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Harkin EE, Browne JA, Murphy BA. Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity. PLoS One 2024; 19:e0294089. [PMID: 38820307 PMCID: PMC11142484 DOI: 10.1371/journal.pone.0294089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
Hair follicles provide an easily accessible tissue for interrogating gene expression for multiple purposes in mammals. RNAlater® is a liquid storage solution that stabilises and preserves cellular RNA, eliminating the need to immediately process or freeze tissue specimens. The manufacturer advises storage of samples at 2-8°C overnight before transfer to -20°C. This study aimed to evaluate RNA integrity in hair follicle samples collected from horses, stabilized in RNAlater®, and stored under three short-term storage conditions. Mane hair samples complete with follicles were collected from four horses at a single time point. Approximately 15 hairs were placed in each of three 2 mL tubes containing 0.75ml RNAlater® solution. Test group A was stored at 4°C for 24-h, then decanted and stored at -20°C. Test groups B and C were stored at 4°C and 19°C (room temperature) respectively for 7 days, then decanted and stored at -20°C. RNA was isolated from all samples and RNA quantity and quality were measured. One-way ANOVA revealed no difference in RNA concentration (A:516 +/-125 ng/ml, B:273+/-93 ng/ml, C:476+/-176 ng/ml;P = 0.2) or quality (A:9.5 +/-0.19, B:9.8+/-0.09, C:9.2+/-0.35 RIN; P = 0.46) between the test groups. There were no group differences in mean Cycle Threshold values from qPCR validation assays confirming high-quality template cDNA. The results suggest that storage of hair follicles for one week in RNAlater® at cool or room temperature conditions will not compromise RNA integrity and will permit extended transport times from remote sampling locations without the need for freezing.
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Affiliation(s)
- Eilís E. Harkin
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - John A. Browne
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Barbara A. Murphy
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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2
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Shihab SR, Iqbal BN, Arunasalam S, Noordeen F. Quality of the sample-based RNA determines the real-time RT-PCR results in the laboratory diagnosis of COVID-19. Diagn Microbiol Infect Dis 2024; 108:116076. [PMID: 37980858 DOI: 10.1016/j.diagmicrobio.2023.116076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 11/21/2023]
Abstract
Effect of the quality of sample-based RNA on COVID-19 real-time RT-PCR results was investigated. The purity of the extracts was dependent on the extraction method (P<0.0001) and affected the test interpretations (P = 0.002). Gross RNA concentration negatively correlated with Ct values (P < 0.0001). The presence of impurities contributed to inconclusive test results.
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Affiliation(s)
- Sibra Rm Shihab
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka; Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Bushran N Iqbal
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Shiyamalee Arunasalam
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Faseeha Noordeen
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
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Caixeta DC, Carneiro MG, Rodrigues R, Alves DCT, Goulart LR, Cunha TM, Espindola FS, Vitorino R, Sabino-Silva R. Salivary ATR-FTIR Spectroscopy Coupled with Support Vector Machine Classification for Screening of Type 2 Diabetes Mellitus. Diagnostics (Basel) 2023; 13:diagnostics13081396. [PMID: 37189497 DOI: 10.3390/diagnostics13081396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 05/17/2023] Open
Abstract
The blood diagnosis of diabetes mellitus (DM) is highly accurate; however, it is an invasive, high-cost, and painful procedure. In this context, the combination of ATR-FTIR spectroscopy and machine learning techniques in other biological samples has been used as an alternative tool to develop a non-invasive, fast, inexpensive, and label-free diagnostic or screening platform for several diseases, including DM. In this study, we used the ATR-FTIR tool associated with linear discriminant analysis (LDA) and a support vector machine (SVM) classifier in order to identify changes in salivary components to be used as alternative biomarkers for the diagnosis of type 2 DM. The band area values of 2962 cm-1, 1641 cm-1, and 1073 cm-1 were higher in type 2 diabetic patients than in non-diabetic subjects. The best classification of salivary infrared spectra was by SVM, showing a sensitivity of 93.3% (42/45), specificity of 74% (17/23), and accuracy of 87% between non-diabetic subjects and uncontrolled type 2 DM patients. The SHAP features of infrared spectra indicate the main salivary vibrational modes of lipids and proteins that are responsible for discriminating DM patients. In summary, these data highlight the potential of ATR-FTIR platforms coupled with machine learning as a reagent-free, non-invasive, and highly sensitive tool for screening and monitoring diabetic patients.
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Affiliation(s)
- Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | | | - Ricardo Rodrigues
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Deborah Cristina Teixeira Alves
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Luís Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Thúlio Marquez Cunha
- School of Medicine, Federal University of Uberlandia (UFU), Uberlandia 38408-100, Minas Gerais, Brazil
| | - Foued Salmen Espindola
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Rui Vitorino
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
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A step towards harmonising human biomonitoring study setup on European level: Materials provided and lessons learnt in HBM4EU. Int J Hyg Environ Health 2023; 249:114118. [PMID: 36773579 DOI: 10.1016/j.ijheh.2023.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
Internal exposure of the human body to potentially harmful chemical substances can be assessed by Human Biomonitoring (HBM). HBM can be used to generate conclusive data that may provide an overview of exposure levels in entire or specific population groups. This knowledge can promote the understanding of potential risks of the substances of interest or help monitoring the success of regulatory measures taken on the political level. Study planning and design are key elements of any epidemiologic study to generate reliable data. In the field of HBM, this has been done using differing approaches on various levels of population coverage so far. Comparison and combined usage of the resulting data would contribute to understanding exposure and its factors on a larger scale, however, the differences between studies make this a challenging and somewhat limited endeavour. This article presents templates for documents that are required to set up an HBM study, thus facilitating the generation of harmonised HBM data as a step towards standardisation of HBM in Europe. They are designed to be modular and adaptable to the specific needs of a single study while emphasising minimum requirements to ensure comparability. It further elaborates on the challenges encountered during the process of creating these documents during the runtime of the European Joint Programme HBM4EU in a multi-national expert team and draws up lessons learnt in the context of knowledge management.
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Loy DS, Spuri Gomes R, Dutta E, Brodersen BW, Loy JD. Time and temperature stability of Tritrichomonas foetus in phosphate-buffered saline as evaluated by a reverse transcription real-time PCR assay and field analysis. Front Vet Sci 2023; 10:1101502. [PMID: 37065215 PMCID: PMC10098177 DOI: 10.3389/fvets.2023.1101502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
Tritrichomonas foetus (TF) is a significant reproductive pathogen of cattle, and sample collection, handling, transport, and testing are significant hurdles to surveillance programs. Recent methods have been developed that allow for the direct detection of TF using a reverse transcription real-time PCR (direct RT-qPCR) approach. To evaluate these methods, a comparative analysis was conducted to assess the technical performance of this assay with a commercially available real-time PCR (qPCR) assay. In addition, the evaluation of two types of collection media (PBS and TF transport tube) was conducted that evaluated sample stability from 0 to 3 days when stored at 4°C or 25°C. Extended incubation times for PBS media were also evaluated (5, 7, and 14 days) at both refrigeration and frozen temperatures to evaluate the effect of extended transport time on samples. Limits of detection (LODs), dynamic range, and RNA stability were assessed using lab-cultured TF spiked into samples of normal bovine smegma collected in PBS or TF transport media, and performance was assessed on field samples collected in parallel. 100% agreement was found between direct RT-qPCR and qPCR at 10 parasites/extraction and a LOD of 1 parasite/extraction. Differences in detection were not observed in either collection media when incubated at either temperatures for up to 3 days of incubation. In addition, the extended incubation experiments indicate that samples containing 10 parasites/extraction can be detected at 4°C for 5 days with a mean Cq 26.34 (95% CI: 23.11–29.58) and detected at −20°C for 7 or 14 days, with a mean Cq 29.55 (95% CI: 27.73–31.37). A significant decrease in detectable RNA was observed in samples containing <10 parasites/extraction at −20°C for 14 days, which should be considered for long-term storage. In summary, direct RT-qPCR was found to be equivalent or superior to qPCR and PBS was not significantly different from TF transport media. The findings of the current study allows for more flexibility during sample collection and transport and ultimately enhancement of TF surveillance programs.
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Affiliation(s)
- Duan S. Loy
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
- *Correspondence: Duan S. Loy
| | - Renata Spuri Gomes
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Enakshy Dutta
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bruce W. Brodersen
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - John Dustin Loy
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
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The Association Between Sleep Disturbance and Proinflammatory Markers in Patients With Cancer: A Meta-analysis. Cancer Nurs 2023; 46:E91-E98. [PMID: 35728010 DOI: 10.1097/ncc.0000000000001055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Sleep disturbance is one of the symptoms with high incidence and negative influence in patients with cancer. A better understanding of the biological factors associated with sleep disturbance is critical to predict, treat, and manage this condition. OBJECTIVE The aim of this study was to determine the correlation between sleep disturbance and proinflammatory markers in adult patients with cancer. METHODS A systematic search was conducted in 7 databases from inception to March 1, 2020, for this meta-analysis. Two reviewers independently screened the studies, extracted data, and appraised the quality of the studies. Meta-analyses were conducted using Stata 12.0 software. RESULTS Sixteen studies were included. Results indicated that sleep disturbance was associated with higher levels of the overall proinflammatory markers and that the effect size was small yet significant. Further subgroup analyses suggested that sleep disturbance was significantly associated with interleukin-6 and C-reactive protein, but not with interleukin-1β or tumor necrosis factor-α. Meta-regression results indicated that only the sample source affected the association between sleep disturbance and proinflammatory markers. CONCLUSION There was a positive relationship between sleep disturbance and selected proinflammatory markers in adult patients with cancer. IMPLICATION FOR PRACTICE This review provides empirical support for the association between sleep disturbance and certain proinflammatory markers. Healthcare providers can further explore specific biomarkers to precisely identify the individuals at risk of sleep disturbance and develop targeted strategies for therapeutic and clinical interventions.
