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Barzegar M, Farsani MA, Rafiee M, Amiri V, Parkhihdeh S, Rad F, Mohammadi MH. Acute promyelocytic leukemia derived extracellular vesicles conserve PML-RARα transcript from storage-inflicted degradation: a stable diagnosis tool in APL patients. Ann Hematol 2021; 100:2241-2252. [PMID: 34236496 DOI: 10.1007/s00277-021-04579-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 06/15/2021] [Indexed: 10/20/2022]
Abstract
The early death, which is more common in acute promyelocytic leukemia (APL) patients rather than other types of acute myelocytic leukemia (AML) highlights the importance of appropriate diagnostic method for early detection of this disease. The low sensitivity of the conventional methods, low tumor burden in some patients, and the need for bone marrow sampling are some of the diagnostic challenges on the way of proper detection of APL. Given these, we aimed to compare the efficacy of extracellular vesicles (EVs), as a diagnostic tool, with the existing methods. RT-PCR, qPCR, and flow cytometry were applied on EVs and their corresponding associated cellular component collected from 18 APL new cases, 23 patients with minimal residual disease (MRD), and NB4 cell line. RT-PCR results were positive in both cellular and vesicular components of all new cases, NB4 cells, and EVs in contrary to MRD cases. Normalized copy numbers (NCN) of PML-RARα were 5100 and 3950 for cell and EVs, respectively (p < 0.05). There was a significant difference in the NCN of PML-RARα between cells and EVs in BM samples. Investigating the effect of storage at room temperature revealed that PML-RARα level was retained near to the baseline level in EVs, but there was a significant reduction in its copy number in the cellular component during 7 days. Taken together, given to the acceptable stability, EVs could be introduced as a non-invasive liquid biopsy that alongside existing methods could remarkably change the paradigm of APL diagnostic approaches.
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Affiliation(s)
- Mohieddin Barzegar
- Laboratory Hematology and Blood Banking, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Darband St, Qods Sq, Tehran, Iran
| | - Mehdi Allahbakhshian Farsani
- Laboratory Hematology and Blood Banking, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Darband St, Qods Sq, Tehran, Iran
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rafiee
- Laboratory Hematology and Blood Banking, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Darband St, Qods Sq, Tehran, Iran
| | - Vahid Amiri
- Laboratory Hematology and Blood Banking, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Darband St, Qods Sq, Tehran, Iran
| | - Sayeh Parkhihdeh
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Rad
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Mohammad Hossein Mohammadi
- Laboratory Hematology and Blood Banking, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Darband St, Qods Sq, Tehran, Iran.
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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2
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Harrington CA, Fei SS, Minnier J, Carbone L, Searles R, Davis BA, Ogle K, Planck SR, Rosenbaum JT, Choi D. RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method. Sci Rep 2020; 10:6271. [PMID: 32286338 PMCID: PMC7156519 DOI: 10.1038/s41598-020-62801-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/18/2020] [Indexed: 11/11/2022] Open
Abstract
Peripheral blood is a highly accessible biofluid providing a rich source of information about human physiology and health status. However, for studies of the blood transcriptome with RNA sequencing (RNA-Seq) techniques, high levels of hemoglobin mRNAs (hgbRNA) present in blood can occupy valuable sequencing space, impacting detection and quantification of non-hgbRNAs. In this study, we evaluated two methods for preparing ribosomal RNA (rRNA)-depleted sequencing libraries for RNA-Seq of whole blood, one of which is also designed to deplete hgbRNAs. Two experiments were performed: one evaluating library performance across 6 human blood samples and the other examining library reproducibility and performance in a two-subject subset. We find that addition of hgbRNA depletion to the rRNA-depletion protocol for library preparation from blood RNA effectively reduces highly abundant hgbRNA reads; however, it does not result in a statistically significant increase in differentially expressed genes in our patient-control study. Bioinformatic removal of globin gene counts in non-hgbRNA depleted libraries provides improvement in overall performance of these libraries. We conclude that use of a standard ribosomal RNA depletion method for library preparation coupled with bioinformatic removal of globin gene counts is sufficient for reproducible and sensitive measurement of both coding and noncoding RNAs in the blood transcriptome.
