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Chen Q, Guo X, Wang H, Sun S, Jiang H, Zhang P, Shang E, Zhang R, Cao Z, Niu Q, Zhang C, Liu Y, Shi L, Yu Y, Hou W, Zheng Y. Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:109-124. [PMID: 38884056 PMCID: PMC11169349 DOI: 10.1007/s43657-023-00121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 06/18/2024]
Abstract
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00121-1.
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Affiliation(s)
- Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Xiaorou Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Shanyue Sun
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, 250021 China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Quanne Niu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Chao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
- The International Human Phenome Institutes, Shanghai, 200438 China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
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Romanyuk SA, Popov OS, Sushentseva NN, Apalko SV, Polkovnikova IA, Shcherbak SG. Optimization of RNA storage in a biobank, as well as methods for manual and automated isolation of RNA from whole blood and leukocyte fraction. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aim. To optimize the technique for the isolation and storage of ribonucleic acid (RNA) from whole blood and leukocyte fraction.Materials and methods. Comparison of isolation quality was carried out for RNA samples obtained from 228 leukocyte samples and 198 whole blood samples. Isolation was performed from fresh and frozen samples using ExtractRNA™ reagent and a MagNA Pure Compact automated system. Various methods of removing erythrocytes (centrifugation and treatment with hemolytic agents from two manufacturers) were tested, as well as freezing with and without preservatives for subsequent RNA isolation.Results. Twenty-one combinations of conditions were tested. The highest quality RNA was isolated by manual extraction using the ExtractRNA™ reagent from a fresh leukocyte fraction, purified by the Amplisens hemolytic agent (successful extraction — 94%, median RIN=8,4); frozen in IntactRNA™, purified by leukocyte fraction centrifugation (successful extraction — 100%, median RIN=8); frozen in ExtractRNA™, purified by leukocyte fraction centrifugation (successful extraction — 100%, median RIN=9,3).Conclusion. RNA can be isolated from frozen blood fractions, which is not inferior in quality to that isolated from fresh samples. Thus, it is not necessary to isolate RNA immediately after the receipt of biological material.
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Guo D, Wang A, Xie T, Zhang S, Cao D, Sun J. Effects of ex vivo ischemia time and delayed processing on quality of specimens in tissue biobank. Mol Med Rep 2020; 22:4278-4288. [PMID: 33000275 PMCID: PMC7533433 DOI: 10.3892/mmr.2020.11503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA quality of tissue biobank is crucial for translational research; however, the effects of the ex vivo ischemia time on RNA integrity and expression of genes related to hypoxia, stress, apoptosis and autophagy remains elusive. A total of 18 carcinoma tissues were stored at room temperature for 15 min, 30 min, 1, 2, 4, 8 and 24 h. The integrity and purity of isolated RNA were analyzed. Furthermore, the gene expression of mTOR, hypoxia-inducible factor 1α, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit β isoform (PI3KCB), threonine kinase 1 (AKT1), NF-κB, protein kinase AMP-activated catalytic subunit α1 (AMPKα1), caspase 8 (CASP8), unc-51 like autophagy activating kinase 1 and Fas cell surface death receptor were analyzed using reverse transcription-quantitative PCR. The results demonstrated that RNA integrity numbers (RINs) remained stable in carcinoma tissues following ex vivo ischemia for 2 h at room temperature and that degradation began at 4 h (P<0.001). Additionally, the expression of PI3KCB, AKT1, AMPKα1 and CASP8 decreased at time points 8–24 h following ex vivo ischemia and delayed processing (P<0.001). In conclusion, >2 h of ex vivo ischemia and delayed processing induced RNA degradation and a decrease in RIN, and the gene expressions of PI3KCB, AKT1, AMPKα1 and CASP8 may be considered as markers to evaluate tissue quality at the gene expression level, providing a method for the standard processing and assessment of tissue specimen.
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Affiliation(s)
- Dan Guo
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Anqi Wang
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Ting Xie
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Sumei Zhang
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Dingyan Cao
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Jian Sun
- Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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5
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Comparison of three different pretreatment methods for blood RNA extraction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Tang R, She Q, Lu Y, Yin R, Zhu P, Zhu L, Zhou M, Zheng C. Quality Control of RNA Extracted from PAXgene Blood RNA Tubes After Different Storage Periods. Biopreserv Biobank 2019; 17:477-482. [PMID: 31343263 DOI: 10.1089/bio.2019.0029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qinying She
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minlin Zhou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Li S, Lu X, Feng JB, Tian M, Wang J, Chen H, Chen DQ, Liu QJ. Developing Gender-Specific Gene Expression Biodosimetry Using a Panel of Radiation-Responsive Genes for Determining Radiation Dose in Human Peripheral Blood. Radiat Res 2019; 192:399-409. [DOI: 10.1667/rr15355.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shuang Li
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
| | - Xue Lu
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
| | - Jiang-Bin Feng
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
| | - Mei Tian
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
| | - Jun Wang
- Department of Hematopoietic Stem Cell Transplantation, 307 Hospital of Chinese People's Liberation Army, Beijing, 100071, China
| | - Hu Chen
- Department of Hematopoietic Stem Cell Transplantation, 307 Hospital of Chinese People's Liberation Army, Beijing, 100071, China
| | - De-Qing Chen
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
| | - Qing-Jie Liu
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing 100088, China
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8
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Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J. The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time. Trends Biotechnol 2019; 37:761-774. [PMID: 30654913 DOI: 10.1016/j.tibtech.2018.12.002] [Citation(s) in RCA: 378] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/20/2022]
Abstract
Quantitative PCR (qPCR) is one of the most common techniques for quantification of nucleic acid molecules in biological and environmental samples. Although the methodology is perceived to be relatively simple, there are a number of steps and reagents that require optimization and validation to ensure reproducible data that accurately reflect the biological question(s) being posed. This review article describes and illustrates the critical pitfalls and sources of error in qPCR experiments, along with a rigorous, stepwise process to minimize variability, time, and cost in generating reproducible, publication quality data every time. Finally, an approach to make an informed choice between qPCR and digital PCR technologies is described.
