A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling

Abstract Extracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amen...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jeremy W. Roy, Catherine A. Taylor, Annie P. Beauregard, Surendar R. Dhadi, D. Craig Ayre, Sheena Fry, Simi Chacko, Gabriel Wajnberg, Andrew P. Joy, Ngoc-Nu Mai-Thi, Nicolas Crapoulet, David A. Barnett, Anirban Ghosh, Stephen M. Lewis, Rodney J. Ouellette
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e9305174dbe849828499522865518299
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:e9305174dbe849828499522865518299
record_format	dspace
spelling	oai:doaj.org-article:e9305174dbe8498284995228655182992021-12-02T14:27:56ZA multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling10.1038/s41598-021-87526-y2045-2322https://doaj.org/article/e9305174dbe8498284995228655182992021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87526-yhttps://doaj.org/toc/2045-2322Abstract Extracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amenable to a clinical diagnostic lab setting and is compatible with multiple types of biomarker analyses. We have previously designed a synthetic peptide, known as Vn96 (ME kit), which efficiently isolates EVs from multiple biofluids in a short timeframe without the use of specialized lab equipment. Moreover, it has recently been shown that Vn96 also facilitates the co-isolation of cell-free DNA (cfDNA) along with EVs. Herein we describe an optimized method for Vn96 affinity-based EV and cfDNA isolation from plasma samples and have developed a multiparametric extraction protocol for the sequential isolation of DNA, RNA, and protein from the same plasma EV and cfDNA sample. We are able to isolate sufficient material by the multiparametric extraction protocol for use in downstream analyses, including ddPCR (DNA) and ‘omic profiling by both small RNA sequencing (RNA) and mass spectrometry (protein), from a minimum volume (4 mL) of plasma. This multiparametric extraction protocol should improve the ability to analyse multiple biomarker materials (DNA, RNA and protein) from the same limited starting material, which may improve the sensitivity and specificity of liquid biopsy tests that exploit EV-based and cfDNA biomarkers for disease detection and monitoring.Jeremy W. RoyCatherine A. TaylorAnnie P. BeauregardSurendar R. DhadiD. Craig AyreSheena FrySimi ChackoGabriel WajnbergAndrew P. JoyNgoc-Nu Mai-ThiNicolas CrapouletDavid A. BarnettAnirban GhoshStephen M. LewisRodney J. OuelletteNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeremy W. Roy Catherine A. Taylor Annie P. Beauregard Surendar R. Dhadi D. Craig Ayre Sheena Fry Simi Chacko Gabriel Wajnberg Andrew P. Joy Ngoc-Nu Mai-Thi Nicolas Crapoulet David A. Barnett Anirban Ghosh Stephen M. Lewis Rodney J. Ouellette A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
description	Abstract Extracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amenable to a clinical diagnostic lab setting and is compatible with multiple types of biomarker analyses. We have previously designed a synthetic peptide, known as Vn96 (ME kit), which efficiently isolates EVs from multiple biofluids in a short timeframe without the use of specialized lab equipment. Moreover, it has recently been shown that Vn96 also facilitates the co-isolation of cell-free DNA (cfDNA) along with EVs. Herein we describe an optimized method for Vn96 affinity-based EV and cfDNA isolation from plasma samples and have developed a multiparametric extraction protocol for the sequential isolation of DNA, RNA, and protein from the same plasma EV and cfDNA sample. We are able to isolate sufficient material by the multiparametric extraction protocol for use in downstream analyses, including ddPCR (DNA) and ‘omic profiling by both small RNA sequencing (RNA) and mass spectrometry (protein), from a minimum volume (4 mL) of plasma. This multiparametric extraction protocol should improve the ability to analyse multiple biomarker materials (DNA, RNA and protein) from the same limited starting material, which may improve the sensitivity and specificity of liquid biopsy tests that exploit EV-based and cfDNA biomarkers for disease detection and monitoring.
format	article
author	Jeremy W. Roy Catherine A. Taylor Annie P. Beauregard Surendar R. Dhadi D. Craig Ayre Sheena Fry Simi Chacko Gabriel Wajnberg Andrew P. Joy Ngoc-Nu Mai-Thi Nicolas Crapoulet David A. Barnett Anirban Ghosh Stephen M. Lewis Rodney J. Ouellette
author_facet	Jeremy W. Roy Catherine A. Taylor Annie P. Beauregard Surendar R. Dhadi D. Craig Ayre Sheena Fry Simi Chacko Gabriel Wajnberg Andrew P. Joy Ngoc-Nu Mai-Thi Nicolas Crapoulet David A. Barnett Anirban Ghosh Stephen M. Lewis Rodney J. Ouellette
author_sort	Jeremy W. Roy
title	A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
title_short	A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
title_full	A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
title_fullStr	A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
title_full_unstemmed	A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
title_sort	multiparametric extraction method for vn96-isolated plasma extracellular vesicles and cell-free dna that enables multi-omic profiling
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e9305174dbe849828499522865518299
work_keys_str_mv	AT jeremywroy amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT catherineataylor amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT anniepbeauregard amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT surendarrdhadi amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT dcraigayre amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT sheenafry amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT simichacko amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT gabrielwajnberg amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT andrewpjoy amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT ngocnumaithi amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT nicolascrapoulet amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT davidabarnett amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT anirbanghosh amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT stephenmlewis amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT rodneyjouellette amultiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT jeremywroy multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT catherineataylor multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT anniepbeauregard multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT surendarrdhadi multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT dcraigayre multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT sheenafry multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT simichacko multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT gabrielwajnberg multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT andrewpjoy multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT ngocnumaithi multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT nicolascrapoulet multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT davidabarnett multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT anirbanghosh multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT stephenmlewis multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling AT rodneyjouellette multiparametricextractionmethodforvn96isolatedplasmaextracellularvesiclesandcellfreednathatenablesmultiomicprofiling
_version_	1718391283999834112

A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling

Ejemplares similares