 117597, Singapore.
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27
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Paiva S, Agbulut O. MiRroring the Multiple Potentials of MicroRNAs in Acute Myocardial Infarction. Front Cardiovasc Med 2017; 4:73. [PMID: 29209617 PMCID: PMC5701911 DOI: 10.3389/fcvm.2017.00073] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/31/2017] [Indexed: 12/28/2022] Open
Abstract
At present, cardiovascular diseases are depicted to be the leading cause of death worldwide according to the World Health Organization. In the future, projections predict that ischemic heart disease will persist in the top main causes of illness. Within this alarming context, some tiny master regulators of gene expression programs, namely, microRNAs (miRNAs) carry three promising potentials. In fact, miRNAs can prove to be useful not only in terms of biomarkers allowing heart injury detection but also in terms of therapeutics to overcome limitations of past strategies and treat the lesions. In a more creative approach, they can even be used in the area of human engineered cardiac tissues as maturation tools for cardiomyocytes (CMs) derived from pluripotent stem cell. Very promising not only for patient-specific cell-based therapies but also to develop biomimetic microsystems for disease modeling and drug screening, these cells greatly contribute to personalized medicine. To get into the heart of the matter, the focus of this review lies primarily on miRNAs as acute myocardial infarction (AMI) biomarkers. Only large cohort studies comprising over 100 individuals to reach a potent statistical value were considered. Certain miRNAs appeared to possibly complement protein-based biomarkers and classical risk factors. Some were even described to bear potential in the discrimination of similar symptomatic pathologies. However, differences between pre-analytical and analytical approaches substantially influenced miRNA data. Further supported by meta-analysis studies, this problem had to be addressed. A detailed critical analysis of each step to define miRNAs biomarker potential is provided to inspire a future improved universal strategy. Interestingly, a recurrent set of cardiomyocyte-enriched miRNAs was found, namely, miR-1; miR-133; miR-208a/b; and miR-499a. Each member of this myomiRs group displayed promising roles either individually or in combination as AMI diagnostic or prognostic biomarkers. Furthermore, a precise combo was shown to be powerful enough to transdifferentiate human fibroblasts into CMs opening doors in the therapeutics. Following these discoveries, they also emerged as optional tools to transfect in order to mature CMs derived from pluripotent stem cells. Ultimately, the multiple potentials carried by the myomiRs miR-1; miR-133; miR-208a/b; and miR-499a still remain to be fully unveiled.
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Affiliation(s)
- Solenne Paiva
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR CNRS 8256, Biological Adaptation and Aging, Paris, France
| | - Onnik Agbulut
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR CNRS 8256, Biological Adaptation and Aging, Paris, France
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28
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Detassis S, Grasso M, Del Vescovo V, Denti MA. microRNAs Make the Call in Cancer Personalized Medicine. Front Cell Dev Biol 2017; 5:86. [PMID: 29018797 PMCID: PMC5614923 DOI: 10.3389/fcell.2017.00086] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022] Open
Abstract
Since their discovery and the advent of RNA interference, microRNAs have drawn enormous attention because of their ubiquitous involvement in cellular pathways from life to death, from metabolism to communication. It is also widely accepted that they possess an undeniable role in cancer both as tumor suppressors and tumor promoters modulating cell proliferation and migration, epithelial-mesenchymal transition and tumor cell invasion and metastasis. Moreover, microRNAs can even affect the tumor surrounding environment influencing angiogenesis and immune system activation and recruitment. The tight association of microRNAs with several cancer-related processes makes them undoubtedly connected to the effect of specific cancer drugs inducing either resistance or sensitization. In this context, personalized medicine through microRNAs arose recently with the discovery of single nucleotide polymorphisms in the target binding sites, in the sequence of the microRNA itself or in microRNA biogenesis related genes, increasing risk, susceptibility and progression of multiple types of cancer in different sets of the population. The depicted scenario implies that the overall variation displayed by these small non-coding RNAs have an impact on patient-specific pharmacokinetics and pharmacodynamics of cancer drugs, pushing on a rising need of personalized treatment. Indeed, microRNAs from either tissues or liquid biopsies are also extensively studied as valuable biomarkers for disease early recognition, progression and prognosis. Despite microRNAs being intensively studied in recent years, a comprehensive review describing these topics all in one is missing. Here we report an up-to-date and critical summary of microRNAs as tools for better understanding personalized cancer biogenesis, evolution, diagnosis and treatment.