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Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada.
| | - Katia Nadeau
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Meysam Abbasi
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Claude Lachance
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Marie Nguyen
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
| | - Joshua Fenrich
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
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9
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Choi H, Gim J, Won S, Kim YJ, Kwon S, Park C. Network analysis for count data with excess zeros. BMC Genet 2017; 18:93. [PMID: 29110633 PMCID: PMC5674822 DOI: 10.1186/s12863-017-0561-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand complex interactions between genes in biological processes of a cell. Local Poisson models seem to be promising in modeling positive as well as negative dependencies for count data. Furthermore, when zero counts are more frequent than are expected, excess zeros should be considered in the model. METHODS We present a penalized Poisson graphical model for zero inflated count data and derive an expectation-maximization (EM) algorithm built on coordinate descent. Our method is shown to be effective through simulated and real data analysis. RESULTS Results from the simulated data indicate that our method outperforms the local Poisson graphical model in the presence of excess zeros. In an application to a RNA sequencing data, we also investigate the gender effect by comparing the estimated networks according to different genders. Our method may help us in identifying biological pathways linked to sex hormone regulation and thus understanding underlying mechanisms of the gender differences. CONCLUSIONS We have presented a penalized version of zero inflated spatial Poisson regression and derive an efficient EM algorithm built on coordinate descent. We discuss possible improvements of our method as well as potential research directions associated with our findings from the RNA sequencing data.
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Affiliation(s)
- Hosik Choi
- Department of Applied Statistics, Kyonggi University, Suwon, 16227 Korea
| | - Jungsoo Gim
- Institute of Health and Environment, Seoul National University, Seoul, 08826 Korea
| | - Sungho Won
- Graduate School of Public Health, Seoul National University, 08826Seoul, Korea
| | - You Jin Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, 03760 Korea
| | - Sunghoon Kwon
- Department of Applied Statistics, Konkuk University, Seoul, 05029 Korea
| | - Changyi Park
- Department of Statistics, University of Seoul, Seoul, 02504 Korea
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10
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The Correlation-Base-Selection Algorithm for Diagnostic Schizophrenia Based on Blood-Based Gene Expression Signatures. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7860506. [PMID: 28280741 PMCID: PMC5322573 DOI: 10.1155/2017/7860506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022]
Abstract
Microarray analysis of gene expression is often used to diagnose different types of disease. Many studies report remarkable achievements in nervous system disease. Clinical diagnosis of schizophrenia (SCZ) still depends on doctors' experience, which is unreliable and needs to be more objective and quantified. To solve this problem, we collected whole blood gene expression data from four studies, including 152 individuals with schizophrenia (SCZ) and 138 normal controls in different regions. The correlation-based feature selection (CFS, one of the machine learning methods) algorithm was applied in this study, and 103 significantly differentially expressed genes between patients and controls, called “feature genes,” were selected; then, a model for SCZ diagnosis was built. The samples were subdivided into 10 groups, and cross-validation showed that the model we constructed achieved nearly 100% classification accuracy. Mathematical evaluation of the datasets before and after data processing proved the effectiveness of our algorithm. Feature genes were enriched in Parkinson's disease, oxidative phosphorylation, and TGF-beta signaling pathways, which were previously reported to be associated with SCZ. These results suggest that the analysis of gene expression in whole blood by our model could be a useful tool for diagnosing SCZ.
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11
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Manning G, Macaeva E, Majewski M, Kriehuber R, Brzóska K, Abend M, Doucha-Senf S, Oskamp D, Strunz S, Quintens R, Port M, Badie C. Comparable dose estimates of blinded whole blood samples are obtained independently of culture conditions and analytical approaches. Second RENEB gene expression study. Int J Radiat Biol 2016; 93:87-98. [DOI: 10.1080/09553002.2016.1227105] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Grainne Manning
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, UK
| | - Ellina Macaeva
- Radiobiology Unit, Institute Environment, Health and Safety, Belgian Nuclear Research Centre, Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | | | - Ralf Kriehuber
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich GmbH, Germany
| | - Kamil Brzóska
- Institute of Nuclear Chemistry and Technology, Centre for Radiobiology and Biological Dosimetry, Warsaw, Poland
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | | | - Dominik Oskamp
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich GmbH, Germany
| | - Sonja Strunz
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Institute Environment, Health and Safety, Belgian Nuclear Research Centre, Mol, Belgium
| | - Matthias Port
- Radiobiology Unit, Institute Environment, Health and Safety, Belgian Nuclear Research Centre, Mol, Belgium
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, UK
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12
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Kwarteng A, Ahuno ST. The Potentials and Pitfalls of Microarrays in Neglected Tropical Diseases: A Focus on Human Filarial Infections. MICROARRAYS 2016; 5:microarrays5030020. [PMID: 27600086 PMCID: PMC5040967 DOI: 10.3390/microarrays5030020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 12/01/2022]
Abstract
Data obtained from expression microarrays enables deeper understanding of the molecular signatures of infectious diseases. It provides rapid and accurate information on how infections affect the clustering of gene expression profiles, pathways and networks that are transcriptionally active during various infection states compared to conventional diagnostic methods, which primarily focus on single genes or proteins. Thus, microarray technologies offer advantages in understanding host-parasite interactions associated with filarial infections. More importantly, the use of these technologies can aid diagnostics and helps translate current genomic research into effective treatment and interventions for filarial infections. Studying immune responses via microarray following infection can yield insight into genetic pathways and networks that can have a profound influence on the development of anti-parasitic vaccines.