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Affiliation(s)
- Christina A Harrington
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA. .,Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.
| | - Suzanne S Fei
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jessica Minnier
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA.,OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon, USA
| | - Lucia Carbone
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.,Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA.,Knight Cardiovascular Institute, Oregon Health & Science University Portland, Oregon, USA.,3181 Sam Jackson Park Rd, Oregon Health & Science University, Portland, Oregon, United States
| | - Robert Searles
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon, USA.,3181 Sam Jackson Park Rd, Oregon Health & Science University, Portland, Oregon, United States
| | - Brett A Davis
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA.,Knight Cardiovascular Institute, Oregon Health & Science University Portland, Oregon, USA
| | - Kimberly Ogle
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Stephen R Planck
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - James T Rosenbaum
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Legacy Devers Eye Institute, Legacy Health System, Portland, Oregon, USA
| | - Dongseok Choi
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon, USA.,Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Graduate School of Dentistry, Kyung Hee University, Seoul, Korea
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Yip L, Fuhlbrigge R, Atkinson MA, Fathman CG. Impact of blood collection and processing on peripheral blood gene expression profiling in type 1 diabetes. BMC Genomics 2017; 18:636. [PMID: 28821222 PMCID: PMC5563008 DOI: 10.1186/s12864-017-3949-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/17/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The natural history of type 1 diabetes (T1D) is challenging to investigate, especially as pre-diabetic individuals are difficult to identify. Numerous T1D consortia have been established to collect whole blood for gene expression analysis from individuals with or at risk to develop T1D. However, with no universally accepted protocol for their collection, differences in sample processing may lead to variances in the results. Here, we examined whether the choice of blood collection tube and RNA extraction kit leads to differences in the expression of genes that are changed during the progression of T1D, and if these differences could be minimized by measuring gene expression directly from the lysate of whole blood. RESULTS Microarray analysis showed that the expression of 901 genes is highly influenced by sample processing using the PAXgene versus the Tempus system. These included a significant number of lymphocyte-specific genes and genes whose expression has been reported to differ in the peripheral blood of at-risk and T1D patients compared to controls. We showed that artificial changes in gene expression occur when control and T1D samples were processed differently. The sample processing-dependent differences in gene expression were largely due to loss of transcripts during the RNA extraction step using the PAXgene system. The majority of differences were not observed when gene expression was measured in whole blood lysates prepared from blood collected in PAXgene and Tempus tubes. CONCLUSION We showed that the gene expression profile of samples processed using the Tempus system is more accurate than that of samples processed using the PAXgene system. Variation in sample processing can result in misleading changes in gene expression. However, these differences can be minimized by measuring gene expression directly in whole blood lysates.
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Affiliation(s)
- Linda Yip
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94305, USA.
| | - Rebecca Fuhlbrigge
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94305, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - C Garrison Fathman
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94305, USA
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Feddersen S, Bastholt L, Pedersen SM. Stabilization of circulating thyroglobulin mRNA transcripts in patients treated for differentiated thyroid carcinoma. Ann Clin Biochem 2016; 54:558-566. [PMID: 27629910 DOI: 10.1177/0004563216671538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background The clinical utility of serum thyroglobulin in the follow-up of patients with differentiated thyroid carcinoma may be compromised by the presence of endogenous antithyroglobulin antibodies. To prevent interference by antithyroglobulin antibodies several groups have developed real-time PCR-based assays for quantification of blood thyroglobulin mRNA levels. For accurate quantification of thyroglobulin mRNA in blood preanalytical factors must be recognized and controlled. In this study, we evaluate the effect of different blood RNA stabilizing systems - the Tempus Blood RNA system and the PAXgene Blood RNA system - and storage time on RNA yield and quality, and thyroglobulin mRNA stability. Methods Blood samples from 11 patients previously treated for differentiated thyroid carcinoma were collected in K2-EDTA, Tempus and PAXgene tubes and maintained at room temperature. RNA was isolated following storage for 0 and 72 h, and RNA yield, integrity and purity was determined. Thyroglobulin, GAPDH and ACTB mRNA levels were quantified by semi-quantitative real-time PCR. Results The RNA yield was significantly higher for blood collected in Tempus tubes compared with PAXgene tubes following storage for 72 h at room temperature ( P = 0.0011). High-quality RNA could be extracted from blood collected in PAXgene and Tempus tubes. Blood collected in K2-EDTA tubes, but not in PAXgene and Tempus tubes, showed significant changes in thyroglobulin mRNA levels following storage for 72 h at room temperature ( P = 0.0263). Conclusions Stabilization of blood in PAXgene and Tempus tubes enables storage at room temperature for up to 72 h, without compromising thyroglobulin mRNA levels.
