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Gambarino S, Galliano I, Clemente A, Calvi C, Montanari P, Pau A, Dini M, Bergallo M. Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection. Diagnostics (Basel) 2024; 14:971. [PMID: 38786269 PMCID: PMC11120318 DOI: 10.3390/diagnostics14100971] [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: 03/15/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at -80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at -80, -20, 4 °C, or room temperature for up to 2 months after, and then could be stored at -80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.
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Affiliation(s)
- Stefano Gambarino
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Clemente
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Pau
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Maddalena Dini
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
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Chakkingal Bhaskaran B, Meyermans R, Gorssen W, Maes GE, Buyse J, Janssens S, Buys N. The forgotten variable? Does the euthanasia method and sample storage condition influence an organisms transcriptome - a gene expression analysis on multiple tissues in pigs. BMC Genomics 2023; 24:769. [PMID: 38093185 PMCID: PMC10720124 DOI: 10.1186/s12864-023-09794-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Transcriptomic studies often require collection of fresh tissues post euthanasia. The chosen euthanasia method might have the potential to induce variations in gene expressions that are unlinked with the experimental design. The present study compared the suitability of 'nitrogen gas in foam' (ANOXIA) in comparison to a non-barbiturate anaesthetic, T-61® (T61), for euthanizing piglets used in transcriptome research. Further, the effect of common tissue storage conditions, RNAlater™ (RL) and snap freezing in liquid nitrogen (LN2), on gene expression profiles were also analysed. RESULTS On comparison of the 3'mRNA-Seq data generated from pituitary, hypothalamus, liver and lung tissues, no significant differential expression in the protein coding genes were detected between the euthanasia methods. This implies that the nitrogen anoxia method could be a suitable alternative for euthanasia of piglets used in transcriptomic research. However, small nuclear RNAs (snRNAs) that constitute the eukaryotic spliceosomal machinery were found to be significantly higher (log2fold change ≥ 2.0, and adjusted p value ≤ 0.1) in pituitary samples collected using ANOXIA. Non-protein coding genes like snRNAs that play an important role in pre-mRNA splicing can subsequently modify gene expression. Storage in RL was found to be superior in preserving RNA compared to LN2 storage, as evidenced by the significantly higher RIN values in representative samples. However, storage in RL as opposed to LN2, also influenced differential gene expression in multiple tissues, perhaps as a result of its inability to inhibit biological activity during storage. Hence such external sources of variations should be carefully considered before arriving at research conclusions. CONCLUSIONS Source of biological variations like euthanasia method and storage condition can confound research findings. Even if we are unable to prevent the effect of these external factors, it will be useful to identify the impact of these variables on the parameter under observation and thereby prevent misinterpretation of our results.
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Affiliation(s)
- B Chakkingal Bhaskaran
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
| | - R Meyermans
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - W Gorssen
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - G E Maes
- Centre for Human Genetics, Genomics Core, UZ-KU Leuven, Leuven, Belgium
| | - J Buyse
- Department of Biosystems, Laboratory of Livestock Physiology, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - S Janssens
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - N Buys
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
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A Comparative Study on the Effect of Euthanasia Methods and Sample Storage Conditions on RNA Yield and Quality in Porcine Tissues. Animals (Basel) 2023; 13:ani13040698. [PMID: 36830485 PMCID: PMC9952302 DOI: 10.3390/ani13040698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Animals used in research often have to be euthanised, especially when tissue sampling is essential. Recently, a euthanasia method, utilizing an inhalant anaesthetic 'nitrogen gas in foam' in an anoxia box (ANOXIATM), has gained considerable interest as it claimed to be more animal-friendly. However, it is not clear whether the use of this euthanasia method has an influence on RNA measurements. Moreover, there are no studies on the interaction effect of different euthanasia methods on the tissue sample storage conditions. The current study compared RNA measurements from two euthanasia methods (ANOXIATM vs. T-61® injection) and two storage conditions (RNAlater™ vs. snap freezing) in 12 male piglets. The nitrogen anoxia method had a significantly higher RNA yield (p < 0.01) compared to the T-61® method. However, no effect of the euthanasia methods on the A260/230 ratio and RIN value was observed. Tissues stored in RNAlater™ had significantly higher RIN values (p < 0.001) compared to snap frozen samples. The present study could not find a significant difference between the two euthanasia methods in piglets, with regard to RNA quality measurements. Hence, the nitrogen anoxia technique (ANOXIATM) might be considered as a suitable alternative to T-61® for euthanasia of piglets used in research.
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Vanhaverbeke M, Attard R, Bartekova M, Ben-Aicha S, Brandenburger T, de Gonzalo-Calvo D, Emanueli C, Farrugia R, Grillari J, Hackl M, Kalocayova B, Martelli F, Scholz M, Wettinger SB, Devaux Y. Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129. Cardiovasc Res 2022; 118:3183-3197. [PMID: 34648023 PMCID: PMC9799060 DOI: 10.1093/cvr/cvab327] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/25/2023] Open
Abstract
Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners.
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Affiliation(s)
- Maarten Vanhaverbeke
- Department of Cardiovascular Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ritienne Attard
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Monika Bartekova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
- Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, 81372 Bratislava, Slovakia
| | - Soumaya Ben-Aicha
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Av. Alcalde Rovira Roure 80, 25198, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 28029, Madrid, Spain
| | - Costanza Emanueli
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Rosienne Farrugia
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU - University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | | | - Barbora Kalocayova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Milan 20097, Italy
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Stephanie Bezzina Wettinger
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
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Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, Doolan DL. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples. Int J Mol Sci 2022; 23:ijms231810609. [PMID: 36142559 PMCID: PMC9503649 DOI: 10.3390/ijms231810609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.
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Affiliation(s)
- Yomani D. Sarathkumara
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ashton M. Kelly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J. Pattinson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Catherine M. Rush
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Jeffrey Warner
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Carla Proietti
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Denise L. Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- Correspondence:
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Nyaruaba R, Hong W, Li X, Yang H, Wei H. Long-Term Preservation of SARS-CoV-2 RNA in Silk for Downstream RT-PCR Tests. Anal Chem 2022; 94:4522-4530. [PMID: 35235308 PMCID: PMC8903213 DOI: 10.1021/acs.analchem.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
Positive controls made of viral gene components are essential to validate the performance of diagnostic assays for pathogens like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, most of them are target-specific, limiting their application spectrum when validating assays beyond their specified targets. The use of an inactivated whole-virus RNA reference standard could be ideal, but RNA is a labile molecule that needs cold chain storage and transportation to preserve its integrity and activity. The cold chain process stretches the already dwindling storage capacities, incurs huge costs, and limits the distribution of reference materials to low-resource settings. To circumvent these issues, we developed an inactivated whole-virus SARS-CoV-2 RNA reference standard and studied its stability in silk fibroin matrices, i.e., silk solution (SS) and silk film (SF). Compared to preservation in nuclease-free water (ddH2O) and SS, SF was more stable and could preserve the SARS-CoV-2 RNA reference standard at room temperature for over 21 weeks (∼6 months) as determined by reverse transcription polymerase chain reaction (RT-PCR). The preserved RNA reference standard in SF was able to assess the limits of detection of four commercial SARS-CoV-2 RT-PCR assays. In addition, SF is compatible with RT-PCR reactions and can be used to preserve a reaction-ready primer and probe mix for RT-PCR at ambient temperatures without affecting their activity. Taken together, these results offer extensive flexibility and a simpler mechanism of preserving RNA reference materials for a long time at ambient temperatures of ≥25 °C, with the possibility of eliminating cold chains during storage and transportation.
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Affiliation(s)
- Raphael Nyaruaba
- CAS
Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety
Mega-Science, Wuhan Institute of Virology,
Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Africa
Joint Research Center, 6200-00200 Nairobi, Kenya
| | - Wei Hong
- CAS
Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety
Mega-Science, Wuhan Institute of Virology,
Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Li
- CAS
Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety
Mega-Science, Wuhan Institute of Virology,
Chinese Academy of Sciences, Wuhan 430071, China
| | - Hang Yang
- CAS
Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety
Mega-Science, Wuhan Institute of Virology,
Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS
Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety
Mega-Science, Wuhan Institute of Virology,
Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
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Shokri Bousjein N, Tierney SM, Gardner MG, Schwarz MP. Does effective population size affect rates of molecular evolution: Mitochondrial data for host/parasite species pairs in bees suggests not. Ecol Evol 2022; 12:e8562. [PMID: 35154650 PMCID: PMC8820120 DOI: 10.1002/ece3.8562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 11/08/2022] Open
Abstract
Adaptive evolutionary theory argues that organisms with larger effective population size (N e) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases, species with much smaller N e may be able to survive besides their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small N e are due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit N e that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein-coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between N e and rate of molecular evolution are discussed.