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Affiliation(s)
| | | | | | - Michela A. Denti
- Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of TrentoTrento, Italy
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29
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Morais Junior GS, Souza VC, Machado-Silva W, Henriques AD, Melo Alves A, Barbosa Morais D, Nóbrega OT, Brito CJ, dos Santos Silva RJ. Acute strength training promotes responses in whole blood circulating levels of miR-146a among older adults with type 2 diabetes mellitus. Clin Interv Aging 2017; 12:1443-1450. [PMID: 28979106 PMCID: PMC5608226 DOI: 10.2147/cia.s141716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) consists of a set of metabolic and endocrine disorders which evolve into deficiency in insulin action and hyperglycemia. Physical exercise is considered the main intervention to prevent and control T2DM. Literature has suggested that circulating microRNAs (miRs) help to understand responses to physical activity among diabetic patients. Thus, the aim of this study was to analyze the acute effect of two interventions (strength and cardiovascular) on the total, whole blood circulating concentrations of miR-126, miR-146a and miR-155 in older adults with and without T2DM. A total of 23 male and female older adults (68.2±5.3 years) participated in the trial, 13 of whom presented with controlled T2DM and 10 were nondiabetics. They underwent both interventions separately, performed with intensity from 60% to 70% of reserve heart rate. Glucose and miRs levels were quantified and compared across groups with baseline titers as covariables. Diabetic patients showed more reduction in serum blood glucose than nondiabetics, with a great magnitude of reduction after the strength training intervention, which was paralleled by a positive change of the whole blood circulating levels of miR-146a, but not of the other miRs. Our report supports evidence that miR-146a levels in peripheral blood leukocytes are negatively associated with a state of insulin resistance, which is suggested as a novel marker to trace response to antidiabetic interventions.
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Affiliation(s)
| | | | | | | | | | | | | | - Ciro José Brito
- Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
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30
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Ali HEA, Abdel Hameed R, Effat H, Ahmed EK, Atef AA, Sharawi SK, Ali M, Abd Elmageed ZY, Abdel Wahab AH. Circulating microRNAs panel as a diagnostic tool for discrimination of HCV-associated hepatocellular carcinoma. Clin Res Hepatol Gastroenterol 2017; 41:e51-e62. [PMID: 28750770 DOI: 10.1016/j.clinre.2017.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/09/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023]
Abstract
Early diagnosis of hepatocellular carcinoma (HCC) can significantly improve the overall survival of HCC patients. However, current diagnostic markers are compromised and limited by their low sensitivity and specificity. In this work, circulating microRNAs (miRs) were utilized as a diagnostic tool to test their efficiency to segregate HCC and hepatitis C virus (HCV)-infected patients from healthy subjects. Nine HCC-related miRs (miR-21, miR-30c, miR-93, miR-122, miR-125b, miR-126, miR-130a, miR-193b and miR-222) were analyzed by Real-Time PCR in 86 serum samples; 34 HCC and 52 HCV patients in addition to 25 healthy subjects. The sensitivity and specificity of these miRs were assessed. Our results demonstrated that the median serum level of seven miRs was significantly reduced (P ranges from <0.01 to<0.001) in HCC patients whereas nine miRs were reduced (P<0.001) in HCV compared to healthy controls. Receiver operating characteristic (ROC) curve analyses had shown high diagnostic accuracy (AUC=1.0) when seven and nine combined miRs were considered in HCC and HCV groups, respectively compared to their counterparts. However, a combination of differentially expressed miRs did not improve the discriminatory power (AUC=0.742) when HCC compared to non-HCC groups. miR-122 showed the highest sensitivity and specificity to stratify HCC and HCV versus normal individuals and HCC versus HCV patients. We conclude that differentially expressed miRs in the serum of HCV and HCC patients can be utilized as surrogate and non-invasive biomarker for segregation of HCV and HCC patients from healthy subjects.
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Affiliation(s)
- Hamdy E Abouzeid Ali
- Department of Radiobiological Applications, Nuclear Research Centre, Atomic Energy Authority, Cairo, Egypt; Department of Pharmaceutical Sciences, Texas A&M Health Science Center, 78363, Kingsville, TX USA
| | - Rehab Abdel Hameed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Heba Effat
- Department of Cancer Biology, National Cancer Institute, Cairo University, 1, Kasr El Eini Street Fom El Khalig, 11796 Cairo, Egypt
| | - Emad K Ahmed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Azza A Atef
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sabry K Sharawi
- Department of Cancer Biology, National Cancer Institute, Cairo University, 1, Kasr El Eini Street Fom El Khalig, 11796 Cairo, Egypt
| | - Mohamed Ali
- Department of Chemistry, Faculty of Science, Cairo University, Cairo, Egypt
| | - Zakaria Y Abd Elmageed
- Department of Pharmaceutical Sciences, Texas A&M Health Science Center, 78363, Kingsville, TX USA.
| | - Abdel Hady Abdel Wahab
- Department of Cancer Biology, National Cancer Institute, Cairo University, 1, Kasr El Eini Street Fom El Khalig, 11796 Cairo, Egypt.
