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Ortega-Pinazo J, Pacheco-Rodríguez MJ, Serrano-Castro PJ, Martínez B, Pinto-Medel MJ, Gómez-Zumaquero JM, Lago-Sampedro A, García-Díaz B, Estivill-Torrús G, Emilio Ferro Gallego P. Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices. Mol Biol Rep 2023; 50:9263-9271. [PMID: 37812354 DOI: 10.1007/s11033-023-08761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples. METHODS AND RESULTS In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used. DISCUSSION QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.
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Affiliation(s)
- J Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - M J Pacheco-Rodríguez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - P J Serrano-Castro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - B Martínez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Intercentros de Oncología Médica, Hospitales Universitarios Regional de Málaga y Virgen de la Victoria, Málaga, Spain
| | - M J Pinto-Medel
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - J M Gómez-Zumaquero
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - A Lago-Sampedro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - B García-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Guillermo Estivill-Torrús
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain.
| | - Pedro Emilio Ferro Gallego
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Biobank ECAI, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain.
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Vega Thurber R, Schmeltzer ER, Grottoli AG, van Woesik R, Toonen RJ, Warner M, Dobson KL, McLachlan RH, Barott K, Barshis DJ, Baumann J, Chapron L, Combosch DJ, Correa AMS, DeCarlo TM, Hagedorn M, Hédouin L, Hoadley K, Felis T, Ferrier-Pagès C, Kenkel C, Kuffner IB, Matthews J, Medina M, Meyer C, Oster C, Price J, Putnam HM, Sawall Y. Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration. PeerJ 2022; 10:e14176. [PMID: 36345483 PMCID: PMC9636870 DOI: 10.7717/peerj.14176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/13/2022] [Indexed: 12/15/2022] Open
Abstract
Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at -80 °C to -20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.
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Affiliation(s)
- Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Emily R. Schmeltzer
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Andréa G. Grottoli
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Robert van Woesik
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, Fl, United States
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States
| | - Mark Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Kerri L. Dobson
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Rowan H. McLachlan
- Department of Microbiology, Oregon State University, Corvallis, OR, United States,School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Katie Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Daniel J. Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States
| | - Justin Baumann
- Biology Department, Bowdoin College, Brunswick, ME, United States
| | - Leila Chapron
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | | | | | - Thomas M. DeCarlo
- College of Natural and Computational Sciences, Hawai’i Pacific University, Honolulu, HI, United States
| | - Mary Hagedorn
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States,Conservation Biology Institute, Smithsonian, Kāne’ohe, HI, United States
| | - Laetitia Hédouin
- Centre de Recherches Insulaires et Observatoire de l’Environnement, Chargée de Recherches CNRS, Papetō’ai, Moorea, French Polynesia
| | - Kenneth Hoadley
- Department of Biological Sciences, University of Alabama – Tuscaloosa, Tuscaloosa, AL, United States
| | - Thomas Felis
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | - Carly Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | | | - Jennifer Matthews
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian, Washington DC, United States
| | - Corinna Oster
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - James Price
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Yvonne Sawall
- Bermuda Institute of Ocean Sciences, St. George’s, St. George’s, Bermuda
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Browne DJ, Kelly AM, Brady JL, Doolan DL. A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs. Front Immunol 2022; 13:962220. [PMID: 36110843 PMCID: PMC9469018 DOI: 10.3389/fimmu.2022.962220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4+ or CD8+ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells (i.e., 100 Spot Forming Cells/106 PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration.
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Morocco's First Biobank: Establishment, Ethical Issues, Biomedical Research Opportunities, and Challenges. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8812609. [PMID: 33376744 PMCID: PMC7738781 DOI: 10.1155/2020/8812609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Background Biobanks are highly organized infrastructures that allow the storage of human biological specimens associated with donors' personal and clinical data. These infrastructures play a key role in the development of translational medical research. In this context, we launched, in November 2015, the first biobank in Morocco (BRO Biobank) in order to promote biomedical research and provide opportunities to include Moroccan and North African ethnic groups in international biomedical studies. Here, we present the setup and the sample characteristics of BRO Biobank. Methods Patients were recruited at several departments of two major health-care centers in the city of Oujda. Healthy donors were enrolled during blood donation campaigns all over Eastern Morocco. From each participant, personal, clinical, and biomedical data were collected, and several biospecimens were stored. Standard operating procedures have been established in accordance with international guidelines on human biobanks. Results Between November 2015 and July 2020, 2446 participants were recruited into the BRO Biobank, of whom 2013 were healthy donors, and 433 were patients. For healthy donors, the median age was 35 years with a range between 18 and 65 years and the consanguinity rate was 28.96%. For patients, the median age was 11 years with a range between 1 day and 83 years. Among these patients, 55% had rare diseases (hemoglobinopathies, intellectual disabilities, disorders of sex differentiation, myopathies, etc.), 13% had lung cancer, 4% suffered from hematological neoplasms, 3% were from the kidney transplantation project, and 25% had unknown diagnoses. The BRO Biobank has collected 5092 biospecimens, including blood, white blood cells, plasma, serum, urine, frozen tissue, FFPE tissue, and nucleic acids. A sample quality control has been implemented and suggested that samples of the BRO Biobank are of high quality and therefore suitable for high-throughput nucleic acid analysis. Conclusions The BRO Biobank is the largest sample collection in Morocco, and it is ready to provide samples to national and international research projects. Therefore, the BRO Biobank is a valuable resource for advancing translational medical research.
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Ferro P, Ortega-Pinazo J, Martínez B, Jiménez Á, Gómez-Zumaquero JM, Hortas ML, Díaz T. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank 2019; 17:577-582. [PMID: 31429592 DOI: 10.1089/bio.2019.0024] [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
Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.
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Affiliation(s)
- Pedro Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Jesús Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - Beatriz Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Álvaro Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | | | | | - Tatiana Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
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