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Affiliation(s)
- Nahid Shokri Bousjein
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
- Faculty of Biological SciencesKharazmi UniversityTehranIran
| | - Simon M. Tierney
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Michael G. Gardner
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
- Evolutionary Biology Unit South Australian MuseumNorth Terrace AdelaideSouth AustraliaAustralia
| | - Michael P. Schwarz
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
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Abstract
Systematic bio- and databanks are key prerequisites for modern radiation research to investigate radiation response mechanisms in the context of genetic, environmental and lifestyle-associated factors. This report presents the current status of the German Uranium Miners’ Biobank. In 2008, the bio- and databank was established at the Federal Office for Radiation Protection, and the sampling of biological materials from former uranium miners with and without lung cancer was initiated. For this purpose, various biological specimens, such as DNA and RNA, were isolated from blood samples as well as from formalin-fixed paraffin-embedded lung tissue. High-quality biomaterials suitable for OMICs research and the associated data on occupational radiation and dust exposure, and medical and lifestyle data from over 1000 individuals have been stored so far. Various experimental data, e.g., genome-wide SNPs, whole genome transcriptomic and miRNA data, as well as individual chromosomal aberration data from subgroups of biobank samples, are already available upon request for in-depth research on radiation-induced long-term effects, individual radiation susceptibility to lung cancer and radon-induced fingerprints in lung cancer. This biobank is the first systematic uranium miners´ biobank worldwide that is suitable for OMICs research on radiation-exposed workers. It offers the opportunity to link radiation-induced perturbations of biological pathways or processes and putative adverse outcome(s) by OMICs profiling at different biological organization levels.
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Timmerman DM, Gillis AJM, Mego M, Looijenga LHJ. Comparative Analyses of Liquid-Biopsy MicroRNA371a-3p Isolation Protocols for Serum and Plasma. Cancers (Basel) 2021; 13:cancers13174260. [PMID: 34503070 PMCID: PMC8428229 DOI: 10.3390/cancers13174260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023] Open
Abstract
Simple Summary The active disease status of patients with a malignant germ cell tumor can be evaluated using detection of specific body-circulating microRNAs. However, various methods are reported to isolate and detect microRNAs from blood, possibly influencing the score as positive or negative. Here, we investigated two frequently used techniques for microRNA isolation from blood, either serum or plasma, to evaluate possible differences. These data are required to compare published studies and to select the best methods in the future. No effect of either starting with plasma or serum was found, indicating that both blood products can be used. The bead-based method was more stable and applicable on small blood volumes, whereas the total RNA method exhibited a higher sensitivity due to a larger starting volume. These results are important to develop the optimal method for the detection of microRNAs in blood to monitor malignant germ cell tumor patients in clinic practice. Abstract MicroRNAs (miRNAs) are short, non-coding RNAs involved in translation regulation. Dysregulation has been identified in cancer cells. miRNAs can be secreted and detectable in body fluids; therefore, they are potential liquid-biopsy biomarkers. The miR-371a-3 cluster members are an example, monitoring the presence of malignant germ cell tumors based on patient serum/plasma analyses. However, a large variety of isolation techniques on sample types (serum vs. plasma) are reported, hampering interstudy comparisons. Therefore, we analyzed the impact of using the miRNeasy Serum/Plasma Kit (cell-free total RNA purification) Qiagen extraction kit and the TaqMan anti-miRNA bead-capture procedure of ThermoFisher for miRNA isolation. Ten normal male matched serum and plasma samples and seventeen testicular germ cell tumor patient serum samples were investigated. The Qiagen kit requires a higher input volume (200 µL vs. 50 µL), resulting in higher sensitivity. Serum and plasma comparison demonstrated high similarity in miRNA levels. Titration experiments showed that the bead-capture procedure is superior in cases of lower starting volumes (<100 µL). This study highlights the strengths and limitations of two different isolation protocols, relevant for in vivo analysis with small starting volumes. In summary, miRNA detection levels results varied little between plasma and serum, whereas for low volumes the bead capture isolation method is preferable.
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Affiliation(s)
- Dennis M. Timmerman
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (D.M.T.); (A.J.M.G.)
| | - Ad J. M. Gillis
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (D.M.T.); (A.J.M.G.)
| | - Michal Mego
- Translational Research Unit and 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, 84505 Bratislava, Slovakia;
| | - Leendert H. J. Looijenga
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (D.M.T.); (A.J.M.G.)
- Correspondence: ; Tel.: +31-88-972-5211
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GENEŞ D, PEKKOLAY Z, BEYAZ C, KILINÇ F, TUZCU AK. Is HbA1c Misleading and 90-Minute Glucose Tolerance Test a Better Indicator in the Diagnosis of Diabetes Mellitus? DICLE MEDICAL JOURNAL 2020. [DOI: 10.5798/dicletip.706051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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YILMAZ K, GUNDUZ Z, KUTUK MS, DUSUNSEL R, DURSUN İ, YEL S. The Relationship Between MicroRNAs And Congenital Kidney Anomalies. DICLE MEDICAL JOURNAL 2020. [DOI: 10.5798/dicletip.706048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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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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13
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Abstract
Objectives: Research on the genetic basis of tinnitus is still in its first steps. A group of scientists dedicated to tinnitus genetics within European Tinnitus Network (TINNET) network recognize that further progress requires multicenter collaborative efforts for defining contributing genes. The purpose of the present work is to provide instructions regarding collection, processing, storage, and shipment of samples intended for genetic studies in auditory research. Design: One part of the recommendations has a general character; another part is of particular importance for auditory healthcare practitioners such as otolaryngology physicians, audiologists, and general practitioners. Results: We provide a set of instructions and various options for obtaining samples. We give advice regarding sample processing, storage, and shipment and define the minimal and essential clinical information that should accompany the samples collected for genetic processing. Conclusions: These recommendations offer a basis to standardize and optimize collaborations between geneticists and healthcare practitioners specialized in tinnitus and hearing disorders.
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14
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Ramón Y Cajal S, Segura MF, Hümmer S. Interplay Between ncRNAs and Cellular Communication: A Proposal for Understanding Cell-Specific Signaling Pathways. Front Genet 2019; 10:281. [PMID: 31001323 PMCID: PMC6454836 DOI: 10.3389/fgene.2019.00281] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/14/2019] [Indexed: 01/09/2023] Open
Abstract
Intercellular communication is essential for the development of specialized cells, tissues, and organs and is critical in a variety of diseases including cancer. Current knowledge states that different cell types communicate by ligand–receptor interactions: hormones, growth factors, and cytokines are released into the extracellular space and act on receptors, which are often expressed in a cell-type-specific manner. Non-coding RNAs (ncRNAs) are emerging as newly identified communicating factors in both physiological and pathological states. This class of RNA encompasses microRNAs (miRNAs, well-studied post-transcriptional regulators of gene expression), long non-coding RNAs (lncRNAs) and other ncRNAs. lncRNAs are diverse in length, sequence, and structure (linear or circular), and their functions are described as transcriptional regulation, induction of epigenetic changes and even direct regulation of protein activity. They have also been reported to act as miRNA sponges, interacting with miRNA and modulating its availability to endogenous mRNA targets. Importantly, lncRNAs may have a cell-type-specific expression pattern. In this paper, we propose that lncRNA–miRNA interactions, analogous to receptor–ligand interactions, are responsible for cell-type-specific outcomes. Specific binding of miRNAs to lncRNAs may drive cell-type-specific signaling cascades and modulate biochemical feedback loops that ultimately determine cell identity and response to stress factors.
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Affiliation(s)
- Santiago Ramón Y Cajal
- Department of Pathology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain.,Translational Molecular Pathology, Vall d'Hebron Research Institute, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Miguel F Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology, Vall d'Hebron Research Institute, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
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15
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Charvet S, Riemann L, Alneberg J, Andersson AF, von Borries J, Fischer U, Labrenz M. AFISsys - An autonomous instrument for the preservation of brackish water samples for microbial metatranscriptome analysis. WATER RESEARCH 2019; 149:351-361. [PMID: 30469021 DOI: 10.1016/j.watres.2018.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Microbial communities are the main drivers of biogeochemical cycling of multiple elements sustaining life in the ocean. The rapidity of their response to stressors and abrupt environmental changes implies that even fast and infrequent events can affect local transformations of organic matter and nutrients. Modern molecular techniques now allow for monitoring of microbial activities and functions in the environment through the analysis of genes and expressed genes contained in natural microbial assemblages. However, messenger RNA turnover in cells can be as short as 30 seconds and stability varies greatly between transcripts. Sampling of in situ communities involves an inevitable delay between the collection of seawater and the extraction of its RNA, leaving the bacterial communities plenty of time to alter their gene expression. The characteristics of microbial RNA turnover make time-series very difficult because samples need to be processed immediately to limit alterations to the metatranscriptomes. To address these challenges we designed an autonomous in situ fixation multi-sampler (AFISsys) for the reliable sampling of microbial metatranscriptomes at frequent intervals, for refined temporal resolution. To advance the development of this instrument, we examined the minimal seawater volume necessary for adequate coverage of community gene expression, and the suitability of phenol/ethanol fixation for immediate and long-term preservation of transcripts from a microbial community. We then evaluated the field eligibility of the instrument itself, with two case studies in a brackish system. AFISsys is able to collect, fix, and store water samples independently at a predefined temporal resolution. Phenol/ethanol fixation can conserve metatranscriptomes directly in the environment for up to a week, for later analysis in the laboratory. Thus, the AFISsys constitutes an invaluable tool for the integration of molecular functional analyses in environmental monitoring in brackish waters and in aquatic environments in general.