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Affiliation(s)
- Alexander Kwarteng
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Private Mail Bag, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
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13
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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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Shaughnessy RG, Farrell D, Riepema K, Bakker D, Gordon SV. Analysis of Biobanked Serum from a Mycobacterium avium subsp paratuberculosis Bovine Infection Model Confirms the Remarkable Stability of Circulating miRNA Profiles and Defines a Bovine Serum miRNA Repertoire. PLoS One 2015; 10:e0145089. [PMID: 26675426 PMCID: PMC4682966 DOI: 10.1371/journal.pone.0145089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/26/2015] [Indexed: 12/17/2022] Open
Abstract
Johne's Disease (JD) is a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current disease control strategies are hampered by the lack of sensitive and specific diagnostic modalities. Therefore, novel diagnostic and prognostic tools are needed, and circulating microRNAs (miRNAs) may hold potential in this area. The aims of this study were twofold: (i) to address the stability of miRNA in bovine sera from biobanked samples, and (ii) to assess the potential of miRNAs as biomarkers for JD disease progression. To address these aims we used bovine sera from an experimental MAP infection model that had been stored at -20°C for over a decade, allowing us to also assess the stability of miRNA profiles in biobanked serum samples through comparison with fresh sera. Approximately 100-200 intact miRNAs were identified in each sample with 83 of these being consistently detected across all 57 samples. The miRNA profile of the biobanked sera stored at -20°C for over 10 years was highly similar to the profile of <1 year-old sera stored at -80°C, with an overlap of 73 shared miRNAs. IsomiR analysis also indicated a distinct bovine serum-specific isomiR profile as compared to previously reported bovine macrophage miRNA profiles. To explore the prognostic potential of miRNA profiles cattle defined as seropositive for anti-MAP antibodies (n = 5) were compared against seronegative cattle (n = 7). No significant differential expressed miRNAs were detected at either the early (6 months) or late (43, 46 and 49 months) intervals (FDR≤0.05, fold-change≥1.5) across seropositive or seronegative animals. However, comparing pre-infection sera to the early and late time-points identified increased miR-29a and miR-92b abundance (2-fold) that may be due to blood-cell population changes over time (P<0.001). In conclusion our study has demonstrated that bovine circulating miRNAs retain their integrity under long-term sub-optimal storage temperatures opening the way for increased miRNA analyses from biobanked samples for a range of infectious and non-infectious diseases.
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Affiliation(s)
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
| | - Karel Riepema
- Department of Bacteriology and TSEs, Central Veterinary Institute of Wageningen University, Edelhertweg 15, 8200 AB Lelystad, The Netherlands
| | - Douwe Bakker
- Buitenplaats 116, 8212 AM Lelystad, The Netherlands
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- * E-mail:
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15
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Abstract
CONTEXT Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling. OBJECTIVE To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study. DATA SOURCES We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review. CONCLUSION -Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.
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Affiliation(s)
- Jane H Zhou
- From the Departments of Pathology (Drs Zhou and Sahin) and Head and Neck Surgery (Dr Myers), University of Texas MD Anderson Cancer Center, Houston. Dr Zhou is now with Human Genome Sequencing Center, Baylor College of Medicine, Houston
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16
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Ellervik C, Vaught J. Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking. Clin Chem 2015; 61:914-34. [DOI: 10.1373/clinchem.2014.228783] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Abstract
BACKGROUND
Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized medicine for diagnostic or prognostic purposes.
CONTENT
The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues.
SUMMARY
The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
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Affiliation(s)
- Christina Ellervik
- Department of Research, Nykoebing Falster Hospital, Nykoebing Falster, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA
| | - Jim Vaught
- International Society for Biological and Environmental Repositories, Vancouver, Canada
- Editor-in-Chief, Biopreservation and Biobanking, Vancouver, Canada
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17
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Malentacchi F, Pazzagli M, Simi L, Orlando C, Wyrich R, Günther K, Verderio P, Pizzamiglio S, Ciniselli CM, Zhang H, Korenková V, Rainen L, Bar T, Kubista M, Gelmini S. SPIDIA-RNA: second external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses. PLoS One 2014; 9:e112293. [PMID: 25384019 PMCID: PMC4226503 DOI: 10.1371/journal.pone.0112293] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 10/11/2014] [Indexed: 11/19/2022] Open
Abstract
One purpose of the EC funded project, SPIDIA, is to develop evidence-based quality guidelines for the pre-analytical handling of blood samples for RNA molecular testing. To this end, two pan-European External Quality Assessments (EQAs) were implemented. Here we report the results of the second SPIDIA-RNA EQA. This second study included modifications in the protocol related to the blood collection process, the shipping conditions and pre-analytical specimen handling for participants. Participating laboratories received two identical proficiency blood specimens collected in tubes with or without an RNA stabilizer. For pre-defined specimen storage times and temperatures, laboratories were asked to perform RNA extraction from whole blood according to their usual procedure and to return extracted RNA to the SPIDIA facility for further analysis. These RNA samples were evaluated for purity, yield, integrity, stability, presence of interfering substances, and gene expression levels for the validated markers of RNA stability: FOS, IL1B, IL8, GAPDH, FOSB and TNFRSF10c. Analysis of the gene expression results of FOS, IL8, FOSB, and TNFRSF10c, however, indicated that the levels of these transcripts were significantly affected by blood collection tube type and storage temperature. These results demonstrated that only blood collection tubes containing a cellular RNA stabilizer allowed reliable gene expression analysis within 48 h from blood collection for all the genes investigated. The results of these two EQAs have been proposed for use in the development of a Technical Specification by the European Committee for Standardization.
