Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling
(1) Background: Extracellular vesicles (EVs) have emerged as crucial players in the communication between cells in both physiological and pathological scenarios. The functions of EVs are strongly determined by their molecular content, which includes all bioactive molecules, such as proteins, lipids,...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/14/13/3258 |
| _version_ | 1797480619047911424 |
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| author | Julia Elzanowska Laura Berrocal Beatriz García-Peláez Marta Vives-Usano Beatriz Passos Sebo Joana Maia Silvia Batista Jaakko Teppo Markku Varjosalo Maria Carolina Strano Moraes Miguel Ángel Molina-Vila Bruno Costa-Silva |
| author_facet | Julia Elzanowska Laura Berrocal Beatriz García-Peláez Marta Vives-Usano Beatriz Passos Sebo Joana Maia Silvia Batista Jaakko Teppo Markku Varjosalo Maria Carolina Strano Moraes Miguel Ángel Molina-Vila Bruno Costa-Silva |
| author_sort | Julia Elzanowska |
| collection | DOAJ |
| description | (1) Background: Extracellular vesicles (EVs) have emerged as crucial players in the communication between cells in both physiological and pathological scenarios. The functions of EVs are strongly determined by their molecular content, which includes all bioactive molecules, such as proteins, lipids, RNA, and, as more recently described, double-stranded DNA. It has been shown that in oncological settings DNA associated with EVs (EV-DNA) is representative of the genome of parental cells and that it reflects the mutational status of the tumor, gaining much attention as a promising source of biomarker mutant DNA. However, one of the challenges in studies of EV-DNA is the lack of standardization of protocols for the DNA extraction from EVs, as well as ways to assess quality control, which hinders its future implementation in clinics. (2) Methods: We performed a comprehensive comparison of commonly used approaches for EV-DNA extraction by assessing DNA quantity, quality, and suitability for downstream analyses. (3) Results: We here established strategic points to consider for EV-DNA preparation for mutational analyses, including qPCR and NGS. (4) Conclusions: We put in place a workflow that can be applied for the detection of clinically relevant mutations in the EV-DNA of cancer patients. |
| first_indexed | 2024-03-09T22:02:39Z |
| format | Article |
| id | doaj.art-7fd3a23597ab44da87f8e0575995c12d |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-09T22:02:39Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-7fd3a23597ab44da87f8e0575995c12d2023-11-23T19:46:59ZengMDPI AGCancers2072-66942022-07-011413325810.3390/cancers14133258Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation ProfilingJulia Elzanowska0Laura Berrocal1Beatriz García-Peláez2Marta Vives-Usano3Beatriz Passos Sebo4Joana Maia5Silvia Batista6Jaakko Teppo7Markku Varjosalo8Maria Carolina Strano Moraes9Miguel Ángel Molina-Vila10Bruno Costa-Silva11Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, PortugalLaboratorio de Oncología/Pangaea Oncology, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, SpainLaboratorio de Oncología/Pangaea Oncology, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, SpainLaboratorio de Oncología/Pangaea Oncology, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, SpainChampalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, PortugalChampalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, PortugalChampalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, PortugalDrug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, FinlandMolecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, FinlandChampalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, PortugalLaboratorio de Oncología/Pangaea Oncology, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, SpainChampalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, Portugal(1) Background: Extracellular vesicles (EVs) have emerged as crucial players in the communication between cells in both physiological and pathological scenarios. The functions of EVs are strongly determined by their molecular content, which includes all bioactive molecules, such as proteins, lipids, RNA, and, as more recently described, double-stranded DNA. It has been shown that in oncological settings DNA associated with EVs (EV-DNA) is representative of the genome of parental cells and that it reflects the mutational status of the tumor, gaining much attention as a promising source of biomarker mutant DNA. However, one of the challenges in studies of EV-DNA is the lack of standardization of protocols for the DNA extraction from EVs, as well as ways to assess quality control, which hinders its future implementation in clinics. (2) Methods: We performed a comprehensive comparison of commonly used approaches for EV-DNA extraction by assessing DNA quantity, quality, and suitability for downstream analyses. (3) Results: We here established strategic points to consider for EV-DNA preparation for mutational analyses, including qPCR and NGS. (4) Conclusions: We put in place a workflow that can be applied for the detection of clinically relevant mutations in the EV-DNA of cancer patients.https://www.mdpi.com/2072-6694/14/13/3258extracellular vesicles (EVs)DNAmutation profilingliquid biopsy |
| spellingShingle | Julia Elzanowska Laura Berrocal Beatriz García-Peláez Marta Vives-Usano Beatriz Passos Sebo Joana Maia Silvia Batista Jaakko Teppo Markku Varjosalo Maria Carolina Strano Moraes Miguel Ángel Molina-Vila Bruno Costa-Silva Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling Cancers extracellular vesicles (EVs) DNA mutation profiling liquid biopsy |
| title | Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling |
| title_full | Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling |
| title_fullStr | Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling |
| title_full_unstemmed | Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling |
| title_short | Defining Optimal Conditions for Tumor Extracellular Vesicle DNA Extraction for Mutation Profiling |
| title_sort | defining optimal conditions for tumor extracellular vesicle dna extraction for mutation profiling |
| topic | extracellular vesicles (EVs) DNA mutation profiling liquid biopsy |
| url | https://www.mdpi.com/2072-6694/14/13/3258 |
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