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Affiliation(s)
- Sophie Charvet
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Denmark
| | - Johannes Alneberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | - Anders F Andersson
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | | | - Uwe Fischer
- HYDRO-BIOS Apparatebau GmbH, Altenholz, Germany
| | - Matthias Labrenz
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany.
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16
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Diener C, Galata V, Keller A, Meese E. MicroRNA profiling from dried blood samples. Crit Rev Clin Lab Sci 2019; 56:111-117. [DOI: 10.1080/10408363.2018.1561641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Medical Faculty, Saarland University, Homburg, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, Center for Bioinformatics, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, Center for Bioinformatics, Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Medical Faculty, Saarland University, Homburg, Germany
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17
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Abstract
PURPOSE OF REVIEW Islet transplantation, an important approach to achieve insulin independence for individuals with type 1 diabetes, is limited by the lack of accurate biomarkers to track beta-cell death post islet infusion. In this review, we will discuss existing and recently described biomarkers. RECENT FINDINGS As beta cells are killed by the immune system, fragments of beta cell-specific cell-free DNA and proteins are released into the periphery. Several different strategies to identify these fragments have been described. Some circulating, non-coding microRNAs, particularly miRNA-375 are also showing potential to reflect the rate of beta cell loss post-clinical islet transplantation. Recent advances in identifying accurate beta cell-specific biomarkers such as differentially methylated insulin cell-free DNA and circulating miRNA-375 may help predict clinical outcomes. More studies are required to examine the robustness of these biomarkers to detect chronic beta-cell loss in islet transplantation recipients.
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Affiliation(s)
- Fatimah T. AlRashidi
- Diabetes and Metabolism, Bristol Medical School, University of Bristol, Level 2, Learning and Research, Southmead Hospital, Bristol, BS10 5NB UK
| | - Kathleen M. Gillespie
- Diabetes and Metabolism, Bristol Medical School, University of Bristol, Level 2, Learning and Research, Southmead Hospital, Bristol, BS10 5NB UK
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18
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He J, Yavuz B, Kluge JA, Li AB, Omenetto FG, Kaplan DL. Stabilization of RNA Encapsulated in Silk. ACS Biomater Sci Eng 2018; 4:1708-1715. [DOI: 10.1021/acsbiomaterials.8b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jiuyang He
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Burcin Yavuz
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Jonathan A. Kluge
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
- Vaxess Technologies, c/o Pagliuca Harvard Life Lab, 127 Western Avenue, Allston, Massachusetts 02134, United States
| | - Adrian B. Li
- Vaxess Technologies, c/o Pagliuca Harvard Life Lab, 127 Western Avenue, Allston, Massachusetts 02134, United States
| | - Fiorenzo G. Omenetto
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
- Department of Chemical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
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19
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Chen IH, Chou LS, Chou SJ, Wang JH, Stott J, Blanchard M, Jen IF, Yang WC. Sound exposure-induced cytokine gene transcript profile changes in captive bottlenose dolphin (Tursiops truncatus) blood identified by a probe-based qRT-PCR. J Vet Med Sci 2018; 80:601-605. [PMID: 29479043 PMCID: PMC5938186 DOI: 10.1292/jvms.17-0548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cetacean health may be potentially affected by anthropogenic sound. We have initiated investigations on the effect of low-frequency underwater sound on immunological gene transcript profiles of captive bottlenose dolphins (Tursiops truncatus) using a probe-based quantitative gene expression assay. Six immunologic genes (IL-2Rα, -4, -10, -12, TNFα and IFNγ) were selected for analysis using two validated housekeeping genes (PGK1 and HPRT1) as reference genes. Twenty-four blood samples from six clinically healthy individuals and six blood samples from individuals after sound exposures were available. The gene transcript profile of sound-exposed dolphins was consistent with a stress-induced TH2 shift profile as compared to controls. This study may lead to better understanding of the effects of anthropogenic sound on immune responses of cetaceans.
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Affiliation(s)
- I-Hua Chen
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Lien-Siang Chou
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan (R.O.C.)
| | - Shih-Jen Chou
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jiann-Hsiung Wang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jeffrey Stott
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - Myra Blanchard
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - I-Fan Jen
- Farglory Ocean Park, No.189, Yenliao Village, Shoufong, Hualien, Taiwan (R.O.C.)
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
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20
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Wu C, Xu B, Zhou Y, Ji M, Zhang D, Jiang J, Wu C. Correlation between serum IL-1β and miR-144-3p as well as their prognostic values in LUAD and LUSC patients. Oncotarget 2018; 7:85876-85887. [PMID: 27811377 PMCID: PMC5349881 DOI: 10.18632/oncotarget.13042] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND IL-1β is an essential factor of inflammation initiation, and it also promotes malignant transformation, indicating its tumorigenic property. We aimed to investigate the correlation between IL-1β and miR-144-3p as well as their prognostic values in LUAD and LUSC patients. RESULTS The IL-1β level in both LUAD and LUSC patients was significantly higher than that of healthy donors (P < 0.001). In both populations, patients with low IL-1β level had better prognosis than high IL-1β level (P < 0.001 and P = 0.010, respectively). In A549 cells, miR-144 showed the biggest expression change (-4.38 fold) after IL-1β exposure. In LUAD patients, a negative correlation was detected between IL-1β and miR-144-3p (r = -0.540, P < 0.001) and the high miR-144-3p group had better prognosis (P = 0.003), which was validated by TCGA data. Clinical stage, IL-1β and miR-144-3p were independent risk factors in LUAD patients. In vitro, IL-1β and miR-144-3p antagomir could enhance proliferation and miR-144-3p mimics would attenuate the promoting effect of IL-1β. MATERIALS AND METHODS ELISA and qRT-PCR were applied respectively to detected cytokines and miR-144-3p in 129 LUAD, 54 LUSC and 40 healthy donors. Moreover, miRNA array was carried out for miRNA profiling. TCGA database was employed for validation, and follow up data were collected for prognosis evaluation. MTT assay and western-blot were carried out for proliferation evaluation. CONCLUSIONS In LUAD patients, the serum IL-1β level was correlated with miR-144-3p may affect miR-144-3p at transcriptional level. Both of them were independent risk factors for LUAD prognosis. In addition, IL-1β and miR-144-3p might mediate inflammation-promoted tumorigenesis in LUAD patients.
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Affiliation(s)
- Chen Wu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China.,Institute of Cell Therapy, Soochow University, Changzhou, 213003, P.R.China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China
| | - Bin Xu
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China.,Department of Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China
| | - You Zhou
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China.,Department of Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China
| | - Mei Ji
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China
| | - Dachuan Zhang
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China
| | - Jingting Jiang
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, P.R.China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China.,Department of Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China
| | - Changping Wu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R.China.,Institute of Cell Therapy, Soochow University, Changzhou, 213003, P.R.China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, P.R.China
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21
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Impact of Preanalytical Handling and Timing for Peripheral Blood Mononuclear Cells Isolation and RNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Int J Biol Markers 2018; 27:e90-8. [DOI: 10.5301/jbm.2012.9235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2012] [Indexed: 02/04/2023]
Abstract
Multicenter studies and biobanking projects require blood transportation from the participating center to a central collection or diagnostic laboratory. The impact of time delays between venous blood collection and peripheral blood mononuclear cells (PBMC) isolation prior to RNA extraction may affect the quality and quantity of isolated nucleic acids for genomic applications. Thus, standard operating procedure (SOP) optimization for the treatment of biological samples before RNA extraction is crucial in a biological repository. In order to define SOPs for whole blood preservation prior to RNA extraction, we sought to determine whether different blood storage times (0, 3, 6, 10, 24, and 30 hours) prior to PBMCs isolation and storage at –80°C, could affect the quality and quantity of extracted RNA. After spectrophotometric quantification, the quality and integrity of RNA were assessed by agarose gel electrophoresis, RNA integrity number and real time-PCR (RT-PCR). Across the different time points we did not observe significant differences within the first 24 hours of blood storage at room temperature, while a significant loss in RNA yield and integrity was detected between 24 and 30 hours. We conclude that time delays before PBMCs isolation prior to RNA extraction may have a significant impact on downstream molecular biological applications.