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Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
- * E-mail:
| | - Mario Pazzagli
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Lisa Simi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Claudio Orlando
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | | | | | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Maura Ciniselli
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Vlasta Korenková
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lynne Rainen
- Becton Dickinson (BD), Franklin Lakes, New Jersey, United States of America
| | - Tzachi Bar
- Labonnet Ltd, St. Ramat-Hasharon, Israel
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- TATAA Biocenter AB, Gothenburg, Sweden
| | - Stefania Gelmini
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
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18
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Franconi F, Rosano G, Campesi I. Need for gender-specific pre-analytical testing: the dark side of the moon in laboratory testing. Int J Cardiol 2014; 179:514-35. [PMID: 25465806 DOI: 10.1016/j.ijcard.2014.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/27/2014] [Accepted: 11/03/2014] [Indexed: 01/16/2023]
Abstract
Many international organisations encourage studies in a sex-gender perspective. However, research with a gender perspective presents a high degree of complexity, and the inclusion of sex-gender variable in experiments presents many methodological questions, the majority of which are still neglected. Overcoming these issues is fundamental to avoid erroneous results. Here, pre-analytical aspects of the research, such as study design, choice of utilised specimens, sample collection and processing, animal models of diseases, and the observer's role, are discussed. Artefacts in this stage of research could affect the predictive value of all analyses. Furthermore, the standardisation of research subjects according to their lifestyles and, if female, to their life phase and menses or oestrous cycle, is urgent to harmonise research worldwide. A sex-gender-specific attention to pre-analytical aspects could produce a decrease in the time for translation from the bench to bedside. Furthermore, sex-gender-specific pre-clinical pharmacological testing will enable adequate assessment of pharmacokinetic and pharmacodynamic actions of drugs and will enable, where appropriate, an adequate gender-specific clinical development plan. Therefore, sex-gender-specific pre-clinical research will increase the gender equity of care and will produce more evidence-based medicine.
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Affiliation(s)
- Flavia Franconi
- Department of Biomedical Sciences, University of Sassari, National Laboratory of Gender Medicine of the National Institute of Biostructures and Biosystems, Osilo, Sassari, Italy; Vicepresident of Basilicata Region.
| | - Giuseppe Rosano
- Cardiovascular and Cell Sciences Research Institute, St George's University of London, United Kingdom
| | - Ilaria Campesi
- Department of Biomedical Sciences, University of Sassari, National Laboratory of Gender Medicine of the National Institute of Biostructures and Biosystems, Osilo, Sassari, Italy
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19
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Zhang H, Korenková V, Sjöback R, Švec D, Björkman J, Kruhøffer M, Verderio P, Pizzamiglio S, Ciniselli CM, Wyrich R, Oelmueller U, Kubista M, Lindahl T, Lönneborg A, Rian E. Biomarkers for monitoring pre-analytical quality variation of mRNA in blood samples. PLoS One 2014; 9:e111644. [PMID: 25369468 PMCID: PMC4219744 DOI: 10.1371/journal.pone.0111644] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 09/24/2014] [Indexed: 12/28/2022] Open
Abstract
There is an increasing need for proper quality control tools in the pre-analytical phase of the molecular diagnostic workflow. The aim of the present study was to identify biomarkers for monitoring pre-analytical mRNA quality variations in two different types of blood collection tubes, K2EDTA (EDTA) tubes and PAXgene Blood RNA Tubes (PAXgene tubes). These tubes are extensively used both in the diagnostic setting as well as for research biobank samples. Blood specimens collected in the two different blood collection tubes were stored for varying times at different temperatures, and microarray analysis was performed on resultant extracted RNA. A large set of potential mRNA quality biomarkers for monitoring post-phlebotomy gene expression changes and mRNA degradation in blood was identified. qPCR assays for the potential biomarkers and a set of relevant reference genes were generated and used to pre-validate a sub-set of the selected biomarkers. The assay precision of the potential qPCR based biomarkers was determined, and a final validation of the selected quality biomarkers using the developed qPCR assays and blood samples from 60 healthy additional subjects was performed. In total, four mRNA quality biomarkers (USP32, LMNA, FOSB, TNRFSF10C) were successfully validated. We suggest here the use of these blood mRNA quality biomarkers for validating an experimental pre-analytical workflow. These biomarkers were further evaluated in the 2nd ring trial of the SPIDIA-RNA Program which demonstrated that these biomarkers can be used as quality control tools for mRNA analyses from blood samples.
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Affiliation(s)
| | - Vlasta Korenková
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - David Švec
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- TATAA Biocenter, Gothenburg, Sweden
| | | | | | - Paolo Verderio
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Sara Pizzamiglio
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | | | | | | | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- TATAA Biocenter, Gothenburg, Sweden
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20
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El-Saghire H, Vandevoorde C, Ost P, Monsieurs P, Michaux A, De Meerleer G, Baatout S, Thierens H. Intensity modulated radiotherapy induces pro-inflammatory and pro-survival responses in prostate cancer patients. Int J Oncol 2014; 44:1073-83. [PMID: 24435511 PMCID: PMC3977809 DOI: 10.3892/ijo.2014.2260] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 12/21/2022] Open
Abstract
Intensity modulated radiotherapy (IMRT) is one of the modern conformal radiotherapies that is widely used within the context of cancer patient treatment. It uses multiple radiation beams targeted to the tumor, however, large volumes of the body receive low doses of irradiation. Using γ-H2AX and global genome expression analysis, we studied the biological responses induced by low doses of ionizing radiation in prostate cancer patients following IMRT. By means of different bioinformatics analyses, we report that IMRT induced an inflammatory response via the induction of viral, adaptive, and innate immune signaling. In response to growth factors and immune-stimulatory signaling, positive regulation in the progression of cell cycle and DNA replication were induced. This denotes pro-inflammatory and pro-survival responses. Furthermore, double strand DNA breaks were induced in every patient 30 min after the treatment and remaining DNA repair and damage signaling continued after 18-24 h. Nine genes belonging to inflammatory responses (TLR3, SH2D1A and IL18), cell cycle progression (ORC4, SMC2 and CCDC99) and DNA damage and repair (RAD17, SMC6 and MRE11A) were confirmed by quantitative RT-PCR. This study emphasizes that the risk assessment of health effects from the out-of-field low doses during IMRT should be of concern, as these may increase the risk of secondary cancers and/or systemic inflammation.