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31
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Garcia-Elias A, Alloza L, Puigdecanet E, Nonell L, Tajes M, Curado J, Enjuanes C, Díaz O, Bruguera J, Martí-Almor J, Comín-Colet J, Benito B. Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs. Sci Rep 2017; 7:7725. [PMID: 28798363 PMCID: PMC5552704 DOI: 10.1038/s41598-017-08134-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 07/05/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples.
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Affiliation(s)
- Anna Garcia-Elias
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.
| | - Leonor Alloza
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Marta Tajes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Joao Curado
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cristina Enjuanes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Oscar Díaz
- Cardiovascular Risk and Nutrition Group, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Jordi Bruguera
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Julio Martí-Almor
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Josep Comín-Colet
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Begoña Benito
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
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32
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Sebastiani G, Nigi L, Grieco GE, Mancarella F, Ventriglia G, Dotta F. Circulating microRNAs and diabetes mellitus: a novel tool for disease prediction, diagnosis, and staging? J Endocrinol Invest 2017; 40:591-610. [PMID: 28213644 DOI: 10.1007/s40618-017-0611-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/03/2017] [Indexed: 12/19/2022]
Abstract
Diabetes is a complex, multifactorial group of metabolic diseases characterized by chronic hyperglycaemia due to pancreatic beta-cell dysfunction and/or loss. It is characterized by an asymptomatic and highly variable prodromic phase, which renders diabetes mellitus difficult to be predicted with sufficient accuracy. Despite several efforts in the identification and standardization of newly trustable. Biomarkers able to predict and follow-up diabetes and to specifically subtype its different forms, few of them have proven of clinical utility. Recently, a new class of endogenous non-coding small RNAs, namely microRNAs, have been indicated as putative biomarkers, being released by cells and tissues and found in a cell-free circulating form in many biological fluids, including serum and/or plasma. MicroRNAs have been initially identified as promising biomarkers in cancer, and nowadays their application has been extended to other diseases, including diabetes. Although an increasing number of studies focused on the evaluation of circulating microRNAs in diabetes, few reproducibly identified microRNAs as biomarkers for disease prediction or follow-up. Technological problems as well as the need to obtain highly standardized operating procedures and methods are still an issue in such research field. In this review, we comprehensively resume the main and most recent findings on circulating microRNAs, and their possible use as biomarkers to predict and follow-up diabetes and its complications, as well as the methodological challenges to standardize accurate operating procedures for their analysis.
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Affiliation(s)
- G Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - L Nigi
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - G E Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - F Mancarella
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - G Ventriglia
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - F Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy.
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy.
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33
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Castiglia M, Perez A, Serrano MJ, Ciaccio M, Bazan V, Russo A. Technical Aspects for the Evaluation of Circulating Nucleic Acids (CNAs): Circulating Tumor DNA (ctDNA) and Circulating MicroRNAs. CURRENT CLINICAL PATHOLOGY 2017. [DOI: 10.1007/978-3-319-55661-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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34
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Meerson A, Ploug T. Assessment of six commercial plasma small RNA isolation kits using qRT-PCR and electrophoretic separation: higher recovery of microRNA following ultracentrifugation. Biol Methods Protoc 2016; 1:bpw003. [PMID: 32161781 PMCID: PMC6994037 DOI: 10.1093/biomethods/bpw003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/18/2016] [Accepted: 10/03/2016] [Indexed: 02/03/2023] Open
Abstract
Growing interest in blood-borne microRNAs (miRNAs) as biomarkers has led to the introduction of a number of commercial kits for isolating small RNAs from plasma/serum. We sought to compare the efficacy of six such kits in isolating miRNAs from either whole plasma or a plasma-derived ultracentrifugation (UC) fraction from 2 healthy volunteers with some of the results being validated in 10 additional subjects. To assess the overall yield and concentration of isolated small RNAs, we measured the levels of one spiked-in and four endogenous miRNAs by quantitative reverse transcription and polymerase chain reaction (qRT-PCR). We also tested the performance of the Agilent Bioanalyzer small RNA assay with these RNA samples. Additionally, we tested the effects of hemolysis on measured miRNA levels in whole plasma and in the UC fraction. Both the efficiency of RNA isolation and the relative levels of specific miRNAs in different samples varied considerably between the tested extraction methods. Of all kits tested, the QIAGEN miRNeasy kits (Mini and Serum/Plasma kits) and the Macherey-Nagel NucleoSpin kit produced the highest RNA yields. The QIAGEN Exo kit produced lesser yields than what could be extracted from the UC fraction using the QIAGEN miRNeasy kits and the Macherey-Nagel NucleoSpin kit. Bioanalyzer results showed an average correlation of R2 = 0.8 with endogenous miRNA qRT-PCR results, for sample concentrations >40 pg/µl. The levels of the endogenous miRNAs measured in the two volunteer samples were compared with those in a larger group of subjects (n = 10) and found to be typical. Our comparison favors the use of the QIAGEN Serum/Plasma kit and the Macherey-Nagel NucleoSpin kit for plasma miRNA applications. Furthermore, extraction of miRNAs from the UC fraction results in higher yield than extraction from whole plasma.