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Kifaro EG, Kim MJ, Jung S, Jang YH, Moon S, Lee DH, Song CS, Misinzo G, Kim SK. Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance. Diagnostics (Basel) 2023; 13:diagnostics13020261. [PMID: 36673071 PMCID: PMC9857651 DOI: 10.3390/diagnostics13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.
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Affiliation(s)
- Emmanuel George Kifaro
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Mi Jung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Yoon-ha Jang
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungyeon Moon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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Testing for Dihydropyrimidine Dehydrogenase Deficiency to Individualize 5-Fluorouracil Therapy. Cancers (Basel) 2022; 14:cancers14133207. [PMID: 35804978 PMCID: PMC9264755 DOI: 10.3390/cancers14133207] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary 5-Fluorouracil (5-FU) is a chemotherapy drug that is commonly used to treat multiple cancers. Many people who are treated with 5-FU experience severe toxicity to the drug, and in severe cases, patients can die. This review discusses current methods for identifying people who are at high risk for severe side effects to 5-FU therapy. Abstract Severe adverse events (toxicity) related to the use of the commonly used chemotherapeutic drug 5-fluorouracil (5-FU) affect one in three patients and are the primary reason cited for premature discontinuation of therapy. Deficiency of the 5-FU catabolic enzyme dihydropyrimidine dehydrogenase (DPD, encoded by DPYD) has been recognized for the past 3 decades as a pharmacogenetic syndrome associated with high risk of 5-FU toxicity. An appreciable fraction of patients with DPD deficiency that receive 5-FU-based chemotherapy die as a result of toxicity. In this manuscript, we review recent progress in identifying actionable markers of DPD deficiency and the current status of integrating those markers into the clinical decision-making process. The limitations of currently available tests, as well as the regulatory status of pre-therapeutic DPYD testing, are also discussed.
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Knutti N, Neugebauer S, Scherr F, Mathay C, Marchese M, Henry E, Palm J, Betsou F, Kiehntopf M. Introduction of BD Vacutainer ® Barricor™ tubes in clinical biobanking and application of amino acid and cytokine quality indicators to Barricor plasma. Clin Chem Lab Med 2022; 60:689-700. [PMID: 35073617 DOI: 10.1515/cclm-2021-0899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/10/2022] [Indexed: 01/04/2024]
Abstract
OBJECTIVES The use of BD Vacutainer® Barricor™ tubes (BAR) can reduce turnaround time (TAT) and improve separation of plasma from cellular components using a specific mechanical separator. Concentrations of amino acids (AAs) and cytokines, known to be labile during pre-analytical time delays, were compared in heparin (BAR, BD Heparin standard tube [PST]), EDTA and serum gel tubes (SER) to validate previously identified quality indicators (QIs) in BAR. METHODS Samples of healthy individuals (n=10) were collected in heparin, EDTA and SER tubes and exposed to varying pre- and post-centrifugation delays at room temperature (RT). Cytokines (interleukin [IL]-8, IL-16 and sCD40L) were analyzed by enzyme-linked immunosorbent assay (ELISA) and AAs were characterized by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). RESULTS All QIs, AAs/AA ratio and cytokines increased during prolonged blood storage in heparin plasma (PST, BAR) and SER tubes. Comparison of 53 h/1 h pre-centrifugation delay resulted in an increase in taurine (Tau) and glutamic acid (Glu) concentrations by more than three times, soluble CD40L increased by 13.6, 9.2 and 4.3 fold in PST, BAR-CTRL and BAR-FAST, and IL-8 increased even more by 112.8 (PST), 266.1 (BAR-CTRL), 268.1 (BAR-FAST) and 70.0 (SER) fold, respectively. Overall, compared to prolonged blood storage, effects of post-centrifugation delays were less pronounced in all tested materials. CONCLUSIONS BAR tubes are compatible with the use of several established QIs and can therefore be used in clinical biobanking to reduce pre-analytical TAT without compromising QIs and thus pre-analytical sample quality analysis.
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Affiliation(s)
- Nadine Knutti
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Sophie Neugebauer
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Franziska Scherr
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Conny Mathay
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Monica Marchese
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Estelle Henry
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Julia Palm
- Institute of Medical Statistics, Computer and Data Science, Jena University Hospital, Jena, Germany
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
- Laboratoire National de Santé (LNS), Dudelange, Luxembourg
| | - Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
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Streicher JP, Streicher MB, Ramesh T, Downs CT. Diet of a generalist mammalian mesocarnivore in an urban matrix. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2086020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Jarryd P Streicher
- Centre for Functional Biodiversity, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Melanie B Streicher
- Centre for Functional Biodiversity, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Tharmalingam Ramesh
- Centre for Functional Biodiversity, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Sálim Ali Centre for Ornithology and Natural History (SACON), Anaikkatti, Coimbatore, India
| | - Colleen T Downs
- Centre for Functional Biodiversity, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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11
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Successive liquid-phase microextraction of acidic and basic analytes. Anal Chim Acta 2022; 1192:339335. [PMID: 35057942 DOI: 10.1016/j.aca.2021.339335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022]
Abstract
Practical biological and environmental samples always contain both acidic and basic substances, and the samples are always precious. Thus, separation of analytes with different nature from the same sample was of great significance. Successive liquid phase microextraction (sLPME) of acidic and basic analytes under optimal extraction conditions was therefore proposed for the first time. The concept of sLPME was proved by using three acidic analytes (naproxen, flurbiprofen and diclofenac) and three basic analytes (haloperidol, fluoxetine and sertraline) as model analytes, and using polypropylene glycol with an average molecular weight of 4000 (PPG4000) as SLM. The recoveries of all target analytes by sLPME were similar to that by individual LPME due to good affinity of PPG4000 to both acidic and basic analytes. Under optimal extraction conditions, the recoveries for all analytes by sLPME from urine samples were in the range of 62%-95%. Moreover, combined with LC-MS/MS, such sLPME approach was also evaluated with urine samples. The matrix effect of sLPME-LC-MS/MS at different levels for all analytes ranged from -14.1%-13.2%. The linear ranges with R2 > 0.996 were 5-1000 ng mL-1 for basic analytes, and 20-1000 ng mL-1 for acidic analytes except diclofenac (1-1000 ng mL-1). The repeatability and accuracy at four levels were in the range of 3%-10% and 86%-120%, respectively. The limit of detection (LOD, S/N = 3) and limit of quantification (LOQ, S/N = 10) were found to be 0.07-0.49 ng mL-1 and 0.25-1.63 ng mL-1, respectively. Finally, the strategy for constructing a sLPME system was further confirmed with urine, plasma and saliva using another two versatile SLM solvents possessing high affinity to both acidic and basic analytes. Successive LPME enabled separation of acidic and basic analytes from the same sample under optimum extraction conditions for all target analytes. Thus, we believe that the sLPME system will become a potent platform for forensic toxicology analysis, food science, environmental analysis and epidemiology study.
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Agrahari S, Kumar Gautam R, Kumar Singh A, Tiwari I. Nanoscale materials-based hybrid frameworks modified electrochemical biosensors for early cancer diagnostics: An overview of current trends and challenges. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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13
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Dass G, Sharma V, Malla MA, Lukose S, Kori RK. Prevalence and Recovery of Microorganisms from Containers used for the Collection of Forensic Biological Samples. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Microbes play a significant role in the degradation of biological evidence collected for forensic analysis. The present study is aimed to isolate and identify the microbes present inside the empty container used for the biological evidence collection.
Methods:
Bacterial isolation from the selected containers was done by cotton swab over the inner surface of the containers. Streaking was done on the surface of the three different culture plates as a Blood agar plate, Nutrient plate and MacConkey plate. The plates were placed in an incubator shaker at 37ºC for 48 hours. The colonies grown on the surface of the media were counted on and used for further study. Various biochemical assays were performed to characterize isolated bacteria.
Results:
Staining results suggested that the presence of Gram-positive stain (Staphylococcus, Bacillus, Corynebacterium, Clostridium) and Gram negative stain (E. coli, Enterobacteriaceae, Pseudomonas, Salmonella, Shigella, Stenotrophomonas, Bdellovibrio, Acetic acid bacteria). The Catalase and Coagulase test suggested the presence of Staphylococcus aureus, S. epidermis and S. sapropyticus. Moreover, the indole test suggested the presence of Citrobacter koseri, Kebsiella oxytoca, Proteus vulgaris etc. Some of the bacteria were urea metabolizing, including Proteus spp, Helicobacter pylori, Cryptococcus spp, Corynebacterium spp.
Conclusion:
This study recommends that there should be proper maintenance of the chain of custody from the collection to analysis so that evidence properly prevents degradation or contamination in the biological evidence. Extra care is needed for the collection and packing of biological evidence from the crime scene. Moreover, the collection containers, if left wide open, lead to contamination and degradation of biological evidence.
