1
|
Lucien F, Gustafson D, Lenassi M, Li B, Teske JJ, Boilard E, von Hohenberg KC, Falcón‐Perez JM, Gualerzi A, Reale A, Jones JC, Lässer C, Lawson C, Nazarenko I, O'Driscoll L, Pink R, Siljander PR, Soekmadji C, Hendrix A, Welsh JA, Witwer KW, Nieuwland R. MIBlood-EV: Minimal information to enhance the quality and reproducibility of blood extracellular vesicle research. J Extracell Vesicles 2023; 12:e12385. [PMID: 38063210 PMCID: PMC10704543 DOI: 10.1002/jev2.12385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Blood is the most commonly used body fluid for extracellular vesicle (EV) research. The composition of a blood sample and its derivatives (i.e., plasma and serum) are not only donor-dependent but also influenced by collection and preparation protocols. Since there are hundreds of pre-analytical protocols and over forty variables, the development of standard operating procedures for EV research is very challenging. To improve the reproducibility of blood EV research, the International Society for Extracellular Vesicles (ISEV) Blood EV Task Force proposes standardized reporting of (i) the applied blood collection and preparation protocol and (ii) the quality of the prepared plasma and serum samples. Gathering detailed information will provide insight into the performance of the protocols and more effectively identify potential confounders in the prepared plasma and serum samples. To collect this information, the ISEV Blood EV Task Force created the Minimal Information for Blood EV research (MIBlood-EV), a tool to record and report information about pre-analytical protocols used for plasma and serum preparation as well as assays used to assess the quality of these preparations. This tool does not require modifications of established local pre-analytical protocols and can be easily implemented to enhance existing databases thereby enabling evidence-based optimization of pre-analytical protocols through meta-analysis. Taken together, insight into the quality of prepared plasma and serum samples will (i) improve the quality of biobanks for EV research, (ii) guide the exchange of plasma and serum samples between biobanks and laboratories, (iii) facilitate inter-laboratory comparative EV studies, and (iv) improve the peer review process.
Collapse
Affiliation(s)
- Fabrice Lucien
- Department of UrologyMayo ClinicRochesterMinnesotaUSA
- Department of ImmunologyMayo ClinicRochesterMinnesotaUSA
| | - Dakota Gustafson
- Department of Laboratory Medicine & PathobiologyUniversity of TorontoTorontoOntarioCanada
- Toronto General Hospital Research InstituteTorontoOntarioCanada
- Department of Public Health SciencesQueen's UniversityKingstonOntarioCanada
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of MedicineUniversity of LjubljanaLjubljanaSlovenia
| | - Bo Li
- Department of Laboratory MedicineNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Laboratory of Experimental Clinical Chemistry, and Amsterdam Vesicle CenterAmsterdam UMClocation AMCAmsterdamNetherlands
| | | | - Eric Boilard
- Centre de Recherche du CHU de Québec – Université Laval, Département de microbiologie et immunologieFaculté de Médecine de l'Université LavalQuébecQuebecCanada
| | | | - Juan Manual Falcón‐Perez
- Exosomes laboratory and Metabolomics PlatformCIC bioGUNE‐BRTADerioSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | | | - Antonia Reale
- Division of Blood CancersMonash University ‐ Alfred HealthMelbourneVictoriaAustralia
| | - Jennifer C. Jones
- Laboratory of Pathology, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Cecilia Lässer
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | | | - Irina Nazarenko
- Institute for Infection Prevention and Control, Faculty of MedicineUniversity of Freiburg, Freiburg, Germany, German Cancer Consortium
- Partner Site Freiburg and German Cancer Research CenterHeidelbergGermany
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical Sciences & Trinity Biomedical Sciences Institute & Trinity St. James's Cancer InstituteTrinity College DublinDublinIreland
| | - Ryan Pink
- Faculty Health and Life SciencesOxford Brookes UniversityOxfordUnited Kingdom of Great Britain and Northern Ireland
| | - Pia R‐M Siljander
- EV‐group, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, and Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical BiosciencesUniversity of HelsinkiHelsinkiFinland
| | - Carolina Soekmadji
- School of Biomedical Sciences, Faculty of MedicineUniversity of QueenslandBrisbaneAustralia
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent UniversityGhentBelgium