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Affiliation(s)
- Søren Feddersen
- 1 Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,2 Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Bastholt
- 3 Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Susanne M Pedersen
- 1 Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
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Evaluation of Existing Methods for Human Blood mRNA Isolation and Analysis for Large Studies. PLoS One 2016; 11:e0161778. [PMID: 27575051 PMCID: PMC5004844 DOI: 10.1371/journal.pone.0161778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
AIMS Prior to implementing gene expression analyses from blood to a larger cohort study, an evaluation to set up a reliable and reproducible method is mandatory but challenging due to the specific characteristics of the samples as well as their collection methods. In this pilot study we optimized a combination of blood sampling and RNA isolation methods and present reproducible gene expression results from human blood samples. METHODS The established PAXgeneTM blood collection method (Qiagen) was compared with the more recent TempusTM collection and storing system. RNA from blood samples collected by both systems was extracted on columns with the corresponding Norgen and PAX RNA extraction Kits. RNA quantity and quality was compared photometrically, with Ribogreen and by Real-Time PCR analyses of various reference genes (PPIA, β-ACTIN and TUBULIN) and exemplary of SIGLEC-7. RESULTS Combining different sampling methods and extraction kits caused strong variations in gene expression. The use of PAXgeneTM and TempusTM collection systems resulted in RNA of good quality and quantity for the respective RNA isolation system. No large inter-donor variations could be detected for both systems. However, it was not possible to extract sufficient RNA of good quality with the PAXgeneTM RNA extraction system from samples collected by TempusTM collection tubes. Comparing only the Norgen RNA extraction methods, RNA from blood collected either by the TempusTM or PAXgeneTM collection system delivered sufficient amount and quality of RNA, but the TempusTM collection delivered higher RNA concentration compared to the PAXTM collection system. The established Pre-analytix PAXgeneTM RNA extraction system together with the PAXgeneTM blood collection system showed lowest CT-values, i.e. highest RNA concentration of good quality. Expression levels of all tested genes were stable and reproducible. CONCLUSIONS This study confirms that it is not possible to mix or change sampling or extraction strategies during the same study because of large variations of RNA yield and expression levels.
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Interferon stimulated genes as peripheral diagnostic markers of early pregnancy in sheep: a critical assessment. Animal 2016; 10:1856-1863. [PMID: 27150201 DOI: 10.1017/s175173111600077x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated the diagnostic reliability of pregnancy detection using changes in interferon stimulated gene (ISG) messenger RNA (mRNA) levels in circulating immune cells in ewes. Two different groups of ewes (an experimental group, experiment 1 and a farm group, experiment 2) were oestrus-synchronized and blood sampled on day 14 (D0=day of insemination in control animals, experiment 1) and day 15 (experiment 2). Real-time PCR were performed to evaluate the abundance of different ISG mRNAs. In the experimental group, peripheral blood mononuclear cells of 29 ewes born and bred in experimental facilities were isolated using a Percoll gradient method. Gene expression for Chemokine (C-X-C motif) ligand 10 (CXCL10), Myxovirus (influenza virus) resistance 1 (MX1) and Signal transducer and activator of transcription 1 (STAT1) mRNA were, respectively, 8.3-fold, 6.1-fold and 2.7-fold higher (P0.10) in CXCL10, STAT1, MX1, Myxovirus (influenza virus) resistance 2 (MX2) and ISG15 ubiquitin-like modifier (ISG15) mRNA expression were found between pregnant and non-pregnant ewes. The ROC curves and the hierarchical classification generated from the real-time PCR data failed to discriminate between pregnant and non-pregnant animals. In this group of animals, our results show a strong variability in ISG expression patterns: 17% of animals identified as non-pregnant by the five tests were in fact pregnant, only 52% of pregnant animals had at least two positive results (two genes above threshold), whereas up to five positive results (five genes above threshold) were needed to avoid misclassification. In conclusion, this study illustrates the high variability in ISG expression levels in immune circulating cells during early pregnancy and, therefore, highlights the limits of using ISG expression levels in blood samples, collected on PAXgene® tubes on farms, for early pregnancy detection in sheep.