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Affiliation(s)
- Houssein El-Saghire
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | | | - Piet Ost
- Department of Radiation Oncology, Ghent University Hospital, Gent, Belgium
| | - Pieter Monsieurs
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Arlette Michaux
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Gert De Meerleer
- Department of Radiation Oncology, Ghent University Hospital, Gent, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Hubert Thierens
- Department of Basic Medical Sciences, Ghent University, Gent, Belgium
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21
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Lee GE, Sung L, Fisher BT, Sullivan KE, McWilliams T, Tobias JW, Meshinchi S, Alonzo TA, Gamis A, Aplenc R. Gene expression profiling to predict viridans group streptococcal and invasive fungal infection in pediatric acute myeloid leukemia: a brief report from the Children's Oncology Group. Acta Haematol 2013; 131:167-9. [PMID: 24217778 PMCID: PMC4443693 DOI: 10.1159/000353758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022]
Affiliation(s)
- Grace E Lee
- Division of Infectious Diseases, The Children's Hospital of Philadelphia, Philadelphia, Pa., USA
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22
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Pazzagli M, Malentacchi F, Simi L, Orlando C, Wyrich R, Günther K, Hartmann C, Verderio P, Pizzamiglio S, Ciniselli C, Tichopad A, Kubista M, Gelmini S. SPIDIA-RNA: First external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses. Methods 2013; 59:20-31. [DOI: 10.1016/j.ymeth.2012.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/28/2012] [Accepted: 10/20/2012] [Indexed: 11/30/2022] Open
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23
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Munkholm K, Vinberg M, Berk M, Kessing LV. State-related alterations of gene expression in bipolar disorder: a systematic review. Bipolar Disord 2012; 14:684-96. [PMID: 23043691 DOI: 10.1111/bdi.12005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Alterations in gene expression in bipolar disorder have been found in numerous studies. It is unclear whether such alterations are related to specific mood states. As a biphasic disorder, mood state-related alterations in gene expression have the potential to point to markers of disease activity, and trait-related alterations might indicate vulnerability pathways. This review therefore evaluated the evidence for whether gene expression in bipolar disorder is state or trait related. METHODS A systematic review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline for reporting systematic reviews, based on comprehensive database searches for studies on gene expression in patients with bipolar disorder in specific mood states, was conducted. We searched Medline, Embase, PsycINFO, and The Cochrane Library, supplemented by manually searching reference lists from retrieved publications. RESULTS A total of 17 studies were included, comprising 565 patients and 418 control individuals. Six studies evaluated intraindividual alterations in gene expression across mood states. Two of five studies found evidence of intraindividual alterations in gene expression between a depressed state and a euthymic state. No studies evaluated intraindividual differences in gene expression between a manic state and a euthymic state, while only one case study evaluated differences between a manic state and a depressed state, finding altered expression in seven genes. No study investigated intraindividual variations in gene expression between a euthymic state and multiple states of various polarities (depressive, manic, hypomanic). Intraindividual alterations in expression of the same genes were not investigated across studies. Only one gene (the brain-derived neurotrophic factor gene; BDNF) was investigated across multiple studies, showing no alteration between bipolar disorder patients and control individuals. CONCLUSIONS There is evidence of some genes exhibiting state-related alterations in expression in bipolar disorder; however, this finding is limited by the lack of replication across studies. Further prospective studies are warranted, measuring gene expression in various affective phases, allowing for assessment of intraindividual differences.
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Affiliation(s)
- Klaus Munkholm
- Psychiatric Center Copenhagen, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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24
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Resau JH, Ho NT, Dykema K, Faber MS, Busik JV, Nickolov RZ, Furge KA, Paneth N, Jewell S, Khoo SK. Evaluation of sex-specific gene expression in archived dried blood spots (DBS). Int J Mol Sci 2012; 13:9599-9608. [PMID: 22949818 PMCID: PMC3431816 DOI: 10.3390/ijms13089599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 11/16/2022] Open
Abstract
Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.
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Affiliation(s)
- James H. Resau
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Nhan T. Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
| | - Karl Dykema
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Matthew S. Faber
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Julia V. Busik
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Radoslav Z. Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA; E-Mail:
| | - Kyle A. Furge
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
- Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Scott Jewell
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-616-234-5536; Fax: +1-616-234-5537
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25
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Neuberger EWI, Jurkiewicz M, Moser DA, Simon P. Detection of EPO gene doping in blood. Drug Test Anal 2012; 4:859-69. [PMID: 22508654 DOI: 10.1002/dta.1347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 02/27/2012] [Accepted: 03/06/2012] [Indexed: 12/18/2022]
Abstract
Gene doping--or the abuse of gene therapy--will continue to threaten the sports world. History has shown that progress in medical research is likely to be abused in order to enhance human performance. In this review, we critically discuss the progress and the risks associated with the field of erythropoietin (EPO) gene therapy and its applicability to EPO gene doping. We present typical vector systems that are employed in ex vivo and in vivo gene therapy trials. Due to associated risks, gene doping is not a feasible alternative to conventional EPO or blood doping at this time. Nevertheless, it is well described that about half of the elite athlete population is in principle willing to risk its health to gain a competitive advantage. This includes the use of technologies that lack safety approval. Sophisticated detection approaches are a prerequisite for prevention of unapproved and uncontrolled use of gene therapy technology. In this review, we present current detection approaches for EPO gene doping, with a focus on blood-based direct and indirect approaches. Gene doping is detectable in principle, and recent DNA-based detection strategies enable long-term detection of transgenic DNA (tDNA) following in vivo gene transfer.
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Affiliation(s)
- Elmo W I Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, Mainz, Germany
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26
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Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis. Clin Chim Acta 2012; 413:779-86. [DOI: 10.1016/j.cca.2012.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/10/2012] [Accepted: 01/15/2012] [Indexed: 01/24/2023]
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27
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Aldridge S, Hadfield J. Introduction to miRNA profiling technologies and cross-platform comparison. Methods Mol Biol 2012; 822:19-31. [PMID: 22144189 DOI: 10.1007/978-1-61779-427-8_2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
MicroRNA analysis has been widely adopted for basic and applied science. The tools and technologies available for quantifying and analysing miRNAs are still maturing. Here, we give an introductory overview of the main tools and the challenges in their use. We also discuss the importance of basic experimental design, sample handling and analysis methods as the impact of these can be as profound as the choice of miRNA analysis platform. Whether the reader is interested in a gene-by-gene or genome-wide approach choosing the platform to use is not trivial. Careful thought given before starting an experiment will make the execution much easier.
