PXD062837

PXD062837 is an original dataset announced via ProteomeXchange.

Title	Pre-Analytical Framework for Routine Clinical Use of Liquid Biopsies: Combining EVs and cfDNA
Description	Liquid biopsies hold significant potential for the non-invasive diagnostics of tumors and other diseases. While the clinical application of cell-free DNA (cfDNA) methodologies is emerging, the implementation of tumor-derived extracellular vesicles (EVs) as validated biomarkers is hindered by substantial pre-analytical variations. In this work, we are taking a step towards standardizing the pre-analytical procedures of blood collection for subsequent co-isolation of plasma cfDNA and EVs from a single blood collection tube. We compare effects of blood preservation tubes and storage to enable proteomic profiling of resulting EVs in addition to cfDNA extraction and sequencing. Following a stringent method of large EV (lEV) and small EV (sEV) isolation, consisting of differential ultracentrifugation and size exclusion chromatography, we evaluate protein concentration, particle number, quality and integrity of the isolated EVs. Subsequent proteomic analyses of EV isolates unravel the complexity of the respective tube proteomes allowing the interpretation of EV origins as well as contamination sources. While ACD-A and Citrate tubes demonstrate satisfying results in preservation of EV proteomes, only Streck RNA®, Norgen® and PAX® tubes can preserve high cfDNA purity for up to 7 days. When aiming for multi-omics analyses, Streck RNA® tubes show the most stable performance across tested parameters for both bioanalytes. Furthermore, we find more variability in protein composition in sEVs than in lEVs after 7 days of storage; thus, sEVs might be more susceptible to storage effects. Our clinically applicable workflow provides the basis for informed choice of liquid biopsy tubes along with a ready-to-use protocol to retrieve both genomic and EV proteomic biomarker information for multi-omics biomarker-based liquid biopsy studies.
HostingRepository	PRIDE
AnnounceDate	2026-01-23
AnnouncementXML	Submission_2026-01-23_02:23:39.259.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Katharina Clemm von Hohenberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-10 23:52:39	ID requested
⏵ 1	2026-01-23 02:23:40	announced

10.20517/evcna.2025.44;

Simon NK, Volz S, Rios de Los Rios Res, é, ndiz J, Wedig T, Montigel SH, Schwarz N, Richter K, Helm D, Ne, ß, ling M, Zielske L, Berker J, Russeck S, Mauermann M, Hofmann WK, Pfister SM, Pajtler KW, Maa, ß KK, Clemm von Hohenberg K, Preanalytical framework for routine clinical use of liquid biopsies: combining EVs and cfDNA. Extracell Vesicles Circ Nucl Acids, 6(4):626-650(2025) [pubmed]

submitter keyword: extracellular vesicles, liquid biopsy, cfDNA, human plasma,Tube preservation, isolation protocol, pre-analytics, translation

Katharina Clemm
contact affiliation	Junior Clinical Cooperation Unit Translational Lymphoma Research German Cancer Research Center Heidelberg, Germany & Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
contact email	k.clemm@dkfz-heidelberg.de
lab head
Katharina Clemm von Hohenberg
contact affiliation	Junior Clinical Cooperation Unit Translational Lymphoma Research German Cancer Research Center Heidelberg & Medical Faculty Mannheim, Heidelberg University
contact email	k.clemm@dkfz-heidelberg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD062837

PRIDE project URI

• PRIDE
  1. PXD062837
     1. Label: PRIDE project
     2. Name: Pre-Analytical Framework for Routine Clinical Use of Liquid Biopsies: Combining EVs and cfDNA