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Affiliation(s)
- Ari Meerson
- MIGAL Galilee Research Institute, PO Box 831, Kiryat Shmona, 11016 Israel.,Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Thorkil Ploug
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
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35
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Bąkowska-Żywicka K, Mleczko AM, Kasprzyk M, Machtel P, Żywicki M, Twardowski T. The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae. FEBS Open Bio 2016; 6:1186-1200. [PMID: 28203519 PMCID: PMC5302060 DOI: 10.1002/2211-5463.12127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/19/2016] [Accepted: 09/13/2016] [Indexed: 11/10/2022] Open
Abstract
Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA-derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress-dependent changes in the amounts of tRNA fragments pool. Instead, we show the differential processing of almost all individual tRNAs. We also provide evidence that 3'-part-derived tRNA fragments are as abundant as the 5'- one in Saccharomyces cerevisiae. The resulting set of S. cerevisiae tRNA fragments provides a robust basis for further experimental studies on biological functions of tRFs.
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Affiliation(s)
| | - Anna M Mleczko
- Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
| | - Marta Kasprzyk
- Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
| | - Piotr Machtel
- Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
| | - Marek Żywicki
- Department of Computational Biology Institute of Molecular Biology and Biotechnology Faculty of Biology A. Mickiewicz University in Poznan Poland
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
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36
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Alsaweed M, Hepworth AR, Lefèvre C, Hartmann PE, Geddes DT, Hassiotou F. Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation. J Cell Biochem 2016; 116:2397-407. [PMID: 25925799 PMCID: PMC5042114 DOI: 10.1002/jcb.25207] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/21/2015] [Indexed: 01/08/2023]
Abstract
MicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column‐based phenol‐free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. J. Cell. Biochem. 116: 2397–2407, 2015. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Mohammed Alsaweed
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia.,College of Applied Medical Sciences, Majmaah University, Almajmaah, Riyadh, Saudi Arabia
| | - Anna R Hepworth
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Christophe Lefèvre
- Centre for Biotechnology and Interdisciplinary Sciences, Deakin University, Victoria, Australia
| | - Peter E Hartmann
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Donna T Geddes
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Foteini Hassiotou
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
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37
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Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
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Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
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38
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Towards a new standardized method for circulating miRNAs profiling in clinical studies: Interest of the exogenous normalization to improve miRNA signature accuracy. Mol Oncol 2016; 10:981-92. [PMID: 27083764 PMCID: PMC5423189 DOI: 10.1016/j.molonc.2016.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 01/15/2023] Open
Abstract
Circulating miRNAs are promising biomarkers in oncology but have not yet been implemented in the clinic given the lack of concordance across studies. In order to increase the cross‐studies reliability, we attempted to reduce and to control the circulating miRNA expression variability between patients. First, to maximize profiling signals and to reduce miRNA expression variability, three isolation kits were compared and the NucleoSpin® kit provided higher miRNA concentrations than the other widely used kits. Second, to control inter‐sample variability during the profiling step, the exogenous miRNAs normalization method commonly used for RT‐qPCR validation step was adapted to microarray experiments. Importantly, exogenous miRNAs presented two‐fold lower inter‐sample variability than the widely used endogenous miR‐16‐5p reflecting that the latter is subject to both biological and technical variability. Although Caenorhabditis elegans miRNAs isolation yields were heterogeneous, they correlated to each other and to their geometrical mean across samples. The normalization based on the geometrical mean of three exogenous miRNAs increased the correlation up‐to 0.97 between the microarrays and individual RT‐qPCR steps of circulating miRNAs expression. Overall, this new strategy open new avenue to identify reliable circulating miRNA signatures for translation into clinical practice. NucleoSpin kit offers the highest endogenous miRNA concentrations from serum/plasma. A common normalization based on exogenous miRNAs for discovery and validation steps. New strategy to increase both the signature accuracy and the overlap across studies.