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Johnson BW, Takahashi K, Cheng YY. Preclinical Models and Resources to Facilitate Basic Science Research on Malignant Mesothelioma - A Review. Front Oncol 2021; 11:748444. [PMID: 34900693 PMCID: PMC8660093 DOI: 10.3389/fonc.2021.748444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma is an aggressive cancer with poor prognosis, predominantly caused by human occupational exposure to asbestos. The global incidence of mesothelioma is predicted to increase as a consequence of continued exposure to asbestos from a variety of sources, including construction material produced in the past in developed countries, as well as those currently being produced in developing countries. Mesothelioma typically develops after a long latency period and consequently it is often diagnosed in the clinic at an advanced stage, at which point standard care of treatment, such as chemo- and radio-therapy, are largely ineffective. Much of our current understanding of mesothelioma biology, particularly in relation to disease pathogenesis, diagnosis and treatment, can be attributed to decades of preclinical basic science research. Given the postulated rising incidence in mesothelioma cases and the limitations of current diagnostic and treatment options, continued preclinical research into mesothelioma is urgently needed. The ever-evolving landscape of preclinical models and laboratory technology available to researchers have made it possible to study human disease with greater precision and at an accelerated rate. In this review article we provide an overview of the various resources that can be exploited to facilitate an enhanced understanding of mesothelioma biology and their applications to research aimed to improve the diagnosis and treatment of mesothelioma. These resources include cell lines, animal models, mesothelioma-specific biobanks and modern laboratory techniques/technologies. Given that different preclinical models and laboratory technologies have varying limitations and applications, they must be selected carefully with respect to the intended objectives of the experiments. This review therefore aims to provide a comprehensive overview of the various preclinical models and technologies with respect to their advantages and limitations. Finally, we will detail about a highly valuable preclinical laboratory resource to curate high quality mesothelioma biospecimens for research; the biobank. Collectively, these resources are essential to the continued advancement of precision medicine to curtail the increasing health burden caused by malignant mesothelioma.
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Affiliation(s)
| | - Ken Takahashi
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
| | - Yuen Yee Cheng
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
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15
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Whitney KE, Dornan GJ, King J, Chahla J, Evans TA, Philippon MJ, LaPrade RF, Huard J. The Effect of a Single Freeze-Thaw Cycle on Matrix Metalloproteinases in Different Human Platelet-Rich Plasma Formulations. Biomedicines 2021; 9:1403. [PMID: 34680520 PMCID: PMC8533272 DOI: 10.3390/biomedicines9101403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 01/17/2023] Open
Abstract
Storing platelet-rich plasma (PRP) for future use is a compelling approach, presuming the retention of biological properties is maintained. However, certain factors in PRP preparations have deleterious effects for the treatment of certain musculoskeletal conditions. The purpose of this study was to measure and compare matrix metalloproteinase protein (MMP) concentrations between fresh and freeze-thawed leukocyte-rich PRP (LR-PRP) inactivated (LR-I) and activated (LR-A) preparations, and leukocyte-poor PRP (LP-PRP) inactivated (LP-I) and activated (LP-A) preparations. A volume of 60 mL of whole blood was drawn from 19 healthy donors. LP-I and LR-I samples were processed using a manual extraction and centrifugation methodology. LP-A and LR-A products were activated with 10% CaCl2 and recombinant thrombin. Blood fractions were either immediately assayed and analyzed or stored at -80 °C for 24, 72 and 160 h. Multiplex immunoassay was used to measure MMP-1, MMP-2, MMP-3, MMP-9, MMP-10, and MMP-12. MMP-1 concentrations increased in LR-A (p < 0.05) and MMP-9 significantly increased in LR-I (p < 0.05), while MMP-2 significantly decreased in LR-I (p < 0.05) and MMP-3 concentrations significantly decreased in LR-A (p < 0.05). MMP-12 concentrations also significantly decreased in LR-I (p < 0.05) from baseline concentrations. There were no significant differences between LP-A and LP-I preparations and MMP concentrations. MMP-10 concentrations in all PRP samples compared to each freezing time point were also not significantly different. MMPs regulate components of the extracellular matrix (ECM) in the remodeling phase of musculoskeletal injury. In this study, we observed a significant increase and decrease in MMP concentrations in response to a single freeze-thaw cycle in inactivated PRP and activated PRP preparations. This evidence contributes to the growing body of literature on the optimization of PRP preparation and storage strategies prior to delivery. Our findings suggest that specific PRP preparations after a single freeze-thaw may be more advantageous for certain musculoskeletal applications based on the presence of MMP concentrations.
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Affiliation(s)
- Kaitlyn E. Whitney
- Steadman Philippon Research Institute, Vail, CO 81657, USA; (K.E.W.); (G.J.D.); (J.K.)
| | - Grant J. Dornan
- Steadman Philippon Research Institute, Vail, CO 81657, USA; (K.E.W.); (G.J.D.); (J.K.)
| | - Jillian King
- Steadman Philippon Research Institute, Vail, CO 81657, USA; (K.E.W.); (G.J.D.); (J.K.)
| | - Jorge Chahla
- Rush University Medical Center, Midwest Orthopaedics at Rush, Chicago, IL 60612, USA;
| | - Thos A. Evans
- The Steadman Clinic, Vail, CO 81657, USA; (T.A.E.); (M.J.P.)
| | | | | | - Johnny Huard
- Steadman Philippon Research Institute, Vail, CO 81657, USA; (K.E.W.); (G.J.D.); (J.K.)
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16
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Nana RRD, Makoge V, Ngum NL, Amvongo-Adjia N, Singh V, Somo RM. Evaluating the dual reactivity on SD bioline malaria rapid diagnosis tests as a potential indicator of high parasitemia due to Plasmodium falciparum. Pathog Glob Health 2021; 115:487-495. [PMID: 34309493 DOI: 10.1080/20477724.2021.1953684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The co-reactivity of the Plasmodium histidine-rich protein 2 (HRP2) and lactate dehydrogenase (pLDH) in malaria rapid diagnosis tests (mRDTs) as a potential indicator of high parasitemia linked to Plasmodium falciparum was evaluated in the reported study from Cameroon. The samples were screened for malaria using both mRDTs (SD bioline HRP2/pLDH), light microscopy and further confirmed by Plasmodium species-specific PCR assay. Of the 483 patients enrolled, 161 (33.3%) showed a reactive mRDTs amongst which 70 patients were positive by both microscopy and mRDTs with 30.0% (21/70) positive for HRP2 alone, while 70.0% (49/70) showed a dual reaction to HRP2 and pLDH parasite antigens. P. falciparum parasitemia was found to be significantly high among patients with both reactive antigens, (p < 0.0001) suggesting that mRDTs reactivity is influenced by parasite load which could be used as a diagnostic marker for therapeutic management of patients with high parasitemia in field conditions.
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Affiliation(s)
- Roman Rodrigue Dongang Nana
- CWll Biology and Malaria Parasite Bank, ICMR-National Institute of Malaria Research (NIMR), New Delhi, India.,Department of Microbiology, Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
| | - Valerie Makoge
- Department of Microbiology, Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
| | - Ngum Lesley Ngum
- Department of Microbiology, Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
| | - Nathalie Amvongo-Adjia
- Department of Microbiology, Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
| | - Vineeta Singh
- CWll Biology and Malaria Parasite Bank, ICMR-National Institute of Malaria Research (NIMR), New Delhi, India
| | - Roger Moyou Somo
- Department of Microbiology, Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon.,Department of Microbiology, Hematology, Parasitology and Infectious Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
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17
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Yu J, Young RG, Deeth LE, Hanner RH. Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PeerJ 2020; 8:e9974. [PMID: 33150057 PMCID: PMC7587055 DOI: 10.7717/peerj.9974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 11/30/2022] Open
Abstract
Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and assay metadata, often under-examined and under-reported. Here, we present the Molecular Detection Mapping and Analysis Platform for R (MDMAPR), an open-source and fully scalable informatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format, while geospatially visualizing the distribution of the data and relative intensity of the qPCR results. The advance of this approach is in the ability to use MDMAPR to store varied qPCR data. This includes pathogen and environmental qPCR species detection studies ideally suited to geographical visualization. However, it also goes beyond these and can be utilized with other qPCR data including gene expression studies, quantification studies used in identifying health dangers associated with food and water bacteria, and the identification of unknown samples. In addition, MDMAPR’s novel centralized management and geospatial visualization of qPCR data can further enable cross-discipline large-scale qPCR data standardization and accessibility to support research spanning multiple fields of science and qPCR applications.
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Affiliation(s)
- Jiaojia Yu
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lorna E Deeth
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Robert H Hanner
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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18
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Effects of processing conditions on stability of immune analytes in human blood. Sci Rep 2020; 10:17328. [PMID: 33060628 PMCID: PMC7566484 DOI: 10.1038/s41598-020-74274-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022] Open
Abstract
Minimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual’s baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range − 10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for > 20 K genes)—with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.