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28
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Neuberger EWI, Moser DA, Simon P. Principle considerations for the use of transcriptomics in doping research. Drug Test Anal 2011; 3:668-75. [DOI: 10.1002/dta.331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elmo W. I. Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention; Johannes Gutenberg-University; Mainz; Germany
| | - Dirk A. Moser
- Department of Sports Medicine, Rehabilitation and Disease Prevention; Johannes Gutenberg-University; Mainz; Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention; Johannes Gutenberg-University; Mainz; Germany
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29
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Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PLoS One 2011; 6:e26905. [PMID: 22046403 PMCID: PMC3203156 DOI: 10.1371/journal.pone.0026905] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Accepted: 10/06/2011] [Indexed: 01/08/2023] Open
Abstract
Background Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. Methodology/Principal Findings Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R2 methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. Conclusions By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study.
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30
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Fricano MM, Ditewig AC, Jung PM, Liguori MJ, Blomme EAG, Yang Y. Global transcriptomic profiling using small volumes of whole blood: a cost-effective method for translational genomic biomarker identification in small animals. Int J Mol Sci 2011; 12:2502-17. [PMID: 21731455 PMCID: PMC3127131 DOI: 10.3390/ijms12042502] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/28/2011] [Accepted: 04/01/2011] [Indexed: 01/19/2023] Open
Abstract
Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total RNA samples were further processed using the NuGEN Ovation Whole Blood Solution system and cDNA was hybridized to Affymetrix Rat Genome 230 2.0 Arrays. The microarray QC parameters using RNA isolated with the QSI method were within the acceptable range for microarray analysis. The transcriptomic profiles were highly correlated with those using RNA isolated with the PAXgene method and were consistent with expected LPS-induced inflammatory responses. The present study demonstrated that the QSI method coupled with NuGEN Ovation Whole Blood Solution system is cost-effective and particularly suitable for transcriptomic profiling of minimal volumes of whole blood, typical of those obtained with small animal species.
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Affiliation(s)
- Meagan M Fricano
- Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Il 60064, USA; E-Mails: (M.M.F.); (A.C.D.); (P.M.J.); (M.J.L.); (E.A.G.B.)
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31
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cDNA targets improve whole blood gene expression profiling and enhance detection of pharmocodynamic biomarkers: a quantitative platform analysis. J Transl Med 2010; 8:87. [PMID: 20868515 PMCID: PMC2954848 DOI: 10.1186/1479-5876-8-87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 09/25/2010] [Indexed: 12/20/2022] Open
Abstract
Background Genome-wide gene expression profiling of whole blood is an attractive method for discovery of biomarkers due to its non-invasiveness, simple clinical site processing and rich biological content. Except for a few successes, this technology has not yet matured enough to reach its full potential of identifying biomarkers useful for clinical prognostic and diagnostic applications or in monitoring patient response to therapeutic intervention. A variety of technical problems have hampered efforts to utilize this technology for identification of biomarkers. One significant hurdle has been the high and variable concentrations of globin transcripts in whole blood total RNA potentially resulting in non-specific probe binding and high background. In this study, we investigated and quantified the power of three whole blood profiling approaches to detect meaningful biological expression patterns. Methods To compare and quantify the impact of different mitigation technologies, we used a globin transcript spike-in strategy to synthetically generate a globin-induced signature and then mitigate it with the three different technologies. Biological differences, in globin transcript spiked samples, were modeled by supplementing with either 1% of liver or 1% brain total RNA. In order to demonstrate the biological utility of a robust globin artifact mitigation strategy in biomarker discovery, we treated whole blood ex vivo with suberoylanilide hydroxamic acid (SAHA) and compared the overlap between the obtained signatures and signatures of a known biomarker derived from SAHA-treated cell lines and PBMCs of SAHA-treated patients. Results We found cDNA hybridization targets detect at least 20 times more specific differentially expressed signatures (2597) between 1% liver and 1% brain in globin-supplemented samples than the PNA (117) or no treatment (97) method at FDR = 10% and p-value < 3x10-3. In addition, we found that the ex vivo derived gene expression profile was highly concordant with that of the previously identified SAHA pharmacodynamic biomarkers. Conclusions We conclude that an amplification method for gene expression profiling employing cDNA targets effectively mitigates the negative impact on data of abundant globin transcripts and greatly improves the ability to identify relevant gene expression based pharmacodynamic biomarkers from whole blood.
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Millán A, Gómez-Tato A, Fernández C, Pardo BG, Alvarez-Dios JA, Calaza M, Bouza C, Vázquez M, Cabaleiro S, Martínez P. Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:452-465. [PMID: 19844759 DOI: 10.1007/s10126-009-9231-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/08/2009] [Indexed: 05/28/2023]
Abstract
An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 x 15 k (five replicates/gene; eight microarrays/slide) was constructed. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida-challenged fish at 3 days postinfection. Only 48 out of 2,716 probes did not show signal of hybridization on the 32 microarrays employed, thus demonstrating the consistency of the bioinformatic applications of our database. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide, and dye bias) factors using 1C and 2C labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random-effects variance revealed that technical variation was mostly negligible, and biological variation represented the main factor, even using pooled samples. One-color approach performed at least as well as 2C, suggesting their usefulness due to its higher design flexibility and lower cost. A relevant proportion of genes turn out to be differentially labeled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defense response were detected at 3 days postchallenging.
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Affiliation(s)
- Adrián Millán
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain
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Min JL, Barrett A, Watts T, Pettersson FH, Lockstone HE, Lindgren CM, Taylor JM, Allen M, Zondervan KT, McCarthy MI. Variability of gene expression profiles in human blood and lymphoblastoid cell lines. BMC Genomics 2010; 11:96. [PMID: 20141636 PMCID: PMC2841682 DOI: 10.1186/1471-2164-11-96] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/08/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. RESULTS Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range rho = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P < 1*10(-16)) with higher variability (P < 1*10(-16)) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (rho = 0.83; rho = 0.79) of the expression levels of detected probes between LCLs and B-cell subsets were much lower compared to the two B-cell isolation methods (rho = 0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. CONCLUSION Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes, before application in large clinical studies.