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39
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Afonso MB, Rodrigues PM, Simão AL, Castro RE. Circulating microRNAs as Potential Biomarkers in Non-Alcoholic Fatty Liver Disease and Hepatocellular Carcinoma. J Clin Med 2016; 5:jcm5030030. [PMID: 26950158 PMCID: PMC4810101 DOI: 10.3390/jcm5030030] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/26/2016] [Accepted: 02/23/2016] [Indexed: 12/12/2022] Open
Abstract
Obesity and metabolic syndrome are growing epidemics worldwide and greatly responsible for many liver diseases, including nonalcoholic fatty liver disease (NAFLD). NAFLD often progresses to cirrhosis, end-stage liver failure and hepatocellular carcinoma (HCC), the most common primary liver cancer and one of the leading causes for cancer-related deaths globally. Currently available tools for the diagnosis of NAFLD staging and progression towards HCC are largely invasive and of limited accuracy. In light of the need for more specific and sensitive noninvasive molecular markers, several studies have assessed the potential of circulating microRNAs (miRNAs) as biomarkers of liver injury and hepatocarcinogenesis. Indeed, extracellular miRNAs are very stable in the blood, can be easily quantitated and are differentially expressed in response to different pathophysiological conditions. Although standardization procedures and larger, independent studies are still necessary, miRNAs constitute promising, clinically-useful biomarkers for the NAFLD-HCC spectrum.
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Affiliation(s)
- Marta B Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal.
| | - Pedro M Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal.
| | - André L Simão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal.
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal.
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal.
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40
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El-Khoury V, Pierson S, Kaoma T, Bernardin F, Berchem G. Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material. Sci Rep 2016; 6:19529. [PMID: 26787294 PMCID: PMC4726450 DOI: 10.1038/srep19529] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) have emerged as promising cancer biomarkers. However, exploiting their informative potential requires careful optimization of their detection. Here, we compared the efficiency of commonly used RNA extraction kits in miRNA recovery from cells, plasma and urine/plasma-derived exosomes, using single-gene RT-qPCR and miRNA profiling. We used increasing amounts of starting material to investigate the impact of the input material size on miRNA extraction. We showed that miRNA recovery was largely influenced by the isolation method and by the amount of input material. In particular, the miRCURY™ kit provided highly pure RNA. However, its columns poorly recovered miRNAs from limiting amounts of cells and plasma, and rapidly saturated by large RNA species and plasma components, thus impeding miRNA recovery from high input amounts. Overall, the miRNeasy® kit permitted a better miRNA detection despite a less pure extracted RNA. Nevertheless, some miRNAs were preferentially or exclusively isolated by either of the methods. Trizol® LS resulted in very low purity RNA which affected RT-qPCR efficiency. In general, miRCURY™ biofluids kit efficiently extracted miRNAs from plasma. A careful selection of the RNA isolation method and the consideration of the type and size of input material are highly recommended to avoid biased results.
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Affiliation(s)
- Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Sandrine Pierson
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - François Bernardin
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, 4 rue Barblé, L-1210 Luxembourg, Luxembourg
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41
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Nagy ZB, Wichmann B, Kalmár A, Barták BK, Tulassay Z, Molnár B. miRNA Isolation from FFPET Specimen: A Technical Comparison of miRNA and Total RNA Isolation Methods. Pathol Oncol Res 2015; 22:505-13. [PMID: 26678076 DOI: 10.1007/s12253-015-0027-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 12/04/2015] [Indexed: 12/11/2022]
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42
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Saplacan RMM, Mircea PA, Balacescu L, Balacescu O. MicroRNAs as non-invasive screening biomarkers of colorectal cancer. ACTA ACUST UNITED AC 2015; 88:453-6. [PMID: 26733742 PMCID: PMC4689235 DOI: 10.15386/cjmed-568] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022]
Abstract
Colorectal cancer is a major cause of cancer-associated deaths in the world. Early detection would be greatly enhanced if accurate and cost-effective diagnostic biomarkers for this disease were accessible. The development of such a blood test will evidently lower the screening costs in regards of colorectal cancer detection. Lately, it has been suggested that microRNA diagnostic biomarkers are feasible new screening methods for colorectal cancer. This review summarizes the diagnostic potential of circulating microRNA biomarkers in relation with colorectal cancer, as well as current methods to detect them.