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19
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Hasegawa Y, Otoki Y, McClorry S, Coates LC, Lombardi RL, Taha AY, Slupsky CM. Optimization of a Method for the Simultaneous Extraction of Polar and Non-Polar Oxylipin Metabolites, DNA, RNA, Small RNA, and Protein from a Single Small Tissue Sample. Methods Protoc 2020; 3:mps3030061. [PMID: 32859006 PMCID: PMC7564281 DOI: 10.3390/mps3030061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive picture of tissue biology can be obtained through the application and integration of multiple omic technologies. However, the common challenge in working with a precious sample is having a sample too small to separately extract analytes of interest for each experiment. Considering the high heterogeneity that can be present in a single tissue sample, extracting all biomolecules from a single and undivided tissue is preferable because it allows direct comparison of results. Here, we combined a modified Folch extraction method with DNA, RNA, small RNA, and protein extraction using two commercial kits, which allowed us to extract polar metabolites and non-polar oxylipin metabolites, DNA, RNA, small RNA, and protein simultaneously from a small tissue sample. The method was validated in terms of quantity and quality of analytes for downstream analyses.
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Affiliation(s)
- Yu Hasegawa
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Yurika Otoki
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - Shannon McClorry
- Department of Nutrition, University of California-Davis, Davis, CA 95616, USA;
| | - Laurynne C. Coates
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Rachel L. Lombardi
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Ameer Y. Taha
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Carolyn M. Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
- Department of Nutrition, University of California-Davis, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-6804; Fax: +1-530-752-4759
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20
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Cicek MS, Olson JE. Mini-Review of Laboratory Operations in Biobanking: Building Biobanking Resources for Translational Research. Front Public Health 2020; 8:362. [PMID: 32850593 PMCID: PMC7399165 DOI: 10.3389/fpubh.2020.00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/24/2020] [Indexed: 01/05/2023] Open
Abstract
Biobanks have become integral to improving population health. We are in a new era in medicine as patients, health professionals, and researchers increasingly collaborate to gain new knowledge and explore new paradigms for diagnosing and treating disease. Many large-scale biobanking efforts are underway worldwide at the institutional, national, and even international level. When linked with subject data from questionnaires and medical records, biobanks serve as valuable resources in translational research. A biobank must have high quality samples that meet researcher's needs. Biobank laboratory operations require an enormous amount of support—from lab and storage space, information technology expertise, and a laboratory management information system to logistics for sample movement, quality management systems, and appropriate facilities. A paramount metric of success for a biobank is the concept of every biospecimen coming to the repository belongs to a participant who has something to contribute to research for a healthier future. This article will discuss the importance of biorepository operations, specific to the collection and storage of participants materials. Specific focus will be given to maintaining the quality of samples, along with the various levels of support biorepositories need to fulfill their purpose and ensure the integrity of each specimen is maintained.
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Affiliation(s)
- Mine S Cicek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
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21
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Biobanks-A Platform for Scientific and Biomedical Research. Diagnostics (Basel) 2020; 10:diagnostics10070485. [PMID: 32708805 PMCID: PMC7400532 DOI: 10.3390/diagnostics10070485] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
The development of biomedical science requires the creation of biological material collections that allow for the search and discovery of biomarkers for pathological conditions, the identification of new therapeutic targets, and the validation of these findings in samples from patients and healthy people. Over the past decades, the importance and need for biobanks have increased considerably. Large national and international biorepositories have replaced small collections of biological samples. The aim of this work is to provide a basic understanding of biobanks and an overview of how biobanks have become essential structures in modern biomedical research.
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Epigenetic Biomarkers for Environmental Exposures and Personalized Breast Cancer Prevention. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041181. [PMID: 32069786 PMCID: PMC7068429 DOI: 10.3390/ijerph17041181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022]
Abstract
Environmental and lifestyle factors are believed to account for >80% of breast cancers; however, it is not well understood how and when these factors affect risk and which exposed individuals will actually develop the disease. While alcohol consumption, obesity, and hormone therapy are some known risk factors for breast cancer, other exposures associated with breast cancer risk have not yet been identified or well characterized. In this paper, it is proposed that the identification of blood epigenetic markers for personal, in utero, and ancestral environmental exposures can help researchers better understand known and potential relationships between exposures and breast cancer risk and may enable personalized prevention strategies.
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23
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Zolotarenko AD, Chekalin EV, Bruskin SA. Modern Molecular Genetic Methods for Age Estimation in Forensics. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Miszczyk J, Rawojć K. Effects of culturing technique on human peripheral blood lymphocytes response to proton and X-ray radiation. Int J Radiat Biol 2020; 96:424-433. [DOI: 10.1080/09553002.2020.1704907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Justyna Miszczyk
- Department of Experimental Physics of Complex Systems, Institute of Nuclear Physics Polish Academy of Sciences, Kraków, Poland
| | - Kamila Rawojć
- The University Hospital in Kraków, Department of Endocrinology, Nuclear Medicine Unit, Kraków, Poland
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25
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Simpson S, Kaislasuo J, Guller S, Pal L. Thermal stability of cytokines: A review. Cytokine 2019; 125:154829. [PMID: 31472404 DOI: 10.1016/j.cyto.2019.154829] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND The role of cytokines in various disease states is a burgeoning field of academic study and clinical application, however there are no consensus documents on how certain cytokines should be stored prior to quantification. This information is especially of interest to researchers assembling a biobank or clinicians who have to transport specimens to a different location in order to be tested. OBJECTIVE To review the literature and synthesize prior findings on cytokine storage and freeze/thaw stability. DESIGN We searched PubMed for articles related to cytokine storage stability. All articles were analyzed for cytokines studied, source of reported cytokine concentration (i.e., human whole blood or serum, concentrations from other species or bodily sources were excluded), and reported statistical results. RESULTS We identified and synthesized results of 23 peer-reviewed articles which published data on the storage and freeze/thaw stability of 33 different cytokines and chemokines. CONCLUSION There is a wide variety of reported cytokine storage and freeze/thaw stability. Interleukin-6 and tumor necrosis factor alpha are the most widely studied cytokines in regard to temperature stability. In a few cytokines, a clear consensus can be reached as to storage safety at particular temperatures, but in most, more research needs to be done and we advise the clinician or researcher to use caution in interpreting cytokine concentration results after a long period of storage or several freeze/thaw cycles.
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Affiliation(s)
- Samantha Simpson
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.
| | - Janina Kaislasuo
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA; Department of Obstetrics and Gynecology, University of Helsinki and the Helsinki University Hospital, Finland
| | - Seth Guller
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Lubna Pal
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
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Schwarz N, Knutti N, Rose M, Neugebauer S, Geiger J, Jahns R, Klopp N, Illig T, Mathay C, Betsou F, Scherag A, Kiehntopf M. Quality Assessment of the Preanalytical Workflow in Liquid Biobanking: Taurine as a Serum-Specific Quality Indicator for Preanalytical Process Variations. Biopreserv Biobank 2019; 17:458-467. [PMID: 31339743 DOI: 10.1089/bio.2019.0004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The scientific impact of translational biomedical research largely depends on the availability of high-quality biomaterials. However, evidence-based and robust quality indicators (QIs) covering the most relevant preanalytical variations are still lacking. The aim of this study was to identify and validate a QI suitable for assessing time-to-centrifugation (TTC) delays in human liquid biospecimens originating from both healthy and diseased individuals. Serum and plasma samples with varying TTCs were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in a pilot cohort of healthy individuals to identify a suitable QI candidate. Taurine (TAU), as a TTC QI candidate, was validated in healthy individuals and patients with rheumatologic and cardiologic diseases, considering the (1) preanalytical handling temperature, (2) platelet count, and (3) postcentrifugation delay. For discrimination of high TTC (TTC >60 minutes) from low TTC serum specimens, a probability calculation tool was developed (Triple-T-cutoff-model). TTC-dependent changes in healthy individuals were observed for amino acids, particularly TAU. Validation of the TAU levels in an independent cohort of healthy individuals revealed a time-dependent increase in serum, but not in plasma, for a TTC delay of 30-240 minutes. TAU increases were dependent on the handling temperature and platelet count and volume. By contrast, no changes in TAU concentrations were observed for additional postcentrifugation delays. Validation of TAU and the Triple-T-cutoff-model, in rheumatologic/cardiologic patient collectives, allowed the discrimination of samples with TTC ≤60 min/>60 min with estimated AUROC (area under the receiver operating characteristic curve) values of 89% [78%-100%]/86% [71%-100%] and 91% [79%-100%]/84% [68%-100%], respectively. Considering the preanalytical handling temperature and platelet count and volume, TAU and the Triple-T-cutoff-model represent reliable QIs for TTC >60 minutes in serum samples from healthy individuals and selected rheumatologic/cardiologic patients. However, further studies in larger patient collectives with various diseases are needed to assess the robustness and potential of the QIs presented in this article as biobanking quality assurance/quality control tools to support high-quality biomedical research.