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22
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Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells. Nat Commun 2017; 8:1733. [PMID: 29170510 PMCID: PMC5700979 DOI: 10.1038/s41467-017-01705-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 01/13/2023] Open
Abstract
Precise rare-cell technologies require the blood to be processed immediately or be stabilized with fixatives. Such restrictions limit the translation of circulating tumor cell (CTC)-based liquid biopsy assays that provide accurate molecular data in guiding clinical decisions. Here we describe a method to preserve whole blood in its minimally altered state by combining hypothermic preservation with targeted strategies that counter cooling-induced platelet activation. Using this method, whole blood preserved for up to 72 h can be readily processed for microfluidic sorting without compromising CTC yield and viability. The tumor cells retain high-quality intact RNA suitable for single-cell RT-qPCR as well as RNA-Seq, enabling the reliable detection of cancer-specific transcripts including the androgen-receptor splice variant 7 in a cohort of prostate cancer patients with an overall concordance of 92% between fresh and preserved blood. This work will serve as a springboard for the dissemination of diverse blood-based diagnostics. The current FDA-approved whole blood stabilization method for circulating tumor cell (CTC) isolation suffers from RNA degradation. Here the authors combine hypothermic preservation and antiplatelet strategies to stabilize whole blood up to 72 h without compromising CTC yield and RNA integrity.
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23
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Circulating MiRNAs as biomarkers of gait speed responses to aerobic exercise training in obese older adults. Aging (Albany NY) 2017; 9:900-913. [PMID: 28301325 PMCID: PMC5391238 DOI: 10.18632/aging.101199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/03/2017] [Indexed: 01/01/2023]
Abstract
Gait speed is a useful predictor of adverse outcomes, including incident mobility disability and mortality in older adults. While aerobic exercise training (AEX) is generally an effective therapy to improve gait speed, individual responses are highly variable. Circulating microRNAs (miRNAs) may contribute to inter-individual changes in gait speed with AEX. We examined whether plasma miRNAs are associated with gait speed changes (dGaitSp) in 33 obese older adults (age: 69.3±3.6 years, BMI: 34.0±3.1 kg/m2, 85% white, 73% women) who performed treadmill walking, 4 days/week for 5 months. Gait speed (baseline: 1.02±0.19 m/s; range of response: −0.2 to 0.35 m/s) was assessed using a 400 meter-fast-paced walk test. Using Nanostring technology, 120 out of 800 miRNAs were found to be abundantly expressed in plasma and 4 of these were significantly changed after AEX: miR-376a-5p increased, while miR-16-5p, miR-27a-3p, and miR-28-3p all decreased. In addition, baseline miR-181a-5p levels (r=-0.40, p=0.02) and percent changes in miR-92a-3p (r=-0.44, p=0.009) associated negatively with dGaitSp. Linear regression combined baseline miR-181a-5p and miR-92a-3p levels showed even stronger associations with dGaitSp (r=-0.48, p=0.005). These results suggest that circulating miR-181a-5p and miR-92a-3p may predict and/or regulate AEX-induced gait speed changes in obese older adults.
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24
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Tsai MA, Chen IH, Wang JH, Chou SJ, Li TH, Leu MY, Ho HK, Yang WC. A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales ( Delphinapterus leucas). PeerJ 2017; 5:e3840. [PMID: 28970970 PMCID: PMC5622604 DOI: 10.7717/peerj.3840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/01/2017] [Indexed: 12/20/2022] Open
Abstract
Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.
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Affiliation(s)
- Ming-An Tsai
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - I-Hua Chen
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Jiann-Hsiung Wang
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Shih-Jen Chou
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Tsung-Hsien Li
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Ming-Yih Leu
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Hsiao-Kuan Ho
- Department of Biology, Hi-Scene World Enterprise Co. Ltd., Pingtung, Taiwan
| | - Wei Cheng Yang
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
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25
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Zhang K, Wang YW, Wang YY, Song Y, Zhu J, Si PC, Ma R. Identification of microRNA biomarkers in the blood of breast cancer patients based on microRNA profiling. Gene 2017; 619:10-20. [PMID: 28359916 DOI: 10.1016/j.gene.2017.03.038] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/22/2017] [Accepted: 03/25/2017] [Indexed: 12/14/2022]
Abstract
Accumulating evidence indicates that human circulating microRNAs (miRNAs) could serve as diagnostic and prognostic biomarkers in various cancers. We aimed to explore novel miRNA biomarkers in the blood of breast cancer patients based on miRNA profiling. A miRCURY™ LNA Array was used to identify differentially altered miRNAs in the whole blood of breast cancer patients (n=6) and healthy controls (n=6). Levels of candidate miRNAs were quantified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in whole blood specimens of 15 breast cancer patients and 13 age-matched healthy control individuals. The miRWalk database was used to predict miRNA targets and the DAVID tool was used to identify significant enrichment pathways. A total of 171 differentially expressed miRNAs were identified by microarray, including 169 upregulated and 2 downregulated miRNAs in breast cancer. Five upregulated miRNAs (miR-30b-5p, miR-96-5p, miR-182-5p, miR-374b-5p, and miR-942-5p) were confirmed by qRT-PCR. The areas under the receiver operating characteristic curve of miR-30b-5p, miR-96-5p, miR-182-5p, miR-374b-5p, and miR-942-5p were 0.9333, 0.7692, 0.7590, 0.8256, and 0.8128, respectively. Importantly, upregulation of these five miRNAs was observed even in patients with very early-stage breast cancer. A total of 855 genes were predicted to be targeted by the five miRNAs, and the one cut domain family member 2 gene (ONECUT2) was a shared target of the five miRNAs. Analysis of publicly available data revealed that these dysregulated miRNAs and the target genes were associated with the survival of breast cancer patients. Furthermore, the five miRNAs were significantly enriched in numerous cancer-related pathways, including "MicroRNAs in cancer", "Pathways in cancer", "FoxO signaling pathway", "Ras signaling pathway", "Rap1 signaling pathway", "MAPK signaling pathway", and "PI3K-Akt signaling pathway". Our data support the potential of the five identified miRNAs as novel biomarkers for the detection of breast cancer, and indicate that they may be involved in breast cancer development and progression.
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Affiliation(s)
- Kai Zhang
- Department of Breast Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China
| | - Ya-Wen Wang
- Department of Breast Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China
| | - Yan-Yan Wang
- Health Examination Center, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China
| | - Yu Song
- Department of Breast Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China
| | - Jiang Zhu
- Department of Breast Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China
| | - Peng-Chao Si
- Key Laboratory for Liqeuid-Solid Structural Evolution and Processing of Materials, Ministry of Education, School of Materials Science and Engineering, Shandong University, Jinan 250061, People's Republic of China
| | - Rong Ma
- Department of Breast Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan 250012, Shandong, People's Republic of China.
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26
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Johansen JS, Calatayud D, Albieri V, Schultz NA, Dehlendorff C, Werner J, Jensen BV, Pfeiffer P, Bojesen SE, Giese N, Nielsen KR, Nielsen SE, Yilmaz M, Holländer NH, Andersen KK. The potential diagnostic value of serum microRNA signature in patients with pancreatic cancer. Int J Cancer 2016; 139:2312-24. [PMID: 27464352 DOI: 10.1002/ijc.30291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/18/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Biomarkers for early diagnosis of patients with pancreatic cancer (PC) are needed. Our aim was to identify panels of miRNAs in serum in combination with CA 19-9 for use in the diagnosis of PC. Four hundred seventeen patients with PC were included prospectively from Denmark (n = 306) and Germany (n = 111). Controls included 59 patients with chronic pancreatitis (CP) and 248 healthy subjects (HS). MiRNAs were analyzed in pretreatment serum samples from 3 cohorts: discovery cohort (754 human miRNAs, TaqMan(®) Human MicroRNA assay, Applied Biosystem; PC n = 133, controls n = 72); training cohort (34 miRNAs, real-time qPCR using the Fluidigm BioMark™ System; PC n = 198, controls n = 184); validation cohort (13 miRNAs, real-time qPCR using the Fluidigm BioMark™ System; PC n = 86, controls n = 51). We found that 34 miRNAs in serum from PC patients in the discovery cohort were expressed differently than in controls. These miRNAs were tested in the training cohort, and four diagnostic panels were constructed that included 5 or 12 miRNAs (miR-16, -18a, -20a, -24, -25, -27a, -29c, -30a.5p, -191, -323.3p, -345 and -483.5p). Diagnostic accuracy of detecting PC in the training cohort was AUC (Index I 0.85; II 0.87; III 0.85; IV 0.95; CA 19-9 0.93); specificity (I 0.71; II 0.76; III 0.66; IV 0.90 (fixed sensitivity at 0.85); CA 19-9 0.93). Combining serum CA 19-9 and Index II best discriminated Stages I and II PC from HS [AUC 0.93 (0.90-0.96), sensitivity 0.77 (0.69-0.84), specificity 0.94 (0.90-0.96) and accuracy 0.88 (0.84-0.91)]. In conclusion, we identified four diagnostic panels based on 5 or 12 miRNAs in serum that could distinguish patients with PC from HS and CP.