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Affiliation(s)
- Josine L Min
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, Oxford, UK.
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Lönneborg A, Aarøe J, Dumeaux V, Børresen-Dale AL. Found in transcription: gene expression and other novel blood biomarkers for the early detection of breast cancer. Expert Rev Anticancer Ther 2009; 9:1115-23. [PMID: 19671031 DOI: 10.1586/era.09.31] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Early detection of a growing breast tumor is of key importance for patient survival. Despite limitations, mammography screening has improved the detection of breast tumors, however many tumors are not detected. This is especially true for younger women and women with high breast density. Novel diagnostic blood biomarkers either generated by the tumor and released into the blood, or generated by nontumor cells as a response to the tumor presence, can now potentially help improve the accuracy of early-stage breast cancer detection. They include multicomponent biomarkers, circulating tumor cells and RNA expression of peripheral blood. These novel biomarkers and their potential use will be presented and discussed in this review, with special emphasis on gene expression-based markers.
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Cankovic M, Varney RC, Whiteley L, Brown R, D'Angelo R, Chitale D, Zarbo RJ. The Henry Ford production system: LEAN process redesign improves service in the molecular diagnostic laboratory: a paper from the 2008 William Beaumont hospital symposium on molecular pathology. J Mol Diagn 2009; 11:390-9. [PMID: 19661386 DOI: 10.2353/jmoldx.2009.090002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement.
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Affiliation(s)
- Milena Cankovic
- Henry Ford Hospital, Department of Pathology and Laboratory Medicine, 2799 W. Grand Blvd., Detroit, MI 48202, USA.
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Karlovich C, Duchateau-Nguyen G, Johnson A, McLoughlin P, Navarro M, Fleurbaey C, Steiner L, Tessier M, Nguyen T, Wilhelm-Seiler M, Caulfield JP. A longitudinal study of gene expression in healthy individuals. BMC Med Genomics 2009; 2:33. [PMID: 19500411 PMCID: PMC2713969 DOI: 10.1186/1755-8794-2-33] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 06/07/2009] [Indexed: 12/12/2022] Open
Abstract
Background The use of gene expression in venous blood either as a pharmacodynamic marker in clinical trials of drugs or as a diagnostic test requires knowledge of the variability in expression over time in healthy volunteers. Here we defined a normal range of gene expression over 6 months in the blood of four cohorts of healthy men and women who were stratified by age (22–55 years and > 55 years) and gender. Methods Eleven immunomodulatory genes likely to play important roles in inflammatory conditions such as rheumatoid arthritis and infection in addition to four genes typically used as reference genes were examined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), as well as the full genome as represented by Affymetrix HG U133 Plus 2.0 microarrays. Results Gene expression levels as assessed by qRT-PCR and microarray were relatively stable over time with ~2% of genes as measured by microarray showing intra-subject differences over time periods longer than one month. Fifteen genes varied by gender. The eleven genes examined by qRT-PCR remained within a limited dynamic range for all individuals. Specifically, for the seven most stably expressed genes (CXCL1, HMOX1, IL1RN, IL1B, IL6R, PTGS2, and TNF), 95% of all samples profiled fell within 1.5–2.5 Ct, the equivalent of a 4- to 6-fold dynamic range. Two subjects who experienced severe adverse events of cancer and anemia, had microarray gene expression profiles that were distinct from normal while subjects who experienced an infection had only slightly elevated levels of inflammatory markers. Conclusion This study defines the range and variability of gene expression in healthy men and women over a six-month period. These parameters can be used to estimate the number of subjects needed to observe significant differences from normal gene expression in clinical studies. A set of genes that varied by gender was also identified as were a set of genes with elevated expression in a subject with iron deficiency anemia and another subject being treated for lung cancer.
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Affiliation(s)
- Chris Karlovich
- Department of Genomics and Oncology, Roche Molecular Systems, Pleasanton, CA, USA.
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Krawiec JA, Chen H, Alom-Ruiz S, Jaye M. Modified PAXgene method allows for isolation of high-integrity total RNA from microlitre volumes of mouse whole blood. Lab Anim 2009; 43:394-8. [PMID: 19502296 DOI: 10.1258/la.2008.0070157] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of gene expression is often used to evaluate the effects of experimental manipulations in laboratory animals. Blood is a rich source of potential biomarkers, including gene expression information, which may be obtained from whole blood. When compared with the end of a study, when whole blood samples can be easily obtained for gene expression measurements, the limiting volumes of whole blood obtainable from animals during the course of an experiment requires a method for RNA isolation from a minimal volume of whole blood. The PAXgene Blood RNA Extraction System originally designed for isolation of total RNA from 2.5 mL of human whole blood, was modified and successfully used to isolate high-integrity total RNA from as little as 50 microL of mouse whole blood. Fifty microlitres of mouse whole blood yielded an average of 2.3 microg highly intact total RNA, of sufficient quality and quantity allowing for multiple gene expression determinations. The utility of this method was demonstrated by confirming the time- and dose-dependent upregulation of haem oxygenase-1 (Hmox1) mRNA in response to a single injection of cobalt protoporphyrin. The successful isolation of total RNA from small volumes of mouse whole blood can allow for serial sampling on the same animals, thereby reducing the number of animals required for experimentation.