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Affiliation(s)
- Nicolle Schwarz
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Nadine Knutti
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Michael Rose
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Sophie Neugebauer
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), Würzburg, Germany
| | - Roland Jahns
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), Würzburg, Germany
| | - Norman Klopp
- Hannover Unified Biobank (HUB), Hannover, Germany
| | - Thomas Illig
- Hannover Unified Biobank (HUB), Hannover, Germany
| | - Conny Mathay
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - André Scherag
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
| | - Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
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27
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Dubaisi S, Caruso JA, Gaedigk R, Vyhlidal CA, Smith PC, Hines RN, Kocarek TA, Runge-Morris M. Developmental Expression of the Cytosolic Sulfotransferases in Human Liver. Drug Metab Dispos 2019; 47:592-600. [PMID: 30885913 PMCID: PMC6505379 DOI: 10.1124/dmd.119.086363] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
The liver is the predominant organ of metabolism for many endogenous and foreign chemicals. Cytosolic sulfotransferases (SULTs) catalyze the sulfonation of drugs and other xenobiotics, as well as hormones, neurotransmitters, and sterols, with consequences that include enhanced drug elimination, hormone inactivation, and procarcinogen bioactivation. SULTs are classified into six gene families, but only SULT1 and SULT2 enzymes are expressed in human liver. We characterized the developmental expression patterns of SULT1 and SULT2 mRNAs and proteins in human liver samples using reverse transcription quantitative polymerase chain reaction (RT-qPCR), RNA sequencing, and targeted quantitative proteomics. Using a set of prenatal, infant, and adult liver specimens, RT-qPCR analysis demonstrated that SULT1A1 (transcript variant 1) expression did not vary appreciably during development; SULT1C2, 1C4, and 1E1 mRNA levels were highest in prenatal and/or infant liver, and 1A2, 1B1, and 2A1 mRNA levels were highest in infant and/or adult. Hepatic SULT1A1 (transcript variant 5), 1C3, and 2B1 mRNA levels were low regardless of developmental stage. Results obtained with RNA sequencing of a different set of liver specimens (prenatal and pediatric) were generally comparable results to those of the RT-qPCR analysis, with the additional finding that SULT1A3 expression was highest during gestation. Analysis of SULT protein content in a library of human liver cytosols demonstrated that protein levels generally corresponded to the mRNAs, with the major exception that SULT1C4 protein levels were much lower than expected based on mRNA levels. These findings further support the concept that hepatic SULTs play important metabolic roles throughout the human life course, including early development.
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Affiliation(s)
- Sarah Dubaisi
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Joseph A Caruso
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Roger Gaedigk
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Carrie A Vyhlidal
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Philip C Smith
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Ronald N Hines
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Thomas A Kocarek
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
| | - Melissa Runge-Morris
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.); Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, North Carolina (P.C.S.); and Office of Research and Development, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina (R.N.H.)
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Coppola L, Cianflone A, Grimaldi AM, Incoronato M, Bevilacqua P, Messina F, Baselice S, Soricelli A, Mirabelli P, Salvatore M. Biobanking in health care: evolution and future directions. J Transl Med 2019; 17:172. [PMID: 31118074 PMCID: PMC6532145 DOI: 10.1186/s12967-019-1922-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/15/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The aim of the present review is to discuss how the promising field of biobanking can support health care research strategies. As the concept has evolved over time, biobanks have grown from simple biological sample repositories to complex and dynamic units belonging to large infrastructure networks, such as the Pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Biobanks were established to support scientific knowledge. Different professional figures with varied expertise collaborate to obtain and collect biological and clinical data from human subjects. At same time biobanks preserve the human and legal rights of each person that offers biomaterial for research. METHODS A literature review was conducted in April 2019 from the online database PubMed, accessed through the Bibliosan platform. Four primary topics related to biobanking will be discussed: (i) evolution, (ii) bioethical issues, (iii) organization, and (iv) imaging. RESULTS Most biobanks were founded as local units to support specific research projects, so they evolved in a decentralized manner. The consequence is an urgent needing for procedure harmonization regarding sample collection, processing, and storage. Considering the involvement of biomaterials obtained from human beings, different ethical issues such as the informed consent model, sample ownership, veto rights, and biobank sustainability are debated. In the face of these methodological and ethical challenges, international organizations such as BBMRI play a key role in supporting biobanking activities. Finally, a unique development is the creation of imaging biobanks that support the translation of imaging biomarkers (identified using a radiomic approach) into clinical practice by ensuring standardization of data acquisition and analysis, accredited technical validation, and transparent sharing of biological and clinical data. CONCLUSION Modern biobanks permit large-scale analysis for individuation of specific diseases biomarkers starting from biological or digital material (i.e., bioimages) with well-annotated clinical and biological data. These features are essential for improving personalized medical approaches, where effective biomarker identification is a critical step for disease diagnosis and prognosis.
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Affiliation(s)
- Luigi Coppola
- IRCCS SDN, Naples Via Emanuele Gianturco, 11, 80143, Naples, Italy
| | | | | | | | - Paolo Bevilacqua
- IRCCS SDN, Naples Via Emanuele Gianturco, 11, 80143, Naples, Italy
| | | | - Simona Baselice
- IRCCS SDN, Naples Via Emanuele Gianturco, 11, 80143, Naples, Italy.,Ospedale Evangelico Betania, Naples, Italy
| | - Andrea Soricelli
- IRCCS SDN, Naples Via Emanuele Gianturco, 11, 80143, Naples, Italy.,Department of Sport Sciences & Healthiness, University of Naples Parthenope, Naples, Italy
| | | | - Marco Salvatore
- IRCCS SDN, Naples Via Emanuele Gianturco, 11, 80143, Naples, Italy
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Santos Ferreira DL, Maple HJ, Goodwin M, Brand JS, Yip V, Min JL, Groom A, Lawlor DA, Ring S. The Effect of Pre-Analytical Conditions on Blood Metabolomics in Epidemiological Studies. Metabolites 2019; 9:metabo9040064. [PMID: 30987180 PMCID: PMC6523923 DOI: 10.3390/metabo9040064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 11/16/2022] Open
Abstract
Serum and plasma are commonly used in metabolomic-epidemiology studies. Their metabolome is susceptible to differences in pre-analytical conditions and the impact of this is unclear. Participant-matched EDTA-plasma and serum samples were collected from 37 non-fasting volunteers and profiled using a targeted nuclear magnetic resonance (NMR) metabolomics platform (n = 151 traits). Correlations and differences in mean of metabolite concentrations were compared between reference (pre-storage: 4 °C, 1.5 h; post-storage: no buffer addition delay or NMR analysis delay) and four pre-storage blood processing conditions, where samples were incubated at (i) 4 °C, 24 h; (ii) 4 °C, 48 h; (iii) 21 °C, 24 h; and (iv) 21 °C, 48 h, before centrifugation; and two post-storage sample processing conditions in which samples thawed overnight (i) then left for 24 h before addition of sodium buffer followed by immediate NMR analysis; and (ii) addition of sodium buffer, then left for 24 h before NMR profiling. We used multilevel linear regression models and Spearman’s rank correlation coefficients to analyse the data. Most metabolic traits had high rank correlation and minimal differences in mean concentrations between samples subjected to reference and the different conditions tested, that may commonly occur in studies. However, glycolysis metabolites, histidine, acetate and diacylglycerol concentrations may be compromised and this could bias results in association/causal analyses.
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Affiliation(s)
- Diana L Santos Ferreira
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Hannah J Maple
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Matt Goodwin
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Judith S Brand
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, 701 85 Örebro, Sweden.
| | - Vikki Yip
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Alix Groom
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
- Bristol National Institute of Health Research Biomedical Research Centre, Bristol BS1 3NU, UK.
| | - Susan Ring
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK.
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Wyatt LA, Nwosu LN, Wilson D, Hill R, Spendlove I, Bennett AJ, Scammell BE, Walsh DA. Molecular expression patterns in the synovium and their association with advanced symptomatic knee osteoarthritis. Osteoarthritis Cartilage 2019; 27:667-675. [PMID: 30597276 DOI: 10.1016/j.joca.2018.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is a major source of knee pain. Mechanisms of OA knee pain are incompletely understood but include synovial pathology. We aimed to identify molecular expression patterns in the synovium associated with symptomatic knee OA. DESIGN Snap frozen synovia were from people undergoing total knee replacement (TKR) for advanced OA, or from post-mortem (PM) cases who had not sought help for knee pain. Associations with OA symptoms were determined using discovery and validation samples, each comprising TKR and post mortem (PM) cases matched for chondropathy (Symptomatic or Asymptomatic Chondropathy). Associations with OA were determined by comparing age matched TKR and PM control cases. Real-time quantitative PCR for 96 genes involved in inflammation and nerve sensitisation used TaqMan® Array Cards in discovery and validation samples, and protein expression for replicated genes was quantified using Luminex bead assay. RESULTS Eight genes were differentially expressed between asymptomatic and symptomatic chondropathy cases and replicated between discovery and validation samples (P<0.05 or >3-fold change). Of these, matrix metalloprotease (MMP)-1 was also increased whereas interleukin-1 receptor 1 (IL1R1) and vascular endothelial growth factor (VEGF) were decreased at the protein level in the synovium of symptomatic compared to asymptomatic chondropathy cases. MMP1 protein expression was also increased in OA compared to PM controls. CONCLUSION Associations of symptomatic OA may suggest roles of MMP1 expression and IL1R1 and VEGF pathways in OA pain. Better understanding of which inflammation-associated molecules mediate OA pain should inform refinement of existing therapies and development of new treatments.