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Affiliation(s)
- Julia S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark. .,Department of Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark.
| | - Dan Calatayud
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Vanna Albieri
- Danish Cancer Society Research Center, Danish Cancer Society, Denmark
| | - Nicolai A Schultz
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, Copenhagen University Hospital, Denmark
| | | | - Jens Werner
- Department of General, Visceral, and Transplant Surgery, University of Heidelberg, Germany
| | - Benny V Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | | | - Stig E Bojesen
- Department of Oncology, Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Nathalia Giese
- Department of General, Visceral, and Transplant Surgery, University of Heidelberg, Germany
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Denmark
| | | | - Mette Yilmaz
- Department of Oncology, Aalborg University Hospital, Denmark
| | | | - Klaus K Andersen
- Danish Cancer Society Research Center, Danish Cancer Society, Denmark
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27
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Pop LA, Pileczki V, Cojocneanu-Petric RM, Petrut B, Braicu C, Jurj AM, Buiga R, Achimas-Cadariu P, Berindan-Neagoe I. Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors. Onco Targets Ther 2016; 9:3369-80. [PMID: 27330317 PMCID: PMC4898429 DOI: 10.2147/ott.s97519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors). Nanotechnologies help improve the quality and quantity control for gene expression studies. Patients and methods The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three housekeeping genes and one small nuclear RNA gene using the ViiA 7 platform, with specific primers. Results Every step of the sample handling protocol, which begins with sample harvest and ends with the data analysis, is of utmost importance due to the fact that it is time consuming, labor intensive, and highly expensive. High temperature of the surgical procedure does not affect the small nucleic acid sequences in comparison with the mRNA. Conclusion Gene expression is clearly affected by the RNA quality, but less affected in the case of small nuclear RNAs. We proved that the high-temperature, highly invasive transurethral resection of bladder tumor procedure damages the tissue and affects the integrity of the RNA from biological specimens.
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Affiliation(s)
- Laura A Pop
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Valentina Pileczki
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Analytical Chemistry, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Roxana M Cojocneanu-Petric
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Bogdan Petrut
- Department of Surgery II - Urology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Urology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Cornelia Braicu
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ancuta M Jurj
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Rares Buiga
- Department of Pathology, The Oncology Institute "Prof. Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
| | - Patriciu Achimas-Cadariu
- Department of Surgery, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Surgical Oncology and Gynecological Oncology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ioana Berindan-Neagoe
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
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Malentacchi F, Pizzamiglio S, Wyrich R, Verderio P, Ciniselli C, Pazzagli M, Gelmini S. Effects of Transport and Storage Conditions on Gene Expression in Blood Samples. Biopreserv Biobank 2016; 14:122-8. [DOI: 10.1089/bio.2015.0037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | | | | | - Paolo Verderio
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Mario Pazzagli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | - Stefania Gelmini
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
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29
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Franken C, Remy S, Lambrechts N, Hollanders K, Den Hond E, Schoeters G. Peripheral blood collection: the first step towards gene expression profiling. Biomarkers 2016; 21:458-65. [DOI: 10.3109/1354750x.2016.1153721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Carmen Franken
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
- Department of Biomedical Sciences
| | - Sylvie Remy
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
- Department of Epidemiology and Social Medicine, University of Antwerp, Antwerp, Belgium
| | - Nathalie Lambrechts
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
| | - Karen Hollanders
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
| | - Elly Den Hond
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
| | - Greet Schoeters
- Unit Environmental Risk and Health, Flemish Institute for Technological Research (VITO NV), Mol, Belgium
- Department of Biomedical Sciences
- Department of Environmental Medicine, University of Southern Denmark, Odense, Denmark
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30
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Eikrem O, Beisland C, Hjelle K, Flatberg A, Scherer A, Landolt L, Skogstrand T, Leh S, Beisvag V, Marti HP. Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development. PLoS One 2016; 11:e0149743. [PMID: 26901863 PMCID: PMC4764764 DOI: 10.1371/journal.pone.0149743] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients to investigate feasibility of RNAseq in archival tissue. From each of 16 patients undergoing partial or full nephrectomy, four core biopsies, such as two specimens with ccRCC and two specimens of adjacent normal tissue, were obtained with a 16g needle. One normal and one ccRCC tissue specimen per patient was stored either in FFPE or RNAlater®. RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol. Comparative analysis was done using voom/Limma R-package. The analysis of the FFPE and RNAlater® datasets yielded similar numbers of detected genes, differentially expressed transcripts and affected pathways. The FFPE and RNAlater datasets shared 80% (n = 1106) differentially expressed genes. The average expression and the log2 fold changes of these transcripts correlated with R2 = 0.97, and R2 = 0.96, respectively. Among transcripts with the highest fold changes in both datasets were carbonic anhydrase 9 (CA9), neuronal pentraxin-2 (NPTX2) and uromodulin (UMOD) that were confirmed by immunohistochemistry. IPA revealed the presence of gene signatures of cancer and nephrotoxicity, renal damage and immune response. To simulate the feasibility of clinical biomarker studies with FFPE samples, a classifier model was developed for the FFPE dataset: expression data for CA9 alone had an accuracy, specificity and sensitivity of 94%, respectively, and achieved similar performance in the RNAlater dataset. Transforming growth factor-ß1 (TGFB1)-regulated genes, epithelial to mesenchymal transition (EMT) and NOTCH signaling cascade may support novel therapeutic strategies. In conclusion, in this proof of concept study, RNAseq data obtained from FFPE kidney biopsies are comparable to data obtained from fresh stored material, thereby expanding the utility of archival tissue specimens.
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Affiliation(s)
- Oystein Eikrem
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, Urology, University of Bergen, Bergen, Norway
| | - Karin Hjelle
- Department of Clinical Medicine, Urology, University of Bergen, Bergen, Norway
| | - Arnar Flatberg
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Lea Landolt
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Trude Skogstrand
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Vidar Beisvag
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
- Department of Medicine, Nephrology, Haukeland University Hospital, Bergen, Norway
- * E-mail:
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31
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Petriella D, De Summa S, Lacalamita R, Galetta D, Catino A, Logroscino AF, Palumbo O, Carella M, Zito FA, Simone G, Tommasi S. miRNA profiling in serum and tissue samples to assess noninvasive biomarkers for NSCLC clinical outcome. Tumour Biol 2015; 37:5503-13. [DOI: 10.1007/s13277-015-4391-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022] Open
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32
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Liu X, Li Q, Wang X, Zhou X, Liao Q, He X, Zhang J, Sun J, Wu J, Cheng L, Zhang Y. Comparison of six different pretreatment methods for blood RNA extraction. Biopreserv Biobank 2015; 13:56-60. [PMID: 25686049 DOI: 10.1089/bio.2014.0090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human blood specimens serve as important research materials in the field of translational medicine research. The RNA extracted from blood, for example, represents the gene expression profiles of individuals or groups, and can be indicative of the pathological basis for human diseases. Meanwhile, the RNA quality may have severe impacts on the results of RNA studies. RNA is susceptible to many factors, such as the time of sample collection, transportation conditions, protectants, pretreatments, and extraction methods. In this study, six different pretreatment methods are evaluated for their effects on blood RNA extraction including the RNA yields and quality. Results show that most of these methods meet the basic requirements for RNA studies. While considering the simplicity of the procedure, the cost factor, and how to make full use of the samples, the proper method should be employed by researchers who have specific requirements for their research.
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Affiliation(s)
- Xiaopan Liu
- 1 China National Genebank, BGI-Shenzhen , Shenzhen, China
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33
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Selection of suitable reference genes for normalization of quantitative RT-PCR in peripheral blood samples of bottlenose dolphins (Tursiops truncatus). Sci Rep 2015; 5:15425. [PMID: 26486099 PMCID: PMC4614023 DOI: 10.1038/srep15425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/17/2015] [Indexed: 12/25/2022] Open
Abstract
Quantitative RT-PCR is often used as a research tool directed at gene transcription. Selection of optimal housekeeping genes (HKGs) as reference genes is critical to establishing sensitive and reproducible qRT-PCR-based assays. The current study was designed to identify the appropriate reference genes in blood leukocytes of bottlenose dolphins (Tursiops truncatus) for gene transcription research. Seventy-five blood samples collected from 7 bottlenose dolphins were used to analyze 15 candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ, LDHA, SDHA). HKG stability in qRT-PCR was determined using geNorm, NormFinder, BestKeeper and comparative delta Ct algorithms. Utilization of RefFinder, which combined all 4 algorithms, suggested that PGK1, HPRT1 and RPL4 were the most stable HKGs in bottlenose dolphin blood. Gene transcription perturbations in blood can serve as an indication of health status in cetaceans as it occurs prior to alterations in hematology and chemistry. This study identified HKGs that could be used in gene transcript studies, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans.