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Affiliation(s)
- J A Krawiec
- Cardiovascular Center for Excellence in Drug Discovery, Department of Vascular Inflammatory Diseases, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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Somoza N, Torà M. [Biological safety in the storage and transport of biological specimens from patients with respiratory diseases used in research settings]. Arch Bronconeumol 2009; 45:187-95. [PMID: 19327879 DOI: 10.1016/j.arbres.2009.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 02/05/2009] [Indexed: 02/04/2023]
Abstract
Major advances in genomics and proteomics have prompted the creation of biological specimen collections and biobanks for use in biomedical research. These specimen collections and the wealth of data they generate will allow longitudinal studies to be conducted and subproducts such as DNA or RNA to be obtained. They may even be used in future studies. To ensure specimen integrity, from the outset it is necessary to define procedures for sampling, transport and storage, the subproducts to be obtained, and the end purpose, as well as to address biosafety issues and arrange for suitable equipment monitoring. Strict control of these conditions will confer added value on the specimens, as quality and traceability would be assured. This article aims to provide a general overview of the recommendations concerning biological safety, transport, and storage of biological specimens for biomedical research into respiratory diseases in accordance with current legislation.
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Affiliation(s)
- Nuria Somoza
- Servicios Científico-Técnicos, IMIM-Hospital del Mar, Universitat Autònoma de Barcelona (UDIMAS-UAB), Barcelona, España
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Fan HPY, Di Liao C, Fu BY, Lam LCW, Tang NLS. Interindividual and interethnic variation in genomewide gene expression: insights into the biological variation of gene expression and clinical implications. Clin Chem 2009; 55:774-85. [PMID: 19233909 DOI: 10.1373/clinchem.2008.119107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Analysis of gene expression in peripheral blood samples is increasingly being applied in biomarker studies of disease diagnosis and prognosis. Although knowledge of interindividual and interethnic variation in gene expression is required to set ethnicity-specific reference intervals and to select reference genes and preferred markers from a list of candidate genes, few studies have attempted to characterize such biological variation on a genomewide scale. METHODS The genomewide expression profiles of 11 355 transcripts expressed among 210 multiethnic individuals of the HapMap project were obtained and analyzed; 4 replicates were included for each sample. The total biological CV in gene expression (CV(b)) was partitioned into interindividual (CV(g)), inter-ethnic group (CV(e)), and residual components by random-effects mixed models. RESULTS CV(g) was the major component of CV(b), and the differences among transcripts were large (up to 38%). Distinct groups of genes were characterized by CV values and expression levels. Of the genes with lowest biological variation (CV(b) < 1.5%), 35 genes were highly expressed, whereas 32 had intermediate or low expression. Although CV(g) was almost always greater than CV(e), we identified 10 genes in which ethnic variation predominated (range, 8%-18%). On the other hand, 17 annotated genes were highly variable with CV(g) values ranging between 15% and 38%. CONCLUSIONS Genomewide analysis of gene expression variation demonstrated biological differences among transcripts. Transcripts with the least biological variation are better candidates for reference genes, whereas those with low interindividual variation may be good disease markers. The presence of interethnic variation suggests that ethnicity-specific reference intervals may be necessary.
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Affiliation(s)
- Harris P Y Fan
- Departments of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Beekman JM, Reischl J, Henderson D, Bauer D, Ternes R, Peña C, Lathia C, Heubach JF. Recovery of microarray-quality RNA from frozen EDTA blood samples. J Pharmacol Toxicol Methods 2008; 59:44-9. [PMID: 19028589 DOI: 10.1016/j.vascn.2008.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 10/08/2008] [Indexed: 11/15/2022]
Abstract
INTRODUCTION The availability of blood collection systems with RNA stabilizing additives (e.g. PAXgene) has opened the field for gene expression profiling in large multi-center clinical trials. Here, we investigated whether the PAXgene system also offers a method for extraction of RNA from frozen EDTA blood samples, which do not yield RNA of high enough quality for RNA expression profiling, when extracted with standard protocols. METHODS Whole blood was obtained from six healthy volunteers in conventional EDTA tubes and frozen. The thawed EDTA blood was transferred into PAXgene tubes, and the RNA was extracted using the PAXgene RNA extraction kit. Microarray analysis was performed to asses the effect of RNA quality on gene expression profiles. RESULTS The RNA yield of the transferred samples was 1.76+/-0.88 microg/ml. This yield was clearly lower than the yield from a PAXgene reference group (2.84+/-0.62 microg/ml), but considerably higher than the yield resulting from a standard protocol usually applied to fresh EDTA blood samples (0.07+/-0.06 microg/ml). The RNA integrity number (RIN) of the transferred samples was 6.1+/-0.8 as compared to 9.8+/-0.1 for the PAXgene reference. Microarray analysis of the extracted RNA suggested that samples with RIN values above 5 produce data that fulfill the quality criteria defined by the manufacturer. DISCUSSION The transfer of thawed EDTA blood into PAXgene blood collection tubes offers a method to recover sufficient RNA of acceptable quality for microarray experiments.
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Jahn CE, Charkowski AO, Willis DK. Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J Microbiol Methods 2008; 75:318-24. [DOI: 10.1016/j.mimet.2008.07.004] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 07/09/2008] [Accepted: 07/09/2008] [Indexed: 11/24/2022]
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Nelson PT, Wang WX, Wilfred BR, Tang G. Technical variables in high-throughput miRNA expression profiling: much work remains to be done. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:758-65. [PMID: 18439437 DOI: 10.1016/j.bbagrm.2008.03.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 03/24/2008] [Accepted: 03/26/2008] [Indexed: 12/11/2022]
Abstract
MicroRNA (miRNA) gene expression profiling has provided important insights into plant and animal biology. However, there has not been ample published work about pitfalls associated with technical parameters in miRNA gene expression profiling. One source of pertinent information about technical variables in gene expression profiling is the separate and more well-established literature regarding mRNA expression profiling. However, many aspects of miRNA biochemistry are unique. For example, the cellular processing and compartmentation of miRNAs, the differential stability of specific miRNAs, and aspects of global miRNA expression regulation require specific consideration. Additional possible sources of systematic bias in miRNA expression studies include the differential impact of pre-analytical variables, substrate specificity of nucleic acid processing enzymes used in labeling and amplification, and issues regarding new miRNA discovery and annotation. We conclude that greater focus on technical parameters is required to bolster the validity, reliability, and cultural credibility of miRNA gene expression profiling studies.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology and Sanders-Brown Center, University of Kentucky, Lexington, KY 40536, USA.
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