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Affiliation(s)
- L A Wyatt
- Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, NG5 1PB, UK; Division of Rheumatology, Orthopaedics and Dermatology, University of Nottingham, Nottingham, UK; Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis, University of Nottingham, Nottingham, UK.
| | - L N Nwosu
- Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, NG5 1PB, UK; Division of Rheumatology, Orthopaedics and Dermatology, University of Nottingham, Nottingham, UK
| | - D Wilson
- Department of Rheumatology, Sherwood Forest Hospitals NHS Foundation Trust, Mansfield Road, Sutton in Ashfield, NG17 4JL, UK
| | - R Hill
- Department of Rheumatology, Sherwood Forest Hospitals NHS Foundation Trust, Mansfield Road, Sutton in Ashfield, NG17 4JL, UK
| | - I Spendlove
- Divison of Cancer and Stem Cells, University of Nottingham, UK
| | - A J Bennett
- Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, NG5 1PB, UK; School of Life Sciences, University of Nottingham, Nottingham, NG5 1PB, UK
| | - B E Scammell
- Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, NG5 1PB, UK; Division of Rheumatology, Orthopaedics and Dermatology, University of Nottingham, Nottingham, UK; Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis, University of Nottingham, Nottingham, UK; NIHR Nottingham, Biomedical Research Centre, University of Nottingham, UK
| | - D A Walsh
- Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, NG5 1PB, UK; Division of Rheumatology, Orthopaedics and Dermatology, University of Nottingham, Nottingham, UK; Department of Rheumatology, Sherwood Forest Hospitals NHS Foundation Trust, Mansfield Road, Sutton in Ashfield, NG17 4JL, UK; NIHR Nottingham, Biomedical Research Centre, University of Nottingham, UK
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Clinical performance of Anyplex II HPV28 by human papillomavirus type and viral load in a referral population. PLoS One 2019; 14:e0210997. [PMID: 30673759 PMCID: PMC6343909 DOI: 10.1371/journal.pone.0210997] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/04/2019] [Indexed: 11/28/2022] Open
Abstract
Anyplex II HPV28 (`Anyplex`) is a semi-quantitative DNA PCR assay divided into set A, comprising 14 high risk (hr)HPV types; and set B, comprising 5 possibly hrHPV types and 9 low risk (lr)HPV types. We compared the ability of Anyplex to that of Hybrid Capture 2 (HC2) and PreTect HPV-Proofer (`Proofer`) to detect cervical intraepithelial neoplasia grade two or worse (CIN2+) by HPV types and viral load. This cross-sectional study included 296 women referred to colposcopy with abnormal cervical cytology and/or persistent HPV infection. CIN2+ was identified in 175/296 women. Liquid based cytology samples were used to perform HPV testing. The sensitivity of Anyplex to detect CIN2+ was 98.9% (95% CI 95.9–99.9) and specificity 43.0% (95% CI 34.0–52.3). Restricting to medium and high viral loads in Anyplex set A, sensitivity and specificity were 97.1% (95% CI 93.5–99.1) and 59.5% (95% CI 50.2–68.3) with positive (PPV) and negative predictive value (NPV) 77.6% and 93.5%, respectively, comparable to HC2. Restricting Anyplex to the hrHPV types in Proofer, HPV16, 18, 31, 33 and 45, sensitivity and specificity for CIN2+ were 85.1% (95% CI 79.0–90.1) and 71.1% (95% CI 62.1–79.0), comparable to Proofer`s. When adding HPV52 and 58, the sensitivity for CIN2+ was 92.6% (95% CI 87.6–96.0) and CIN3+ 96.5% (95% CI 92.0–98.8). No value of Anyplex set B was found in detecting CIN2+. In conclusion, the clinical performance of medium and high viral loads in Anyplex set A was comparable to HC2. Restricting the test to the 7 hrHPV types included in the 9-valent HPV-vaccine, HPV16, 18, 31, 33, 45, 52 and 58, satisfies the international criteria for cervical cancer screening with relative sensitivity compared to HC2 for CIN2+ and CIN3+ of 0.98 and 1.01, respectively. Detecting all 28 Anyplex HPV types adds no benefit in a referral population.
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Abstract
Urine is a major repository of biometabolites, some proteins, and DNA. Within the past few decades, it has become increasingly apparent that certain infectious, neoplastic, and congenital diseases can be investigated using urine samples for diagnostic and prognostic purposes. In this chapter, a number of pertinent urine analytes and methods of banking urine samples for future analyses are discussed.
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Shen Q, Björkesten J, Galli J, Ekman D, Broberg J, Nordberg N, Tillander A, Kamali-Moghaddam M, Tybring G, Landegren U. Strong impact on plasma protein profiles by precentrifugation delay but not by repeated freeze-thaw cycles, as analyzed using multiplex proximity extension assays. Clin Chem Lab Med 2018; 56:582-594. [PMID: 29040064 DOI: 10.1515/cclm-2017-0648] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/11/2017] [Indexed: 01/06/2023]
Abstract
Background A number of factors regarding blood collection, handling and storage may affect sample quality. The purpose of this study was to assess the impact on plasma protein profiles by delayed centrifugation and plasma separation and multiple freeze-thaw cycles. Methods Blood samples drawn from 16 healthy individuals were collected into ethylenediaminetetraacetic acid tubes and kept either at 4 °C or 22 °C for 1-36 h prior to centrifugation. Plasma samples prepared 1 h after venipuncture were also subjected to two to eight cycles of freezing at -80 °C and thawing at 22 °C. Multiplex proximity extension assay, an antibody-based protein assay, was used to investigate the influence on plasma proteins. Results Up to 36 h delay before blood centrifugation resulted in significant increases of 16 and 40 out of 139 detectable proteins in samples kept at 4 °C or 22 °C, respectively. Some increases became noticeable after 8 h delay at 4 °C but already after 1 h at 22 °C. For samples stored at 4 °C, epidermal growth factor (EGF), NF-kappa-B essential modulator, SRC, interleukin 16 and CD6 increased the most, whereas the five most significantly increased proteins after storage at 22 °C were CD40 antigen ligand (CD40-L), EGF, platelet-derived growth factor subunit B, C-X-C motif chemokine ligand 5 and matrix metallopeptidase 1 (MMP1). Only matrix metallopeptidase 7 (MMP7) decreased significantly over time and only after storage at 22 °C. No protein levels were found to be significantly affected by up to eight freeze-thaw cycles. Conclusions Plasma should be prepared from blood after a limited precentrifugation delay at a refrigerated temperature. By contrast, the influence by several freeze-thaw cycles on detectable protein levels in plasma was negligible.
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Affiliation(s)
- Qiujin Shen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University,Uppsala, Sweden
| | - Johan Björkesten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University,Uppsala, Sweden
| | - Joakim Galli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University,Uppsala, Sweden
| | | | | | | | - Annika Tillander
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University,Uppsala, Sweden
| | - Gunnel Tybring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University,Uppsala, Sweden
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Li Q, Wang X, Li X, He X, Wan Q, Yin J, Sun J, Yang X, Chen Q, Miao X. Obtaining High-Quality Blood Specimens for Downstream Applications: A Review of Current Knowledge and Best Practices. Biopreserv Biobank 2018; 16:411-418. [PMID: 30383403 DOI: 10.1089/bio.2018.0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood is a biological fluid that contains multiple blood fraction and cellular components. High-quality blood specimens are essential prerequisites for various downstream applications such as molecular epidemiology studies, genomics, and proteomics studies. Currently, protocols and research publications concerning the collection, handling, preservation, and stability of blood or blood fractions are constantly emerging. Moreover, standardized guidelines are a requirement for biorepositories to tightly control preanalytical variables originating from these procedures and obtain high-quality blood specimen for downstream analyses. In this review article, we summarize the best practices and fit-for-purpose protocols regarding blood collection, processing, storage, and stability. In addition, we present some typical quality biomarkers, which could be used to evaluate the integrity of blood specimens.
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Affiliation(s)
- Qiyuan Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qian Wan
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaoping Yang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiaohong Chen
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xinyuan Miao
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
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Landegren U, Al-Amin RA, Björkesten J. A myopic perspective on the future of protein diagnostics. N Biotechnol 2018; 45:14-18. [DOI: 10.1016/j.nbt.2018.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 01/09/2023]
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Abstract
Aim: We tested a large set (n = 181) of wet urine and dried urine samples spotted on regular cosmetic cotton swabs for comparative UHPLC–MS/MS analysis of various metabolites across a wide polarity and structural range. Results/methodology: The agreement of measurements between conventional 24 h urines and dried urine spots made from them in situ was evaluated by Passing–Bablok regression and Bland–Altman analysis after creatinine correction. There was full agreement in qualitative results but quantitative analysis revealed underestimation of dried urine spots in some cases. The dried urine samples contained analytes at measurable levels for at least 9 months. Conclusion: Although this technique seems very promising more methodological studies have to be conducted in order to improve applicability of dried urine microvolume fluidic sampling for quantitative analysis.
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Establishing a Twin Register: An Invaluable Resource for (Behavior) Genetic, Epidemiological, Biomarker, and ‘Omics’ Studies. Twin Res Hum Genet 2018; 21:239-252. [DOI: 10.1017/thg.2018.23] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Twin registers are wonderful research resources for research applications in medical and behavioral genetics, epidemiology, psychology, molecular genetics, and other areas of research. New registers continue to be launched all over the world as researchers from different disciplines recognize the potential to boost and widen their research agenda. In this article, we discuss multiple aspects that need to be taken into account when initiating a register, from its preliminary sketch to its actual development. This encompasses aspects related to the strategic planning and key elements of research designs, promotion and management of a twin register, including recruitment and retaining of twins and family members of twins, phenotyping, database organization, and collaborations between registers. We also present information on questions unique to twin registers and twin-biobanks, such as the assessment of zygosity by SNP arrays, the design of (biomarker) studies involving related participants, and the analyses of clustered data. Altogether, we provide a number of basic guidelines and recommendations for reflection when planning a twin register.