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34
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Balzano F, Deiana M, Dei Giudici S, Oggiano A, Baralla A, Pasella S, Mannu A, Pescatori M, Porcu B, Fanciulli G, Zinellu A, Carru C, Deiana L. miRNA Stability in Frozen Plasma Samples. Molecules 2015; 20:19030-40. [PMID: 26492230 PMCID: PMC6331950 DOI: 10.3390/molecules201019030] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) represent a family of small non-coding ribonucleic acids that post-transcriptionally inhibits the expression of their target messenger RNAs (mRNAs), thereby acting as general gene repressors. In this study we examined the relative quantity and stability of miRNA subjected to a long period of freezing; we compared the stability of eight miRNAs in the plasma of five human healthy controls before freezing and after six and 12 months of storage at −80 °C. In addition, we examined the plasma frozen for 14 years and the amount of miRNA still available. Using a Life Technologies protocol to amplify and quantify plasma miRNAs from EDTA (Ethylene Diamine Tetraacetic Acid)-treated blood, we analyzed the stability of eight miRNAs, (miR-125b-5p, miR-425-5p, miR-200b-5p, miR-200c-3p, miR-579-3p, miR-212-3p, miR-126-3p, and miR-21-5p). The miRNAs analyzed showed a high stability and long frozen half-life.
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Affiliation(s)
- Francesca Balzano
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Marta Deiana
- Associazione "L'Isola dei Centenari", Via Milano 4, Sassari 07100, Italy.
| | - Silvia Dei Giudici
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Vienna 2, Sassari 07100, Italy.
| | - Annalisa Oggiano
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Vienna 2, Sassari 07100, Italy.
| | - Angela Baralla
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Sara Pasella
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Andrea Mannu
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Mario Pescatori
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Baingio Porcu
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Giuseppe Fanciulli
- Department of Clinical and Experimental Medicine, University of Sassari, vl. San Pietro 8, Sassari 07100, Italy.
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
| | - Luca Deiana
- Department of Biomedical Sciences, University of Sassari, vl. San Pietro 43b, Sassari 07100, Italy.
- Associazione "L'Isola dei Centenari", Via Milano 4, Sassari 07100, Italy.
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Maceda-Veiga A, Figuerola J, Martínez-Silvestre A, Viscor G, Ferrari N, Pacheco M. Inside the Redbox: applications of haematology in wildlife monitoring and ecosystem health assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 514:322-332. [PMID: 25668285 DOI: 10.1016/j.scitotenv.2015.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 06/04/2023]
Abstract
Blood analyses have great potential in studies of ecology, ecotoxicology and veterinary science in wild vertebrates based on advances in human and domestic animal medicine. The major caveat for field researchers, however, is that the 'rules' for human or domestic animal haematology do not always apply to wildlife. The present overview shows the strengths and limitations of blood analyses in wild vertebrates, and proposes a standardisation of pre-analytical procedures plus some suggestions for a more systematic examination of blood smears to increase the diagnostic value of blood data. By discussing the common problems that field researchers face with blood variables, we also aim to highlight common ground enabling new researchers in the field to accurately collect blood samples and interpret and place their haematological findings into the overall picture of an ecological or eco-toxicological study. Besides showing the practicality and ecological relevance of simple blood variables, this study illustrates the suitability of blood samples for the application of cutting-edge analytical procedures for expanding the current repertoire of diagnostic tools in wildlife monitoring and ecosystem health assessment.
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Affiliation(s)
- Alberto Maceda-Veiga
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Institute of Research in Biodiversity (IRBio), Facultat de Biologia, Universitat de Barcelona, ES-08028 Barcelona, Spain.
| | - Jordi Figuerola
- Department of Wetland Ecology, Estación Biológica de Doñana-CSIC, ES-41092 Sevilla, Spain
| | | | - Ginés Viscor
- Department of Animal Physiology (Biology), Universitat de Barcelona, ES-08028 Barcelona, Spain
| | - Nicola Ferrari
- Department of Veterinary Sciences and Public Health, Università degli Studi di Milano, IT-16 20133 Milan, Italy
| | - Mário Pacheco
- Department of Biology, Centre for Environmental and Marine Studies-CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Sutton PA, Jones RP, Morrison F, Goldring CE, Park BK, Palmer DH, Malik HZ, Vimalachandran D, Kitteringham NR. Evaluation of a novel tissue stabilization gel to facilitate clinical sampling for translational research in surgical trials. Br J Surg 2015; 102:e124-32. [DOI: 10.1002/bjs.9678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/20/2014] [Accepted: 09/19/2014] [Indexed: 12/19/2022]
Abstract
Abstract
Background
The aim was to establish the feasibility of using a tissue stabilization gel (Allprotect™) as an alternative to liquid nitrogen to facilitate collection of clinical samples for translational research.
Methods
Tumour samples from patients undergoing surgery for primary or metastatic colorectal cancer were either snap-frozen in liquid nitrogen or stored in Allprotect™ under a number of different conditions. Sample integrity was compared across different storage conditions by assessing biomolecule stability and function. DNA quality was assessed spectrophotometrically and by KRas genotyping by pyrosequencing. Total RNA retrieval was determined by nanodrop indices/RNA integrity numbers, and quality assessed by reverse transcription–PCR for two representative genes (high-mobility group box 1, HMGB1; carboxylesterase 1, CES1) and two microRNAs (miR122 and let7d). Western blot analysis of HMGB1 and CES1 was used to confirm protein expression, and the metabolic conversion of irinotecan to its active metabolite, SN-38, was used to assess function.
Results
Under short-term storage conditions (up to 1 week) there was no apparent difference in quality between samples stored in Allprotect™ and those snap-frozen in liquid nitrogen. Some RNA degradation became apparent in tissue archived in Allprotect™ after 1 week, and protein degradation after 2 weeks.
Conclusion
In hospitals that do not have access to liquid nitrogen and –80°C freezers, Allprotect™ provides a suitable alternative for the acquisition and stabilization of clinical samples. Storage proved satisfactory for up to 1 week, allowing transfer of samples without the need for specialized facilities. Surgical relevanceAccess to clinical material is a fundamental component of translational research that requires significant infrastructure (research personnel, liquid nitrogen, specialized storage facilities). The aim was to evaluate a new-to-market tissue stabilization gel (Allprotect™), which offers a simple solution to tissue preservation without the need for complex infrastructure.Allprotect™ offers comparable DNA, RNA and protein stabilization to tissue snap-frozen in liquid nitrogen for up to 1 week. Degradation of biomolecules beyond this highlights its role as a short-term tissue preservative.Allprotect™ has the potential to increase surgeon participation in translational research and surgical trials requiring tissue collection.
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Affiliation(s)
- P A Sutton
- Cancer Research UK Centre, UK
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
- Countess of Chester Hospital NHS Foundation Trust, Chester, UK
| | - R P Jones
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
- Liverpool Hepatobiliary Unit, University Hospitals Aintree, Liverpool, UK
| | - F Morrison
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - C E Goldring
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - B K Park
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - D H Palmer
- Cancer Research UK Centre, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Wirral, UK
| | - H Z Malik
- Liverpool Hepatobiliary Unit, University Hospitals Aintree, Liverpool, UK
| | | | - N R Kitteringham
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
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Iacoviello L, De Curtis A, Donati MB, de Gaetano G. Biobanks for cardiovascular epidemiology and prevention. Future Cardiol 2015; 10:243-54. [PMID: 24762252 DOI: 10.2217/fca.13.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Biobanks for medical research are organized collections of biological samples associated with personal data and information on their donors, to be stored for an indefinite period of time. The storage of biological samples has varied considerably over time, ranging from the informal storage of tissue specimens in a researcher's freezer in the past, to the present well-structured formal repositories. Large-scale population-related biobanks are being set up in several countries and will allow not only research into individual diseases, but also approaches to a wide range of health-related issues, such as physical activity, eating, drinking, education and pollution, among others. The purpose of this article is to discuss how biobanks have improved research in cardiovascular disease epidemiology and prevention, by describing the most relevant population-based epidemiological studies that used set-up biobanks and stored samples for research. The selection of epidemiological studies and biobanks was based on their dimensions and their contribution to the field.
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Affiliation(s)
- Licia Iacoviello
- Unit of Molecular & Nutritional Epidemiology, Department of Epidemiology & Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
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Weber DG, Casjens S, Johnen G, Bryk O, Raiko I, Pesch B, Kollmeier J, Bauer TT, Brüning T. Combination of MiR-103a-3p and mesothelin improves the biomarker performance of malignant mesothelioma diagnosis. PLoS One 2014; 9:e114483. [PMID: 25469901 PMCID: PMC4255020 DOI: 10.1371/journal.pone.0114483] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/10/2014] [Indexed: 12/29/2022] Open
Abstract
Background For the detection of malignant mesothelioma no single biomarker with reasonable sensitivity and specificity has been described so far. Mesothelin, the most prominent blood-based biomarker, is characterized by high specificity but low sensitivity. It might be reasonable to combine biomarkers of different molecular classes in order to improve the overall performance. The aim of this study was to assess the performance of the combination of mesothelin and miR-103a-3p as blood-based biomarker for mesothelioma. Methods/Principal Findings Mesothelin concentration in plasma and miR-103a-3p levels in the cellular blood fraction were analyzed in 43 male mesothelioma patients and 52 male controls formerly exposed to asbestos. For the discrimination of epithelioid and biphasic mesothelioma from asbestos-exposed controls mesothelin and miR-103a-3p showed 74% and 89% sensitivity and 85% and 63% specificity, respectively. For the combination of mesothelin and miR-103a-3p a sensitivity of 95% and a specificity of 81% were calculated. Conclusions/Significance The results of this study show that the combination of mesothelin and miR-103a-3p improves the diagnostic performance of individual blood-based biomarker to detect malignant mesothelioma. The obtained results indicate that the use of biomarkers of different molecular classes might be a reasonable approach to assemble a biomarker panel.