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7
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Soverini S, De Benedittis C, Mancini M, Martinelli G. Best Practices in Chronic Myeloid Leukemia Monitoring and Management. Oncologist 2016; 21:626-33. [PMID: 27032870 DOI: 10.1634/theoncologist.2015-0337] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/21/2016] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED : Optimal use of current therapeutic opportunities for chronic myeloid leukemia patients requires integration of clinical and laboratory monitoring. Assessment of molecular response (MR) by real-time quantitative polymerase chain reaction is the most sensitive way to monitor tyrosine kinase inhibitor (TKI) treatment efficacy. Besides major molecular response, which has emerged as a safe haven for survival since the initial studies of first-line imatinib treatment, two additional MR milestones have recently been defined: early molecular response and deep molecular response. The achievement of such MR milestones within defined time points during therapy is thought to draw the ideal trajectory toward optimal long-term outcome and, possibly, successful treatment discontinuation. Sensitive and reproducible MR measurement and proper interpretation of MR results are therefore critical to correctly inform therapeutic decisions. In patients who do not achieve an optimal response to TKI therapy, BCR-ABL1 mutation screening should also be performed, because it may deliver useful information for TKI choice. This review aims to help clinicians apply and translate the latest response definitions and clinical recommendations into practice. We provide a critical update on how these recommendations have incorporated MR levels in the clinical decision algorithms and how detection of BCR-ABL1 mutations should be interpreted. We also include a practical guide for pathologists and molecular biologists to best perform molecular testing and for hematologists and oncologists to best integrate it into routine practice. IMPLICATIONS FOR PRACTICE Ever-more-potent therapeutic strategies have been developed for chronic myeloid leukemia (CML) in parallel with the evolution of therapeutic goals and the refinement of response definitions and monitoring schemes and procedures. Terminology and methodology continue to evolve rapidly, making it difficult for busy hematology/oncology professionals to keep abreast of the newest developments. Optimal CML patient management results from the timely and rational use of molecular testing, the critical assessment of the power and pitfalls of current technology, and the appropriate interpretation and contextualization of results.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
| | - Caterina De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
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Durussel J, Haile DW, Mooses K, Daskalaki E, Beattie W, Mooses M, Mekonen W, Ongaro N, Anjila E, Patel RK, Padmanabhan N, McBride MW, McClure JD, Pitsiladis YP. Blood transcriptional signature of recombinant human erythropoietin administration and implications for antidoping strategies. Physiol Genomics 2016; 48:202-9. [DOI: 10.1152/physiolgenomics.00108.2015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/07/2016] [Indexed: 01/18/2023] Open
Abstract
Recombinant human erythropoietin (rHuEPO) is frequently abused by athletes as a performance-enhancing drug, despite being prohibited by the World Anti-Doping Agency. Although the methods to detect blood doping, including rHuEPO injections, have improved in recent years, they remain imperfect. In a proof-of-principle study, we identified, replicated, and validated the whole blood transcriptional signature of rHuEPO in endurance-trained Caucasian males at sea level ( n = 18) and Kenyan endurance runners at moderate altitude ( n = 20), all of whom received rHuEPO injections for 4 wk. Transcriptional profiling shows that hundreds of transcripts were altered by rHuEPO in both cohorts. The main regulated expression pattern, observed in all participants, was characterized by a “rebound” effect with a profound upregulation during rHuEPO and a subsequent downregulation up to 4 wk postadministration. The functions of the identified genes were mainly related to the functional and structural properties of the red blood cell. Of the genes identified to be differentially expressed during and post-rHuEPO, we further confirmed a whole blood 34-transcript signature that can distinguish between samples collected pre-, during, and post-rHuEPO administration. By providing biomarkers that can reveal rHuEPO use, our findings represent an advance in the development of new methods for the detection of blood doping.