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Tan P, Pepin É, Lavoie JL. Mouse Adipose Tissue Collection and Processing for RNA Analysis. J Vis Exp 2018. [PMID: 29443083 DOI: 10.3791/57026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Compared to other tissues, white adipose tissue has a considerably less RNA and protein content for downstream applications such as real-time PCR and Western Blot, since it mostly contains lipids. RNA isolation from adipose tissue samples is also challenging as extra steps are required to avoid these lipids. Here, we present a procedure to collect three anatomically different white adipose tissues from mice, to process these samples and perform RNA isolation. We further describe the synthesis of cDNA and gene expression experiments using real-time PCR. The hereby described protocol allows the reduction of contamination from the animal's hair and blood on fat pads as well as cross-contamination between different fat pads during tissue collection. It has also been optimized to ensure adequate quantity and quality of the RNA extracted. This protocol can be widely applied to any mouse model where adipose tissue samples are required for routine experiments such as real-time PCR but is not intended for isolation from primary adipocytes cell culture.
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Affiliation(s)
- Paul Tan
- Centre de Recherche du Centre Hospitalier, Université de Montréal; Department of Biochemistry and Molecular Medicine, Université de Montréal
| | - Émilie Pepin
- Centre de Recherche du Centre Hospitalier, Université de Montréal; Montreal Diabetes Research Center
| | - Julie L Lavoie
- Centre de Recherche du Centre Hospitalier, Université de Montréal; Department of Kinesiology, Université de Montréal; Montreal Diabetes Research Center;
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Ruiz CA, Chaney ME, Tosi AJ. Medical-grade buccal swabs versus drugstore cotton swabs: No difference in DNA yield. MethodsX 2018; 5:39-42. [PMID: 30622908 PMCID: PMC6318096 DOI: 10.1016/j.mex.2018.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/12/2018] [Indexed: 12/01/2022] Open
Abstract
We tested three types of medical-grade buccal swabs against standard cotton swabs for differences in DNA yield. A panel of swab types – one drugstore (Q-tips®) and three medical-grade – was used for buccal cell collection from three different individuals. DNA was extracted from all swabs using a QIAcube robot; quantitation values were measured by an Alu-based qPCR assay; and differences were compared through a 2-way ANOVA. Our results demonstrate that cotton swabs recover as much DNA as medical-grade swabs, but at a tremendously lower cost. Cotton swabs also display the greatest consistency of DNA yield, as indicated by the lowest coefficient of variation among the four tested swab types. These findings suggest that the use of standard cotton swabs for buccal cell collection offers not only a significant cost savings, but a more consistent method compared to the use of medical-grade swabs.
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Affiliation(s)
- Cody A Ruiz
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
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Impact of Preanalytical Handling and Timing for Peripheral Blood Mononuclear Cells Isolation and RNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Int J Biol Markers 2018; 27:e90-8. [DOI: 10.5301/jbm.2012.9235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2012] [Indexed: 02/04/2023]
Abstract
Multicenter studies and biobanking projects require blood transportation from the participating center to a central collection or diagnostic laboratory. The impact of time delays between venous blood collection and peripheral blood mononuclear cells (PBMC) isolation prior to RNA extraction may affect the quality and quantity of isolated nucleic acids for genomic applications. Thus, standard operating procedure (SOP) optimization for the treatment of biological samples before RNA extraction is crucial in a biological repository. In order to define SOPs for whole blood preservation prior to RNA extraction, we sought to determine whether different blood storage times (0, 3, 6, 10, 24, and 30 hours) prior to PBMCs isolation and storage at –80°C, could affect the quality and quantity of extracted RNA. After spectrophotometric quantification, the quality and integrity of RNA were assessed by agarose gel electrophoresis, RNA integrity number and real time-PCR (RT-PCR). Across the different time points we did not observe significant differences within the first 24 hours of blood storage at room temperature, while a significant loss in RNA yield and integrity was detected between 24 and 30 hours. We conclude that time delays before PBMCs isolation prior to RNA extraction may have a significant impact on downstream molecular biological applications.
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41
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Chen WC, Kerr R, May A, Ndlovu B, Sobalisa A, Duze ST, Joseph L, Mathew CG, Babb de Villiers C. The Integrity and Yield of Genomic DNA Isolated from Whole Blood Following Long-Term Storage at -30°C. Biopreserv Biobank 2018; 16:106-113. [PMID: 29298092 DOI: 10.1089/bio.2017.0050] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Long-term storage of whole blood can affect the integrity of DNA if it is not done under optimal conditions. The aim of this study was to determine whether long-term storage (2-19 years) of whole blood samples at -30°C had a negative effect on the quality or quantity of genomic DNA that could be recovered at extraction. Genomic DNA was isolated from 2758 whole blood samples collected in 4 mL EDTA vacutainers from 1997 to 2012. DNA was extracted using the Qiagen® FlexiGene® DNA kit. The average storage duration at -30°C was 12 years. The quality and quantity of the isolated DNA were assessed using spectrophotometry (NanoDrop™), a fluorometric assay for double-stranded DNA (Qubit™), and agarose gel electrophoresis. The mean DNA yield per sample was found to be 114 μg from whole blood volumes that ranged from 0.5 to 4 mL. The mean A260/280 ratio and median A260/280 ratios were both 1.8. No correlation was found between the duration of storage and the total yield or the quality of DNA extracted. These data suggest that high-quality DNA can be extracted from whole blood samples that are stored at -30°C for up to 19 years.
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Affiliation(s)
- Wenlong Carl Chen
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,2 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa .,3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Robyn Kerr
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Andrew May
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Babongile Ndlovu
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa
| | - Anelisa Sobalisa
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Sanelisiwe T Duze
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,5 Centre for Enteric Diseases, National Institute for Communicable Diseases , Johannesburg, South Africa
| | - Lavania Joseph
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa
| | - Christopher G Mathew
- 2 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa .,6 Division of Medical Biochemistry, University of Cape Town , Cape Town, South Africa
| | - Chantal Babb de Villiers
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,7 Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge , Cambridge, United Kingdom
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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43
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Poe A, Duong NT, Bedi K, Kodani M. Stability of hepatitis C virus RNA and anti-HCV antibody in air-dried and freeze-dried human plasma samples. J Virol Methods 2017; 253:53-55. [PMID: 29248530 DOI: 10.1016/j.jviromet.2017.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/06/2023]
Abstract
Diagnosis of hepatitis C virus (HCV) infection is based on testing for antibodies to HCV (anti-HCV), hepatitis C core antigen (HCV cAg) and HCV RNA. To ensure quality control (QC) and quality assurance (QA), proficiency panels are provided by reference laboratories and various international organizations, requiring costly dry ice shipments to maintain specimen integrity. Alternative methods of specimen preservation and transport can save on shipping and handling and help in improving diagnostics by facilitating QA/QC of various laboratories especially in resource limited countries. Plasma samples positive for anti-HCV and HCV RNA were either dried using dried tube specimens (DTS) method or lyophilization for varying durations of time and temperature. Preservation of samples using DTS method resulted in loss of anti-HCV reactivity for low-positive samples and did not generate enough volume for HCV RNA testing. Lyophilized samples tested positive for anti-HCV even after storage at 4 °C and 25 °C for 12 weeks. Further, HCV RNA was detectable in 5 of 5 (100%) samples over the course of 12 week storage at 4, 25, 37 and 45 °C. In conclusion, lyophilization of specimens maintains integrity of plasma samples for testing for markers of HCV infection and can be a potent mode of sharing proficiency samples without incurring huge shipping costs and avoids challenges with dry ice shipments between donor and recipient laboratories.
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Affiliation(s)
- Amanda Poe
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States
| | - Ngocvien Thi Duong
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States
| | - Kanwar Bedi
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States
| | - Maja Kodani
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States.
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44
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Dorta-Estremera S, Nehete PN, Yang G, He H, Nehete BP, Shelton KK, Barry MA, Sastry KJ. Minimally invasive monitoring of CD4 T cells at multiple mucosal tissues after intranasal vaccination in rhesus macaques. PLoS One 2017; 12:e0188807. [PMID: 29220358 PMCID: PMC5722341 DOI: 10.1371/journal.pone.0188807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/12/2017] [Indexed: 02/03/2023] Open
Abstract
Studies in nonhuman primates (NHP) for prospective immune cell monitoring subsequent to infection and/or vaccination usually rely on periodic sampling of the blood samples with only occasional collections of biopsies from mucosal tissues because of safety concerns and practical constraints. Here we present evidence in support of cytobrush sampling of oral, rectal, and genital mucosal tissues as a minimally invasive approach for the phenotypic analyses of different T cells subsets de novo as well as prospectively after intranasal immunization in rhesus macaques. Significant percentages of viable lymphocytes were obtained consistently from both naïve and chronically SIV-infected rhesus macaques. The percentages of CD3+ T cells in the blood were significantly higher compared to those in the mucosal tissues analyzed in the naïve animals, while in the SIV+ animals the CD3+ T cells were significantly elevated in the rectal tissues, relative to all other sites analyzed. In the naïve, but not SIV+ macaques, the rectal and vaginal mucosal tissues, compared to oral mucosa and blood, showed higher diversity and percentages of CD4+ T cells expressing the HIV entry co-receptor CCR5 and mucosal specific adhesion (CD103) as well as activation (HLA-DR) and proliferation (Ki67) markers. Sequential daily cytobrush sampling from the oral, rectal, and genital mucosal tissues was performed in SIV+ animals from an ongoing study where they were administered intranasal immunization with adenoviral vectored vaccines incorporating the green fluorescent protein (GFP) reporter gene. We detected a transient increase in GFP+ CD4 T cells in only oral mucosa suggesting limited mucosal trafficking. In general, CD4+ and CD8+ T cells expressing Ki67 transiently increased in all mucosal tissues, but those expressing the CCR5, HLA-DR, and CD103 markers exhibited minor changes. We propose the minimally invasive cytobrush sampling as a practical approach for effective and prospective immune monitoring of the oral-genital mucosal tissues in NHP.