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Affiliation(s)
- Roberta Maria Manzat Saplacan
- Department of Internal Medicine, 1st Medical Clinic, Cluj-Napoca, Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, Romania
| | - Petru Adrian Mircea
- Department of Internal Medicine, 1st Medical Clinic, Cluj-Napoca, Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, Romania
| | - Loredana Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, Prof. Dr. Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, Prof. Dr. Ion Chiricuta Oncology Institute, Cluj-Napoca, Romania
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43
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Schwarzenbach H, da Silva AM, Calin G, Pantel K. Data Normalization Strategies for MicroRNA Quantification. Clin Chem 2015; 61:1333-42. [PMID: 26408530 DOI: 10.1373/clinchem.2015.239459] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Different technologies, such as quantitative real-time PCR or microarrays, have been developed to measure microRNA (miRNA) expression levels. Quantification of miRNA transcripts implicates data normalization using endogenous and exogenous reference genes for data correction. However, there is no consensus about an optimal normalization strategy. The choice of a reference gene remains problematic and can have a serious impact on the actual available transcript levels and, consequently, on the biological interpretation of data. CONTENT In this review article we discuss the reliability of the use of small RNAs, commonly reported in the literature as miRNA expression normalizers, and compare different strategies used for data normalization. SUMMARY A workflow strategy is proposed for normalization of miRNA expression data in an attempt to provide a basis for the establishment of a global standard procedure that will allow comparison across studies.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumour Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreia Machado da Silva
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX; Instituto de Investigação em Saúde, Universidade do Porto, Porto, Portugal; INEB, Institute of Biomedical Engineering, Universidade do Porto, Porto, Portugal
| | - George Calin
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Klaus Pantel
- Department of Tumour Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
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44
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Makarova JA, Shkurnikov MU, Turchinovich AA, Tonevitsky AG, Grigoriev AI. Circulating microRNAs. BIOCHEMISTRY (MOSCOW) 2015; 80:1117-26. [DOI: 10.1134/s0006297915090035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Laurent LC, Abdel-Mageed AB, Adelson PD, Arango J, Balaj L, Breakefield X, Carlson E, Carter BS, Majem B, Chen CC, Cocucci E, Danielson K, Courtright A, Das S, Abd Elmageed ZY, Enderle D, Ezrin A, Ferrer M, Freedman J, Galas D, Gandhi R, Huentelman MJ, Van Keuren-Jensen K, Kalani Y, Kim Y, Krichevsky AM, Lai C, Lal-Nag M, Laurent CD, Leonardo T, Li F, Malenica I, Mondal D, Nejad P, Patel T, Raffai RL, Rubio R, Skog J, Spetzler R, Sun J, Tanriverdi K, Vickers K, Wang L, Wang Y, Wei Z, Weiner HL, Wong D, Yan IK, Yeri A, Gould S. Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles 2015; 4:26533. [PMID: 26320937 PMCID: PMC4553263 DOI: 10.3402/jev.v4.26533] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 04/17/2015] [Accepted: 05/03/2015] [Indexed: 01/14/2023] Open
Abstract
Extracellular RNAs (exRNAs) have been identified in all tested biofluids and have been associated with a variety of extracellular vesicles, ribonucleoprotein complexes and lipoprotein complexes. Much of the interest in exRNAs lies in the fact that they may serve as signalling molecules between cells, their potential to serve as biomarkers for prediction and diagnosis of disease and the possibility that exRNAs or the extracellular particles that carry them might be used for therapeutic purposes. Among the most significant bottlenecks to progress in this field is the lack of robust and standardized methods for collection and processing of biofluids, separation of different types of exRNA-containing particles and isolation and analysis of exRNAs. The Sample and Assay Standards Working Group of the Extracellular RNA Communication Consortium is a group of laboratories funded by the U.S. National Institutes of Health to develop such methods. In our first joint endeavour, we held a series of conference calls and in-person meetings to survey the methods used among our members, placed them in the context of the current literature and used our findings to identify areas in which the identification of robust methodologies would promote rapid advancements in the exRNA field.