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Affiliation(s)
- Daniel G. Weber
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
- * E-mail:
| | - Swaantje Casjens
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Georg Johnen
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Oleksandr Bryk
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Irina Raiko
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Beate Pesch
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Jens Kollmeier
- HELIOS Clinic Emil von Behring, Respiratory Disease Clinic Heckeshorn, Berlin, Germany
| | - Torsten T. Bauer
- HELIOS Clinic Emil von Behring, Respiratory Disease Clinic Heckeshorn, Berlin, Germany
| | - Thomas Brüning
- Center of Molecular Medicine, Institute of Prevention and Occupational Medicine of the German Social Accident Insurance - Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
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Nair VS, Pritchard CC, Tewari M, Ioannidis JPA. Design and Analysis for Studying microRNAs in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol 2014; 180:140-52. [PMID: 24966218 PMCID: PMC4082346 DOI: 10.1093/aje/kwu135] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/30/2014] [Indexed: 12/18/2022] Open
Abstract
microRNAs (miRNAs) are fundamental to cellular biology. Although only approximately 22 bases long, miRNAs regulate complex processes in health and disease, including human cancer. Because miRNAs are highly stable in circulation when compared with several other classes of nucleic acids, they have generated intense interest as clinical biomarkers in diverse epidemiologic studies. As with other molecular biomarker fields, however, miRNA research has become beleaguered by pitfalls related to terminology and classification; procedural, assay, and study cohort heterogeneity; and methodological inconsistencies. Together, these issues have led to both false-positive and potentially false-negative miRNA associations. In this review, we summarize the biological rationale for studying miRNAs in human disease with a specific focus on circulating miRNAs, which highlight some of the most challenging topics in the field to date. Examples from lung cancer are used to illustrate the potential utility and some of the pitfalls in contemporary miRNA research. Although the field is in its infancy, several important lessons have been learned relating to cohort development, sample preparation, and statistical analysis that should be considered for future studies. The goal of this primer is to equip epidemiologists and clinical researchers with sound principles of study design and analysis when using miRNAs.
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Affiliation(s)
| | | | | | - John P. A. Ioannidis
- Correspondence to Dr. John P. A. Ioannidis, Stanford University School of Medicine, Stanford Prevention Research Center, 1265 Welch Road, MSOB X306, Stanford, CA 94305 ()
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Tao H, Beineke P, Li B, Alberts W, Rosenberg S, Kvam E, Wingrove JA. Evaluation of a solid matrix for collection and ambient storage of RNA from whole blood. BMC Clin Pathol 2014; 14:22. [PMID: 24855452 PMCID: PMC4030268 DOI: 10.1186/1472-6890-14-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 04/22/2014] [Indexed: 12/04/2022] Open
Abstract
Background Whole blood gene expression-based molecular diagnostic tests are becoming increasingly available. Conventional tube-based methods for obtaining RNA from whole blood can be limited by phlebotomy, volume requirements, and RNA stability during transport and storage. A dried blood spot matrix for collecting high-quality RNA, called RNA Stabilizing Matrix (RSM), was evaluated against PAXgene® blood collection tubes. Methods Whole blood was collected from 25 individuals and subjected to 3 sample storage conditions: 18 hours at either room temperature (baseline arm) or 37°C, and 6 days at room temperature. RNA was extracted and assessed for integrity by Agilent Bioanalyzer, and gene expression was compared by RT-qPCR across 23 mRNAs comprising a clinical test for obstructive coronary artery disease. Results RSM produced RNA of relatively high integrity across the various tested conditions (mean RIN ± 95% CI: baseline arm, 6.92 ± 0.24; 37°C arm, 5.98 ± 0.48; 6-day arm, 6.72 ± 0.23). PAXgene samples showed comparable RNA integrity in both baseline and 37°C arms (8.42 ± 0.17; 7.92 ± 0.1 respectively) however significant degradation was observed in the 6-day arm (3.19 ± 1.32). Gene expression scores on RSM were highly correlated between the baseline and 37°C and 6-day study arms (median r = 0.96, 0.95 respectively), as was the correlation to PAXgene tubes (median r = 0.95, p < 0.001). Conclusion RNA obtained from RSM shows little degradation and comparable RT-qPCR performance to PAXgene RNA for the 23 genes analyzed. Further development of this technology may provide a convenient method for collecting, shipping, and storing RNA for gene expression assays.
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Affiliation(s)
- Heng Tao
- CardioDx, Inc., 2500 Faber Place, Palo Alto, CA 94303, USA
| | - Philip Beineke
- CardioDx, Inc., 2500 Faber Place, Palo Alto, CA 94303, USA
| | - Bing Li
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
| | - William Alberts
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
| | | | - Erik Kvam
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
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Vordenbäumen S, Bleck E, Brinks R, Schneider M. Assessment of magnetic bead-based automated whole blood RNA-isolation from a validated RNA stabilization reagent (Tempus Blood RNA). J Immunol Methods 2014; 406:148-9. [DOI: 10.1016/j.jim.2014.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 11/29/2022]
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Abstract
BACKGROUND The recent revolutionary advances made in genome-wide sequencing technology have transformed biology and molecular diagnostics, allowing new sRNA (small RNA) classes to be discovered as potential disease-specific biological indicators. Cell-free microRNAs (miRNAs) have been shown to exist stably in a wide spectrum of body fluids and their expression profiles have been shown to reflect an assortment of physiological conditions, underscoring the utility of this new class of molecules to function as noninvasive biomarkers of disease. CONTENT We summarize information on the known mechanisms of miRNA protection and release into extracellular space and compile the current literature on extracellular miRNAs that have been investigated as biomarkers of 20 different cancers, 11 organ damage conditions and 10 diverse disease states. We also discuss the various strategies involved in the miRNA biomarker discovery workflow and provide a critical opinion on the impediments faced by this advancing field that need to be overcome in the laboratory. SUMMARY The field of miRNA-centered diagnostics is still in its infancy, and basic questions with regard to the exact role of miRNAs in the pathophysiology of diseases, and the mechanisms of their release from affected cells into biological fluids are yet to be completely understood. Nevertheless, these noninvasive micromarkers have immense potential in translational medicine not only for use in monitoring the efficacy and safety of therapeutic regimens but also to guide the diagnosis of diseases, to determine the risk of developing diseases or conditions, and more importantly, to inform treatment options.
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Affiliation(s)
- Janani Saikumar
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, and Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Krithika Ramachandran
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, and Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Vishal S Vaidya
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, and Department of Environmental Health, Harvard School of Public Health, Boston, MA.
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Kirwin SM, Manolakos A, Barnett SS, Gonzalez IL. Tafazzin splice variants and mutations in Barth syndrome. Mol Genet Metab 2014; 111:26-32. [PMID: 24342716 DOI: 10.1016/j.ymgme.2013.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/12/2013] [Accepted: 11/12/2013] [Indexed: 11/23/2022]
Abstract
Barth syndrome is caused by mutations in the TAZ (tafazzin) gene on human chromosome Xq28. The human tafazzin gene produces four major mRNA splice variants; two of which have been shown to be functional (TAZ lacking exon 5 and full-length) in complementation studies with yeast and Drosophila. This study characterizes the multiple alternative splice variants of TAZ mRNA and their proportions in blood samples from a cohort of individuals with Barth syndrome (BTHS). Because it has been reported that collection and processing methods can affect the expression of various genes, we tested and chose a stabilizing medium for collecting, shipping and processing of the blood samples of these individuals. In both healthy controls and in BTHS individuals, we found a greater variety of alternatively spliced forms than previously described, with a sizeable proportion of minor splice variants besides the four dominant isoforms. Individuals with certain exonic and intronic splice mutations produce additional mutant mRNAs that could be translated into two or more proteins with different amino acid substitutions in a single individual. A fraction of the minor splice variants is predicted to be non-productive.