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Affiliation(s)
- Jérôme Durussel
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Kerli Mooses
- Faculty of Sport and Exercise Sciences, University of Tartu, Tartu, Estonia
| | - Evangelia Daskalaki
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Wendy Beattie
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Martin Mooses
- Faculty of Sport and Exercise Sciences, University of Tartu, Tartu, Estonia
| | - Wondyefraw Mekonen
- Department of Medical Physiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Neford Ongaro
- Department of Medical Physiology, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; and
| | - Edwin Anjila
- Department of Medical Physiology, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; and
| | - Rajan K. Patel
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Neal Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Martin W. McBride
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John D. McClure
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Yannis P. Pitsiladis
- FIMS Reference Collaborating Centre of Sports Medicine for Anti-Doping Research, University of Brighton, Eastbourne, United Kingdom
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Stein C, Makarewicz O, Pfeifer Y, Brandt C, Pletz MW. Direct RNA-based detection of CTX-M β-lactamases in human blood samples. Int J Med Microbiol 2015; 305:370-7. [PMID: 25769406 DOI: 10.1016/j.ijmm.2015.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/08/2014] [Accepted: 02/14/2015] [Indexed: 01/04/2023] Open
Abstract
Bloodstream infections with ESBL-producers are associated with increased mortality, which is due to delayed appropriate treatment resulting in clinical failure. Current routine diagnostics for detection of bloodstream infections consists of blood culture followed by species identification and susceptibility testing. In attempts to improve and accelerate diagnostic procedures, PCR-based methods have been developed. These methods focus on species identification covering only a limited number of ESBL coding genes. Therefore, they fail to cover the steadily further evolving genetic diversity of clinically relevant β-lactamases. We have recently designed a fast and novel RNA targeting method to detect and specify CTX-M alleles from bacterial cultures, based on an amplification-pyrosequencing approach. We further developed this assay towards a diagnostic tool for clinical use and evaluated its sensitivity and specificity when applied directly to human blood samples. An optimized protocol for mRNA isolation allows detection of specific CTX-M groups from as little as 100 CFU/mL blood via reverse transcription, amplification, and pyrosequencing directly from human EDTA blood samples as well as from pre-incubated human blood cultures with a turnaround time for test results of <7 h.
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Affiliation(s)
- Claudia Stein
- Center for Infectious Diseases and Infection's Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany.