| | - Joshua A Welsh
- School of Medicine, Department of Molecular and Comparative Pathobiology, and Department of NeurologyJohns Hopkins UniversityBaltimoreMarylandUnited States
| | - Kenneth W. Witwer
- School of Medicine, Department of Molecular and Comparative Pathobiology, and Department of NeurologyJohns Hopkins UniversityBaltimoreMarylandUnited States
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, and Amsterdam Vesicle CenterAmsterdam UMClocation AMCAmsterdamNetherlands
| |
Collapse
|
2
|
Want A, Staniak K, Grabowska-Pyrzewicz W, Fesiuk A, Barczak A, Gabryelewicz T, Kulczyńska-Przybik A, Mroczko B, Wojda U. Optimized RT-qPCR and a novel normalization method for validating circulating miRNA biomarkers in ageing-related diseases. Sci Rep 2023; 13:20869. [PMID: 38012217 PMCID: PMC10682428 DOI: 10.1038/s41598-023-47971-3] [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: 06/06/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Circulating miRNAs have potential as minimally invasive biomarkers for diagnosing various diseases, including ageing-related disorders such as Alzheimer's disease (AD). However, the lack of standardization in the common analysis method, RT-qPCR, and specifically in the normalization step, has resulted in inconsistent data across studies, hindering miRNA clinical implementation as well as basic research. To address this issue, this study proposes an optimized protocol for key steps in miRNA profiling, which incorporates absorbance-based haemolysis detection for assessing sample quality, double spike-in controls for miRNA isolation and reverse transcription, and the use of 7 stable normalizers verified in an aging population, including healthy subjects and individuals at different stages of Alzheimer's disease (140 subjects). The stability of these 7 normalizers was demonstrated using our novel method called BestmiRNorm for identifying optimal normalizers. BestmiRNorm, developed utilizing the Python programming language, enables the assessment of up to 11 potential normalizers. The standardized application of this optimized RT-qPCR protocol and the recommended normalizers are crucial for the development of miRNAs as biomarkers for AD and other ageing-related diseases in clinical diagnostics and basic research.
Collapse
Affiliation(s)
- Andrew Want
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Staniak
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wioleta Grabowska-Pyrzewicz
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Fesiuk
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Dementia Diseases Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Gabryelewicz
- Dementia Diseases Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kulczyńska-Przybik
- Department of Neurodegeneration Diagnostics, Faculty of Medicine, Medical University of Bialystok, Białystok, Poland
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Faculty of Medicine, Medical University of Bialystok, Białystok, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
| |
Collapse
|
3
|
Ma Z, Li Y, Lu Z, Pan J, Li M. A novel biosensor-based method for the detection of p-nitrophenol in agricultural soil. CHEMOSPHERE 2023; 313:137306. [PMID: 36410515 DOI: 10.1016/j.chemosphere.2022.137306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/19/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Directly measurement of the bioavailable concentration of soil contaminants is essential for their accurate risk assessment. In this study, we successfully modified and identified the key genetic elements (pobR1-3) for the bio-detection of p-nitrophenol and synthesized five novel whole-cell biosensors (Escherichia coli BL21/pPNP-mrfp, E. coli BL21/pPNP-CFP, E. coli BL21/pPNP-YFP, E. coli BL21/pPNP-GFP, and E. coli BL21/pPNP-amilCP) to directly detect the concentration of p-nitrophenol in soils. These biosensor methods contained a simple biosensor activation and sample extraction step, a cost-effective detection means, and a fast detection process (5 h) by using a 96-microwell plate with a low background value and high-reliability equation for p-nitrophenol detection. These biosensors had a detection limit of 6.21-25.2 μg/kg and a linear range of 10-10000 μg/kg for p-nitrophenol in four soils. All biosensors showed better detection performance in the detection of p-nitrophenol in soil samples. The biosensors method can help to quickly and directly assess the actual bioavailable fractions of p-nitrophenol in soils, thus facilitating to understand the environmental cycling of p-nitrophenol.