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Affiliation(s)
- Susan M Kirwin
- Molecular Diagnostics Laboratory, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA.
| | - Athena Manolakos
- Molecular Diagnostics Laboratory, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Sarah Swain Barnett
- Molecular Diagnostics Laboratory, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Iris L Gonzalez
- Molecular Diagnostics Laboratory, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
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Weber DG, Johnen G, Casjens S, Bryk O, Pesch B, Jöckel KH, Kollmeier J, Brüning T. Evaluation of long noncoding RNA MALAT1 as a candidate blood-based biomarker for the diagnosis of non-small cell lung cancer. BMC Res Notes 2013; 6:518. [PMID: 24313945 PMCID: PMC4029199 DOI: 10.1186/1756-0500-6-518] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is described as a potential biomarker for NSCLC (non-small cell lung cancer). Diagnostic biomarkers need to be detectable in easily accessible body fluids, should be characterized by high specificity, sufficient sensitivity, and robustness against influencing factors. The aim of this study was to evaluate the performance of MALAT1 as a blood based biomarker for NSCLC. RESULTS MALAT1 was shown to be detectable in the cellular fraction of peripheral human blood, showing different expression levels between cancer patients and cancer-free controls. For the discrimination of NSCLC patients from cancer-free controls a sensitivity of 56% was calculated conditional on a high specificity of 96%. No impact of tumor stage, age, gender, and smoking status on MALAT1 levels could be observed, but results based on small numbers. CONCLUSIONS The results of this study indicate that MALAT1 complies with key characteristics of diagnostic biomarkers, i.e., minimal invasiveness, high specificity, and robustness. Due to its relatively low sensitivity MALAT1 might not be feasible as a single biomarker for the diagnosis of NSCLC in the cellular fraction of blood. Alternatively, MALAT1 might be applicable as a complementary biomarker within a panel in order to improve the entire diagnostic performance.
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Affiliation(s)
- Daniel Gilbert Weber
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum (IPA), Bürkle-de-la-Camp-Platz 1, 44789 Bochum, Germany.
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Zhu S, Cao L, Zhu J, Kong L, Jin J, Qian L, Zhu C, Hu X, Li M, Guo X, Han S, Yu Z. Identification of maternal serum microRNAs as novel non-invasive biomarkers for prenatal detection of fetal congenital heart defects. Clin Chim Acta 2013; 424:66-72. [DOI: 10.1016/j.cca.2013.05.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
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McHale CM, Zhang L, Thomas R, Smith MT. Analysis of the transcriptome in molecular epidemiology studies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:500-517. [PMID: 23907930 PMCID: PMC5142298 DOI: 10.1002/em.21798] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/07/2013] [Accepted: 06/08/2013] [Indexed: 05/29/2023]
Abstract
The human transcriptome is complex, comprising multiple transcript types, mostly in the form of non-coding RNA (ncRNA). The majority of ncRNA is of the long form (lncRNA, ≥ 200 bp), which plays an important role in gene regulation through multiple mechanisms including epigenetics, chromatin modification, control of transcription factor binding, and regulation of alternative splicing. Both mRNA and ncRNA exhibit additional variability in the form of alternative splicing and RNA editing. All aspects of the human transcriptome can potentially be dysregulated by environmental exposures. Next-generation RNA sequencing (RNA-Seq) is the best available methodology to measure this although it has limitations, including experimental bias. The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental and bioinformatic methodologies. A limited number of toxicogenomic studies have been conducted to date using RNA-Seq. This review describes the complexity of the human transcriptome, the application of transcriptomics by RNA-Seq or microarray in molecular epidemiology studies, and limitations of these approaches including the type of cell or tissue analyzed, experimental variation, and confounding. By using good study designs with precise, individual exposure measurements, sufficient power and incorporation of phenotypic anchors, studies in human populations can identify biomarkers of exposure and/or early effect and elucidate mechanisms of action underlying associated diseases, even at low doses. Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum.
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Affiliation(s)
- Cliona M McHale
- Division of Environmental Health Sciences, Genes and Environment Laboratory, School of Public Health, University of California, Berkeley, California 94720, USA.
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Xu L, Yang BF, Ai J. MicroRNA transport: a new way in cell communication. J Cell Physiol 2013; 228:1713-9. [PMID: 23460497 DOI: 10.1002/jcp.24344] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/04/2013] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) can efficiently regulate gene expression by targeting mRNA to cause mRNA cleavage or translational repression. Growing evidence indicates that miRNAs exist not only in cells but also in a variety of body fluids, which stimulates substantial interest in the transport mechanism and regulating process of extracellular miRNAs. This article reviews the basic biogenesis of miRNAs in detail to explore the origin of extracellular miRNAs. Different miRNA transporters have been summarized (e.g., exosomes, microvesicles, apoptosis bodies, and RNA-binding proteins). In addition, we discuss the regulators affecting miRNA transport (e.g., ATP and ceramide) and the selection mechanism for different miRNA transporters. Studies about miRNA transporters and the transport mechanism are new and developing. With the progress of the research, new functions of extracellular miRNAs may be uncovered in the future.
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Affiliation(s)
- Ling Xu
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, Heilongjiang Province, China
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Pérez-Portela R, Riesgo A. Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing. Mol Ecol Resour 2013; 13:884-9. [PMID: 23683108 DOI: 10.1111/1755-0998.12122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/02/2013] [Accepted: 04/23/2013] [Indexed: 11/26/2022]
Abstract
Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high-quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash-frozen and stored at -80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at -80 °C, RNAlater and storage at -20 °C, preservation in TRIzol reagent and storage at -80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips.
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Affiliation(s)
- Rocío Pérez-Portela
- Center for Advanced Studies of Blanes (CEAB-CSIC), Acces a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain.
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Duale N, Brunborg G, Rønningen KS, Briese T, Aarem J, Aas KK, Magnus P, Stoltenberg C, Susser E, Lipkin WI. Human blood RNA stabilization in samples collected and transported for a large biobank. BMC Res Notes 2012; 5:510. [PMID: 22988904 PMCID: PMC3503553 DOI: 10.1186/1756-0500-5-510] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/13/2012] [Indexed: 11/17/2022] Open
Abstract
Background The Norwegian Mother and Child Cohort Study (MoBa) is a nation-wide population-based pregnancy cohort initiated in 1999, comprising more than 108.000 pregnancies recruited between 1999 and 2008. In this study we evaluated the feasibility of integrating RNA analyses into existing MoBa protocols. We compared two different blood RNA collection tube systems – the PAXgene™ Blood RNA system and the Tempus™ Blood RNA system - and assessed the effects of suboptimal blood volumes in collection tubes and of transportation of blood samples by standard mail. Endpoints to characterize the samples were RNA quality and yield, and the RNA transcript stability of selected genes. Findings High-quality RNA could be extracted from blood samples stabilized with both PAXgene and Tempus tubes. The RNA yields obtained from the blood samples collected in Tempus tubes were consistently higher than from PAXgene tubes. Higher RNA yields were obtained from cord blood (3 – 4 times) compared to adult blood with both types of tubes. Transportation of samples by standard mail had moderate effects on RNA quality and RNA transcript stability; the overall RNA quality of the transported samples was high. Some unexplained changes in gene expression were noted, which seemed to correlate with suboptimal blood volumes collected in the tubes. Temperature variations during transportation may also be of some importance. Conclusions Our results strongly suggest that special collection tubes are necessary for RNA stabilization and they should be used for establishing new biobanks. We also show that the 50,000 samples collected in the MoBa biobank provide RNA of high quality and in sufficient amounts to allow gene expression analyses for studying the association of disease with altered patterns of gene expression.
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Affiliation(s)
- Nur Duale
- The Norwegian Institute of Public Health, Oslo, Norway.
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Performance of survivin mRNA as a biomarker for bladder cancer in the prospective study UroScreen. PLoS One 2012; 7:e35363. [PMID: 22530010 PMCID: PMC3328337 DOI: 10.1371/journal.pone.0035363] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/14/2012] [Indexed: 12/18/2022] Open
Abstract
Background Urinary biomarkers have the potential to improve the early detection of bladder cancer. Most of the various known markers, however, have only been evaluated in studies with cross-sectional design. For proper validation a longitudinal design would be preferable. We used the prospective study UroScreen to evaluate survivin, a potential biomarker that has multiple functions in carcinogenesis. Methods/Results Survivin was analyzed in 5,716 urine samples from 1,540 chemical workers previously exposed to aromatic amines. The workers participated in a surveillance program with yearly examinations between 2003 and 2010. RNA was extracted from urinary cells and survivin was determined by Real-Time PCR. During the study, 19 bladder tumors were detected. Multivariate generalized estimation equation (GEE) models showed that β-actin, representing RNA yield and quality, had the strongest influence on survivin positivity. Inflammation, hematuria and smoking did not confound the results. Survivin had a sensitivity of 21.1% for all and 36.4% for high-grade tumors. Specificity was 97.5%, the positive predictive value (PPV) 9.5%, and the negative predictive value (NPV) 99.0%. Conclusions In this prospective and so far largest study on survivin, the marker showed a good NPV and specificity but a low PPV and sensitivity. This was partly due to the low number of cases, which limits the validity of the results. Compliance, urine quality, problems with the assay, and mRNA stability influenced the performance of survivin. However, most issues could be addressed with a more reliable assay in the future. One important finding is that survivin was not influenced by confounders like inflammation and exhibited a relatively low number of false-positives. Therefore, despite the low sensitivity, survivin may still be considered as a component of a multimarker panel.
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