| | - Oliwia Makarewicz
- Center for Infectious Diseases and Infection's Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Burgstraße 37, D-38855 Wernigerode, Germany
| | - Christian Brandt
- Center for Infectious Diseases and Infection's Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases and Infection's Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
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Duale N, Lipkin WI, Briese T, Aarem J, Rønningen KS, Aas KK, Magnus P, Harbak K, Susser E, Brunborg G. Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank--evaluation of RNA quality and stability. BMC Res Notes 2014; 7:633. [PMID: 25214016 PMCID: PMC4168124 DOI: 10.1186/1756-0500-7-633] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Establishing methods for secure long term storage of RNA is critical to realizing the promise of biobanks in biomedical research. Here, we describe the results of yearly analyses of the same set of umbilical cord and adult whole blood RNA collected in Tempus Blood RNA tubes and stored at -80°C, over a period of up to six years. We systematically investigated the effects of long-term storage of samples (75 Tempus tubes form three adult donors and 30 Tempus tubes from three cord blood donors) on the RNA quality and transcript stability of six selected genes (CDKN1A, FOS, IL1B, IL8, MYC and TP53). This is the first systematic study of both cord and adult blood samples stored for many years. Findings The RNA purity and integrity, expressed as RIN-values, were stable up to six years of storage, and there were no storage-related deleterious effects on RNA purity. There were limited intra- and inter-individual variations in RNA yields; however, no consistent trend of decreasing RNA yield was observed with the duration of storage. Some long-term storage effects were found on the relative transcript levels of the six genes when compared to the year 0 samples. However, these changes were within ± 2–fold for both types of blood samples, except for two genes. Our results show that storage of these samples for up to six years did not have significant effects on the RNA quality and transcript stability of the six genes. Conclusions Blood RNA is stable in Tempus tubes stored at -80°C over a period of six years. Intact and good-quality RNA suitable for transcript profiling analyses in epidemiological studies was obtained from blood samples stored in Tempus tubes. This suggests that blood samples collected in large biobanks–such as the Mother and Child (MoBa) Cohort at Norwegian Institute of Public Health (NIPH) and frozen in suitable collection tubes for total RNA stabilization, can be used for quantitative studies after at least six years of storage. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-633) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nur Duale
- The Norwegian Institute of Public Health, PO Box 4404, Nydalen, NO-0403, Oslo, Norway.
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11
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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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12
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Bayatti N, Cooper-Knock J, Bury JJ, Wyles M, Heath PR, Kirby J, Shaw PJ. Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis. PLoS One 2014; 9:e87508. [PMID: 24475299 PMCID: PMC3903649 DOI: 10.1371/journal.pone.0087508] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/26/2013] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that causes death within a mean of 2–3 years from symptom onset. There is no diagnostic test and the delay from symptom onset to diagnosis averages 12 months. The identification of prognostic and diagnostic biomarkers in ALS would facilitate earlier diagnosis and faster monitoring of treatments. Gene expression profiling (GEP) can help to identify these markers as well as therapeutic targets in neurological diseases. One source of genetic material for GEP in ALS is peripheral blood, which is routinely accessed from patients. However, a high proportion of globin mRNA in blood can mask important genetic information. A number of methods allow safe collection, storage and transport of blood as well as RNA stabilisation, including the PAXGENE and TEMPUS systems for the collection of whole blood and LEUKOLOCK which enriches for the leukocyte population. Here we compared these three systems and assess their suitability for GEP in ALS. We collected blood from 8 sporadic ALS patients and 7 controls. PAXGENE and TEMPUS RNA extracted samples additionally underwent globin depletion using GlobinClear. RNA was amplified and hybridised onto Affymetrix U133 Plus 2.0 arrays. Lists of genes differentially regulated in ALS patients and controls were created for each method using the R package PUMA, and RT-PCR validation was carried out on selected genes. TEMPUS/GlobinClear, and LEUKOLOCK produced high quality RNA with sufficient yield, and consistent array expression profiles. PAXGENE/GlobinClear yield and quality were lower. Globin depletion for PAXGENE and TEMPUS uncovered the presence of over 60% more transcripts than when samples were not depleted. TEMPUS/GlobinClear and LEUKOLOCK gene lists respectively contained 3619 and 3047 genes differentially expressed between patients and controls. Real-time PCR validation revealed similar reliability between these two methods and gene ontology analyses revealed similar pathways differentially regulated in disease compared to controls.