Collapse
Affiliation(s)
- Zhao Ma
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, 518060, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Yuanbo Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China.
| |
Collapse
|
4
|
Nuñez-Borque E, Betancor D, Pastor-Vargas C, Fernández-Bravo S, Martin-Blazquez A, Casado-Navarro N, López-Domínguez D, Gómez-López A, Rodriguez Del Rio P, Tramón P, Beitia JM, Moreno-Aguilar C, González-de-Olano D, Goikoetxea MJ, Ibáñez-Sandín MD, Laguna JJ, Cuesta-Herranz J, Esteban V. Personalized diagnostic approach and indirect quantification of extravasation in human anaphylaxis. Allergy 2023; 78:202-213. [PMID: 35841381 PMCID: PMC10087983 DOI: 10.1111/all.15443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Anaphylaxis is the most acute and life-threatening manifestation of allergic disorders. Currently, there is a need to improve its medical management and increase the understanding of its molecular mechanisms. This study aimed to quantify the extravasation underlying human anaphylactic reactions and propose new theragnostic approaches. METHODS Molecular determinations were performed in paired serum samples obtained during the acute phase and at baseline from patients presenting with hypersensitivity reactions. These were classified according to their severity as Grades 1, 2 and 3, the two latter being considered anaphylaxis. Tryptase levels were measured by ImmunoCAP, and serum protein concentration was quantified by Bradford assay. Human serum albumin (HSA) and haemoglobin beta subunit (HBB) levels were determined by Western blot and polyacrylamide gel electrophoresis, respectively. RESULTS A total of 150 patients were included in the study. Of them, 112 had experienced anaphylaxis (83 and 29 with Grade 2 and 3 reactions, respectively). Tryptase diagnostic efficiency substantially improved when considering patients' baseline values (33%-54%) instead of the acute value threshold (21%). Serum protein concentration and HSA significantly decreased in anaphylaxis (p < .0001). HSA levels dropped with the severity of the reaction (6% and 15% for Grade 2 and 3 reactions, respectively). Furthermore, HBB levels increased during the acute phase of all hypersensitivity reactions (p < .0001). CONCLUSIONS For the first time, the extravasation underlying human anaphylaxis has been evaluated based on the severity of the reaction using HSA and protein concentration measurements. Additionally, our findings propose new diagnostic and potential therapeutic approaches for this pathological event.
Collapse
Affiliation(s)
- Emilio Nuñez-Borque
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | - Diana Betancor
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Department of Allergy, Fundación Jiménez Díaz University Hospital, UAM, Madrid, Spain
| | | | | | | | - Natalia Casado-Navarro
- Department of Clinical Analysis, Fundación Jiménez Díaz University Hospital, UAM, Madrid, Spain
| | - David López-Domínguez
- Clinical Biostatistics Unit, IDIPHIM, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Alicia Gómez-López
- Department of Allergy, Fundación Jiménez Díaz University Hospital, UAM, Madrid, Spain
| | - Pablo Rodriguez Del Rio
- Allergy Department, Hospital Infantil Universitario Niño Jesús, Fundación HNJ, IIS-P, Madrid, Spain
| | - Paloma Tramón
- Department of Clinical Analysis, Fundación Jiménez Díaz University Hospital, UAM, Madrid, Spain
| | | | | | | | | | | | - José Julio Laguna
- Allergy Unit, Allergo-Anaesthesia Unit, Hospital Central de la Cruz Roja, Madrid, Spain.,Faculty of Medicine and Biomedicine, Alfonso X El Sabio University, Madrid, Spain
| | - Javier Cuesta-Herranz
- Department of Allergy, Fundación Jiménez Díaz University Hospital, UAM, Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Faculty of Medicine and Biomedicine, Alfonso X El Sabio University, Madrid, Spain
| |
Collapse
|