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Affiliation(s)
- Stephanie Dorta-Estremera
- The University of Texas MD Anderson Cancer Center, Department of Immunology, Houston, TX, United States of America
| | - Pramod N. Nehete
- The University of Texas MD Anderson Cancer Center, Department of Veterinary Sciences, Bastrop, TX, United States of America
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, United States of America
| | - Guojun Yang
- The University of Texas MD Anderson Cancer Center, Department of Immunology, Houston, TX, United States of America
| | - Hong He
- The University of Texas MD Anderson Cancer Center, Department of Stem Cell Transplantation, Houston, TX, United States of America
| | - Bharti P. Nehete
- The University of Texas MD Anderson Cancer Center, Department of Veterinary Sciences, Bastrop, TX, United States of America
| | - Kathryn K. Shelton
- The University of Texas MD Anderson Cancer Center, Department of Veterinary Sciences, Bastrop, TX, United States of America
| | - Michael A. Barry
- Mayo Clinic, Department of Internal Medicine, Division of Infectious Diseases, Rochester, MN, United States of America
- Mayo Clinic, Department of Molecular Medicine, Rochester, MN, United States of America
- Mayo Clinic, Department of Immunology, Rochester, MN, United States of America
- Mayo Clinic, Translational Immunology Virology and Biodefense Program, Rochester, MN, United States of America
| | - K. Jagannadha Sastry
- The University of Texas MD Anderson Cancer Center, Department of Immunology, Houston, TX, United States of America
- The University of Texas MD Anderson Cancer Center, Department of Veterinary Sciences, Bastrop, TX, United States of America
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, United States of America
- * E-mail:
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Hoenderboom BM, van Ess EF, van den Broek IVF, van Loo IHM, Hoebe CJPA, Ouburg S, Morré SA. Chlamydia trachomatis antibody detection in home-collected blood samples for use in epidemiological studies. J Microbiol Methods 2017; 144:164-167. [PMID: 29196272 DOI: 10.1016/j.mimet.2017.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/24/2017] [Accepted: 11/26/2017] [Indexed: 11/18/2022]
Abstract
Capillary blood collected in serum tubes was subjected to centrifugation delay while stored at room temperature. Chlamydia trachomatis (CT) IgG concentrations in aliquoted serum of these blood samples remained stable for seven days after collection. CT IgG concentrations can reliably be measured in mailed blood samples in epidemiological studies.
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Affiliation(s)
- B M Hoenderboom
- Epidemiology and Surveillance Unit, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Laboratory of Immunogenetics, Department Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
| | - E F van Ess
- Laboratory of Immunogenetics, Department Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - I V F van den Broek
- Epidemiology and Surveillance Unit, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - I H M van Loo
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - C J P A Hoebe
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands; Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Geleen, The Netherlands
| | - S Ouburg
- Laboratory of Immunogenetics, Department Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - S A Morré
- Laboratory of Immunogenetics, Department Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands; Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Maastricht, The Netherlands
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Ochmann SE, Vietz C, Trofymchuk K, Acuna GP, Lalkens B, Tinnefeld P. Optical Nanoantenna for Single Molecule-Based Detection of Zika Virus Nucleic Acids without Molecular Multiplication. Anal Chem 2017; 89:13000-13007. [DOI: 10.1021/acs.analchem.7b04082] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sarah E. Ochmann
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Carolin Vietz
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Kateryna Trofymchuk
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Guillermo P. Acuna
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Birka Lalkens
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
- Department
of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5-13, 81377 Muenchen, Germany
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47
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Implementation of daily chlorhexidine bathing to reduce colonization by multidrug-resistant organisms in a critical care unit. Am J Infect Control 2017; 45:1014-1017. [PMID: 28431846 DOI: 10.1016/j.ajic.2017.02.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND Colonized patients are a reservoir for transmission of multidrug-resistant organisms (MDROs). Not many studies have examined the effectiveness of daily chlorhexidine gluconate (CHG) bathing under routine care conditions. We present a descriptive analysis of the trends of MDRO colonization following implementation of daily CHG bathing under routine clinical conditions in an intensive care unit (ICU). METHODS From May 2010-January 2011, we screened patients admitted to a 24-bed ICU for and methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and fluoroquinolone-resistant gram-negative bacilli (FQRGNB). We calculated and plotted monthly incidence and prevalence of colonization of these MDROs. RESULTS Prevalence decreased in the immediate aftermath of daily CHG bathing implementation and generally remained at that level throughout the observation period. We observed low rates of incidence of MDRO colonization with VRE>FQRGNB>MRSA. Monthly prevalence of colonization and incidence for the composite of MRSA, VRE, and/or FQRGNB was 1.9%-27.9% and 0-1.1/100 patient-days, respectively. CONCLUSIONS Following the implementation of daily CHG bathing, the incidence of MDROs remained low and constant over time, whereas the prevalence decreased immediately after the implementation.
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Dudzik D, Barbas-Bernardos C, García A, Barbas C. Quality assurance procedures for mass spectrometry untargeted metabolomics. a review. J Pharm Biomed Anal 2017; 147:149-173. [PMID: 28823764 DOI: 10.1016/j.jpba.2017.07.044] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 12/16/2022]
Abstract
Untargeted metabolomics, as a global approach, has already proven its great potential and capabilities for the investigation of health and disease, as well as the wide applicability for other research areas. Although great progress has been made on the feasibility of metabolomics experiments, there are still some challenges that should be faced and that includes all sources of fluctuations and bias affecting every step involved in multiplatform untargeted metabolomics studies. The identification and reduction of the main sources of unwanted variation regarding the pre-analytical, analytical and post-analytical phase of metabolomics experiments is essential to ensure high data quality. Nowadays, there is still a lack of information regarding harmonized guidelines for quality assurance as those available for targeted analysis. In this review, sources of variations to be considered and minimized along with methodologies and strategies for monitoring and improvement the quality of the results are discussed. The given information is based on evidences from different groups among our own experiences and recommendations for each stage of the metabolomics workflow. The comprehensive overview with tools presented here might serve other researchers interested in monitoring, controlling and improving the reliability of their findings by implementation of good experimental quality practices in the untargeted metabolomics study.
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Affiliation(s)
- Danuta Dudzik
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Cecilia Barbas-Bernardos
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Antonia García
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
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49
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Recommendations for clinical biomarker specimen preservation and stability assessments. Bioanalysis 2017; 9:643-653. [PMID: 28508714 DOI: 10.4155/bio-2017-0009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
With the wide use of biomarkers to enable critical drug-development decisions, there is a growing concern from scientific community on the need for a 'standardized process' for ensuring biomarker specimen stability and hence, a strong desire to share best practices on preserving the integrity of biomarker specimens in clinical trials and the design of studies to evaluate analyte stability. By leveraging representative industry experience, we have attempted to provide an overview of critical aspects of biomarker specimen stability commonly encountered during clinical development, including: planning of clinical sample collection procedures, clinical site training, selection of sample preservation buffers, shipping logistics, fit-for-purpose stability assessments in the analytical laboratory and presentation of case studies covering widely utilized biomarker specimen types.
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50
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Sinha A, Alfaro J, Kislinger T. Characterization of Protein Content Present in Exosomes Isolated from Conditioned Media and Urine. ACTA ACUST UNITED AC 2017; 87:24.9.1-24.9.12. [PMID: 28150884 DOI: 10.1002/cpps.23] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cells secrete biomolecules into the extracellular space as a way of intercellular communication. Secreted proteins can act as ligands that engage specific receptors-on the same cell, nearby cells, or distant cells-and induce defined signaling pathways. Proteins and other biomolecules can also be packaged as cargo molecules within vesicles that are released to the extracellular space (termed extracellular vesicles or EVs). A subclass of such EVs, exosomes have been shown to horizontally transfer information. In recent years, exosomes have sparked tremendous interest in biological research, both for the discovery of novel biomarkers and for the identification of signaling molecules, as part of their cargo. Although multiple methods have been described for the isolation of exosomes, described here is a simple differential centrifugation approach that is well suited for the isolation of exosomes from conditioned cell culture media and urine. Mass spectrometry provides an ideal method to comprehensively analyze the protein cargo of exosomes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ankit Sinha
- University of Toronto, Department of Medical Biophysics, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Javier Alfaro
- University of Toronto, Department of Medical Biophysics, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Thomas Kislinger
- University of Toronto, Department of Medical Biophysics, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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