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Affiliation(s)
- Louise C Laurent
- Division of Maternal Fetal Medicine, Department of Reproductive Medicine, University of California San Diego, San Diego, CA, USA.,Sanford Consortium for Regenerative Medicine, San Diego, CA, USA;
| | - Asim B Abdel-Mageed
- Department of Urology, Tulane University, School of Medicine, New Orleans, LA, USA
| | | | | | - Leonora Balaj
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Xandra Breakefield
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Carlson
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Bob S Carter
- Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California San Diego, San Diego, CA, USA
| | - Blanca Majem
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Clark C Chen
- Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California San Diego, San Diego, CA, USA
| | - Emanuele Cocucci
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kirsty Danielson
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Amanda Courtright
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Saumya Das
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD, USA
| | - Jane Freedman
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Roopali Gandhi
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yong Kim
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles Lai
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Madhu Lal-Nag
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD, USA
| | - Clara D Laurent
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trevor Leonardo
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Ivana Malenica
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Debasis Mondal
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parham Nejad
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic Florida, Jacksonville, FL, USA.,Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Robert L Raffai
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Veteran's Affairs, San Francisco, CA, USA
| | - Renee Rubio
- Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | | | | | - Jie Sun
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Kahraman Tanriverdi
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kasey Vickers
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yaoyu Wang
- Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Howard L Weiner
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Wong
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Irene K Yan
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Ashish Yeri
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Stephen Gould
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
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46
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Marabita F, de Candia P, Torri A, Tegnér J, Abrignani S, Rossi RL. Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR. Brief Bioinform 2015; 17:204-12. [PMID: 26238539 PMCID: PMC4793896 DOI: 10.1093/bib/bbv056] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/18/2022] Open
Abstract
The high-throughput analysis of microRNAs (miRNAs) circulating within the blood of healthy and diseased individuals is an active area of biomarker research. Whereas quantitative real-time reverse transcription polymerase chain reaction (qPCR)-based methods are widely used, it is yet unresolved how the data should be normalized. Here, we show that a combination of different algorithms results in the identification of candidate reference miRNAs that can be exploited as normalizers, in both discovery and validation phases. Using the methodology considered here, we identify normalizers that are able to reduce nonbiological variation in the data and we present several case studies, to illustrate the relevance in the context of physiological or pathological scenarios. In conclusion, the discovery of stable reference miRNAs from high-throughput studies allows appropriate normalization of focused qPCR assays.
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47
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Gragnani L, Piluso A, Fognani E, Zignego AL. MicroRNA expression in hepatitis C virus-related malignancies: A brief review. World J Gastroenterol 2015; 21:8562-8568. [PMID: 26229398 PMCID: PMC4515837 DOI: 10.3748/wjg.v21.i28.8562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/23/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023] Open
Abstract
Not only is chronic hepatitis C virus (HCV) infection a major public health problem, but also it can cause hepatocellular carcinoma and, more rarely, non-Hodgkin’s lymphoma. These characteristics mean that HCV is the only virus infecting humans that is able to cause two different cancers. The fine pathogenetic and molecular mechanisms by which HCV induces these two malignancies are not completely clear. In the last decade, it has been shown that microRNAs (miRNAs), a class of 21-23-nucleotide molecules modulating post-transcriptional gene expression, make an important contribution to the pathogenesis of several cancers and are also considered highly promising biomarkers. Here, we briefly describe the current knowledge about microRNAs’ involvement in HCV-related molecular oncogenesis. We decided to focus our attention on studies fully conducted on ex vivo samples with this specific etiology, and on cultured cell lines partially or completely expressing the HCV genome. Some of the results reported in this review are controversial, possibly because of methodological issues, differences in sampling size and features, and ethnicity of patients. What is certain is that miRNAs play a remarkable role in regulating gene expression during oncogenetic processes and in viral infection. A clear understanding of their effects is fundamental to elucidating the mechanisms underlying virus-induced malignancies.