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Affiliation(s)
- Nadhim Bayatti
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Joanna J. Bury
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Matthew Wyles
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Paul R. Heath
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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Nikula T, Mykkänen J, Simell O, Lahesmaa R. Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res 2013; 161:181-8. [PMID: 23138105 DOI: 10.1016/j.trsl.2012.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/28/2012] [Accepted: 10/13/2012] [Indexed: 10/27/2022]
Abstract
Peripheral whole blood is relatively easily obtained for monitoring gene expression for biomarker discovery using transcriptomic platforms such as genome-wide microarrays. However, whole blood provides challenges caused by sensitivity for ex vivo incubation and overrepresentation of globin mRNAs. We compared the performance of 2 commercial whole blood preservation methods, TEMPUS (Applied Biosystems, Foster City, CA) and PAXgene (PreAnalytiX, Qiagen BD, Valencia, CA), using 2 RNA amplification protocols and high-density microarrays. Performance of commercial globin mRNA reduction protocol also was studied. Human peripheral blood samples collected with TEMPUS and PAXgene Blood RNA tubes were amplified with the RiboAmp OA 1 Round RNA Amplification Kit (Arcturus; Applied Biosystems) and the Affymetrix (Santa Clara, CA) small sample protocol. Affymetrix globin reduction protocol was applied for total RNA samples. Samples amplified with RiboAmp were hybridized on Illumina Sentrix HumanRef-8 Expression BeadChips (Illumina Inc, San Diego, CA) and subjected to statistical analyses. RiboAmp mRNA amplification did not notably amplify globin mRNA that is overrepresented in RNA isolated by both TEMPUS and PAXgene preservation. Enzymatic depletion of globin transcript reduced the quality of total RNA and is thus not recommendable. Microarray analysis showed acceptable correlation within and between the RNA preservation methods, but altogether 443 transcripts were differentially expressed between RNA samples preserved in TEMPUS and PAXgene tubes. We demonstrated that the 2 tested blood RNA-preservation methods combined with RiboAmp mRNA amplification may be used for microarray experiments without the need for a prior globin RNA reduction. However, because genes involved in immune cell functions and gene regulatory pathways were differentially expressed as a result of the technical bias between the preservation methods, they should not be used in the same analytic setting.
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Affiliation(s)
- Tuomas Nikula
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
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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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15
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Wang IM, Stone DJ, Nickle D, Loboda A, Puig O, Roberts C. Systems biology approach for new target and biomarker identification. Curr Top Microbiol Immunol 2012; 363:169-99. [PMID: 22903568 DOI: 10.1007/82_2012_252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The pharmaceutical industry is spending increasingly large amounts of money on the discovery and development of novel medicines, but this investment is not adequately paying off in an increased rate of newly approved drugs by the FDA. The post-genomic era has provided a wealth of novel approaches for generating large, high-dimensional genetic and transcriptomic data sets from large cohorts of preclinical species as well as normal and diseased individuals. This systems biology approach to understanding disease-related biology is revolutionizing our understanding of the cellular pathways and gene networks underlying the onset of disease, and the mechanisms of pharmacological treatments that ameliorate disease phenotypes. In this article, we review a number of approaches being used by pharmaceutical and biotechnology companies, e.g., high-throughput DNA genotyping, sequencing, and genome-wide gene expression profiling, to enable drug discovery and development through the identification of new drug targets and biomarkers of disease progression, drug pharmacodynamics, and predictive markers for selecting the patients most likely to respond to therapy.
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Affiliation(s)
- I-Ming Wang
- Informatics and Analysis, Merck Research Laboratory, West Point, PA 19486, USA.