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48
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Schulte C, Zeller T. microRNA-based diagnostics and therapy in cardiovascular disease-Summing up the facts. Cardiovasc Diagn Ther 2015; 5:17-36. [PMID: 25774345 DOI: 10.3978/j.issn.2223-3652.2014.12.03] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/10/2014] [Indexed: 12/21/2022]
Abstract
Circulating microRNAs (miRNAs) are discussed as potential disease-specific biomarkers in cardiovascular disease. Their diagnostic value has been examined in numerous studies and animal models with respect to coronary artery disease (CAD) and myocardial infarction (MI) and the prognostic abilities of circulating miRNAs in risk stratification of future disease have been evaluated. Various miRNAs are described to complement protein-based biomarkers or classical risk factors in the diagnosis of CAD or MI and even represent potential new biomarkers in the discrimination of unstable angina pectoris (UAP). Signatures consisting of sets of multiple miRNAs seem to improve the predictive power compared to single miRNAs. Furthermore, the emerging field of miRNA-based therapeutics has reached cardiovascular research. The first promising in vitro results are raising hope for future clinical application. However, methods and material used for RNA isolation, miRNA detection and normalization steps still lack ways of standardization and need to be considered carefully. This article reviews the current knowledge of miRNAs in cardiovascular disease focusing on CAD and MI and will provide an overview regarding the use of circulating miRNAs as biomarkers and potential therapeutic targets in the field of CAD.
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Affiliation(s)
- Christian Schulte
- 1 Department of General and Interventional Cardiology, University Heart Center Hamburg Eppendorf, 20246 Hamburg, Germany ; 2 German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Tanja Zeller
- 1 Department of General and Interventional Cardiology, University Heart Center Hamburg Eppendorf, 20246 Hamburg, Germany ; 2 German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Hamburg, Germany
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Duy J, Koehler JW, Honko AN, Minogue TD. Optimized microRNA purification from TRIzol-treated plasma. BMC Genomics 2015; 16:95. [PMID: 25765146 PMCID: PMC4342875 DOI: 10.1186/s12864-015-1299-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/29/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) represent new and potentially informative diagnostic targets for disease detection and prognosis. However, little work exists documenting the effect of TRIzol, a common viral inactivation and nucleic acid extraction reagent, on miRNA purification. Here, we developed an optimized protocol for miRNA extraction from plasma samples by evaluating five different RNA extraction kits, TRIzol phase separation, purification additives, and initial plasma sample volume. This method was then used for downstream profiling of plasma miRNAs found in archived samples from one nonhuman primate (NHP) experimentally challenged with Ebola virus by the aerosol route. RESULTS Comparison of real-time RT-PCR results for spiked-in and endogenous miRNA sequences determined extraction efficiencies from five different RNA purification kits. These experiments showed that 50 μL plasma processed using the QIAGEN miRNeasy Mini Kit with 5 μg of glycogen as a co-precipitant yielded the highest recovery of endogenous miRNAs. Using this optimized protocol, miRNAs from archived plasma samples of one rhesus macaque challenged with aerosolized Ebola virus was profiled using a targeted real-time PCR array. A total of 519 of the 752 unique miRNAs assayed were present in the plasma samples at day 0 and day 7 (time of death) post-exposure. Statistical analyses revealed 25 sequences significantly up- or down-regulated between day 0 and day 7 post infection, validating the utility of the extraction method for plasma miRNA profiling. CONCLUSIONS This study contributes to the knowledgebase of circulating miRNA extraction methods and expands on the potential applications of cell-free miRNA profiling for diagnostics and pathogenesis studies. Specifically, we optimized an extraction protocol for miRNAs from TRIzol-inactivated plasma samples that can be used for highly pathogenic viruses.
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Affiliation(s)
- Janice Duy
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, Frederick, MD, 21701, USA.
| | - Jeffrey W Koehler
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, Frederick, MD, 21701, USA.
| | - Anna N Honko
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 8200 Research Plaza, Fort Detrick, Frederick, MD, 21701, USA. .,Virology Division, U.S. Army Medical Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, Frederick, MD, 21701, USA.
| | - Timothy D Minogue
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, Frederick, MD, 21701, USA.
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Detection of miRNA as non-invasive biomarkers of colorectal cancer. Int J Mol Sci 2015; 16:2810-23. [PMID: 25633103 PMCID: PMC4346866 DOI: 10.3390/ijms16022810] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/15/2015] [Indexed: 12/15/2022] Open
Abstract
Colorectal Cancer (CRC) is one of the deadliest cancers—ranking as the fourth most common cause of cancer-related deaths in the world. It is such a deadly disease because it is largely asymptomatic until the latter stages—oftentimes when the cancer has metastasized. Thus, a huge emphasis of cancer treatment is placed on early detection. Currently, there is a lack of a noninvasive, reliable, and cost-effective screening method for CRC. In recent years, microRNA (miRNA) diagnostic markers have been suggested as a viable new screening method for CRC. miRNAs play an important role in carcinogenesis, and has been observed to be dysregulated in many cancers including CRC. This review examines the diagnostic potential of circulatory and fecal miRNA markers in relation to CRC, as well as current techniques to detect them.
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