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16
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Ernst T, Hoffmann J, Erben P, Hehlmann R, Hochhaus A, Müller MC. Suitability of the PAXgene system to stabilize bone marrow RNA in imatinib-resistant patients with chronic myeloid leukemia. Clin Chem Lab Med 2008; 46:318-22. [PMID: 18303987 DOI: 10.1515/cclm.2008.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Optimum sample quality is a crucial requirement for molecular monitoring of patients with chronic myeloid leukemia (CML) on therapy. Bedside RNA stabilization systems (e.g., PAXgene) have been developed to inhibit RNA degradation during shipment of samples from the clinical site to the specialized laboratory. In CML, blood but not bone marrow samples have been examined using RNA stabilization in previous studies. Therefore, we sought to investigate the applicability of the PAXgene system for bone marrow samples in CML. METHODS Simultaneously stabilized blood and bone marrow samples were obtained from 55 imatinib-resistant CML patients to compare RNA yield and purity, expression of two housekeeping genes (total ABL and beta-glucuronidase; GUS) by quantitative reverse-transcriptase polymerase chain reaction, BCR-ABL expression (ratios BCR-ABL/ABL and BCR-ABL/GUS), and BCR-ABL kinase domain mutations analyzed by denaturing high-performance liquid chromatography and direct sequencing. RESULTS RNA extraction revealed high-quality RNA derived from both stabilized blood and bone marrow samples. RNA yield was significantly higher in bone marrow (median 9.9 microg RNA/mL bone marrow) than in blood (median 4.3 microg RNA/mL blood) (p=0.0005). The number of housekeeping gene transcripts was comparable in blood and bone marrow (median ABL copies/2 microL cDNA 13,260 vs. 25,590; median GUS copies/2 microL cDNA 35,490 vs. 60,200; n.s.). Further, ratios BCR-ABL/ABL (blood vs. bone marrow, median 47% vs. 57%) and ratios BCR-ABL/GUS (blood vs. bone marrow, median 26% vs. 21%) were not significantly different. Results of mutation analysis corresponded in 51 out of 55 patients (93%), whereas moderate differences were observed in four patients. CONCLUSIONS We conclude that bone marrow can be effectively stabilized using the PAXgene system and shows concordance with blood in terms of BCR-ABL mRNA quantification and mutation analysis in imatinib-resistant CML patients.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Benzamides
- Bone Marrow/metabolism
- DNA Mutational Analysis/methods
- Drug Resistance, Neoplasm/genetics
- Female
- Fusion Proteins, bcr-abl
- Gene Expression Regulation, Neoplastic
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/blood
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Male
- Middle Aged
- Mutation/genetics
- Piperazines/pharmacology
- Piperazines/therapeutic use
- Protein Structure, Tertiary
- Protein-Tyrosine Kinases/chemistry
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- RNA Stability
- RNA, Neoplasm/blood
- RNA, Neoplasm/metabolism
- Reference Standards
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Affiliation(s)
- Thomas Ernst
- III. Medizinische Klinik, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Germany
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Yamada MF, Fujiwara T, Ishikawa I, Kohata K, Katoh C, Miyamura K, Harigae H. Interlaboratory Comparison of Quantitative RT-PCR Based Detection for Minimal Residual Disease in Leukemias: A Standardization Approach in Japan. TOHOKU J EXP MED 2008; 214:97-104. [DOI: 10.1620/tjem.214.97] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Minami F. Yamada
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine
| | | | - Katsura Kohata
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine
| | - Chiaki Katoh
- Department of Internal Medicine, National Hospital Organization Nagoya Medical Center
| | - Koichi Miyamura
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine
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Quinlivan M, Nelly M, Prendergast M, Breathnach C, Horohov D, Arkins S, Chiang YW, Chu HJ, Ng T, Cullinane A. Pro-inflammatory and antiviral cytokine expression in vaccinated and unvaccinated horses exposed to equine influenza virus. Vaccine 2007; 25:7056-64. [PMID: 17825959 DOI: 10.1016/j.vaccine.2007.07.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 03/15/2007] [Accepted: 07/30/2007] [Indexed: 11/15/2022]
Abstract
Most studies of the cytokine response to influenza virus infection have been carried out in human, porcine and murine models, however the data available on equine cytokines is limited. An experimental challenge study was undertaken in unvaccinated naïve horses and horses vaccinated with a commercial inactivated influenza vaccine. The humoral antibody response to vaccination and virus challenge was measured by single radial haemolysis (SRH) assay and clinical signs of influenza and viral shedding were monitored post-challenge. Levels of three equine pro-inflammatory cytokines interleukin (IL)-1beta, IL-6 and tumor necrosis factor (TNF)-alpha and the antiviral cytokine interferon (IFN)-alpha were examined by quantitative RT-PCR of mRNA. Vaccination provided significant clinical and virological protection and resulted in a significant reduction of IFN-alpha and IL-6 expression on day 2 post-challenge. The patterns of cytokine expression observed in control animals suffering from influenza after challenge are comparable to those reported in studies of other species.
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Affiliation(s)
- Michelle Quinlivan
- Virology Unit, Irish Equine Centre, Johnstown, Naas, Co. Kildare, Ireland
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