Dataset Information

Surface Proteome of Extracellular Vesicles and Correlation Analysis for Identification of Breast Cancer Biomarkers

ABSTRACT: Breast cancer (BC) is the second leading cause of death in Canadian women. Despite this, non-invasive early detection methods for BC have yet to be developed. Cells release various types of extracellular vesicles (EVs) as intercellular signals into biofluids, such as blood, reflecting the physiological state of the origin cell. It is by transmitting bioactive molecules between cells that EVs may regulate multiple pathologies in human diseases, including cancer. The detection of protein biomarkers present on the surface of EVs in depleted or enriched biofluids could enable the early diagnosis of BC. Therefore, we used two different approaches to study the surfactome of EVs from cancerous and non-cancerous cells. We found several potential biomarkers that may be involved in the early diagnosis of BC.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Nico Hüttmann

LAB HEAD: Maxim Valentinovich Berezovski

PROVIDER: PXD048074 | Pride | 2024-05-21

REPOSITORIES: Pride

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Surface Proteome of Extracellular Vesicles and Correlation Analysis Reveal Breast Cancer Biomarkers.

Hüttmann Nico N Li Yingxi Y Poolsup Suttinee S Zaripov Emil E D'Mello Rochelle R Susevski Vanessa V Minic Zoran Z Berezovski Maxim V MV

Cancers 20240125 3

Breast cancer (BC) is the second most frequently diagnosed cancer and accounts for approximately 25% of new cancer cases in Canadian women. Using biomarkers as a less-invasive BC diagnostic method is currently under investigation but is not ready for practical application in clinical settings. During the last decade, extracellular vesicles (EVs) have emerged as a promising source of biomarkers because they contain cancer-derived proteins, RNAs, and metabolites. In this study, EV proteins from sm ...[more]

PMID: 38339272

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Project description:Background: Acute coronary syndromes (ACS) are associated with aberrant gene expression and epigenetic mechanisms. In particular, de novo DNA methylation is typically linked to gene silencing, but its role in heart disease remains not fully understood. Extracellular vesicles (EVs) are active components in cellular communication for their ability to carry a plethora of signalling biomolecules, thus representing a promising new diagnostic/therapeutic approach in cardiovascular diseases (CVDs). Indeed, there is the need of novel biomarkers for ACS prediction and timely detection. Purpose: We hypothesized that specific epigenetic signals can be carried by EVs. In this regard, we isolated and characterized circulating EVs from ACS patients and evaluated their potential role to influence DNA methylation in target cells. Methods: Circulating EVs were recovered, by ultracentrifugation, from plasma samples of 19 ACS patients and 50 healthy subjects (HS). Nanoparticle tracking analysis (NTA) and western blot (WB) were used to confirm the EVs integrity and purity. Peripheral blood mononuclear cells (PBMCs) of volunteer donors were treated with both ACS and HS derived EVs and genomic DNA was extracted to perform epigenome wide analysis through Reduced Representation Bisulfite Sequencing. ShinyGO, PANTHER, and STRING tools were interrogated to perform GO and PPI network analyses. Flow Cytometry, qRT-PCR, and WB analysis were also performed to evaluate and validate both intra-vesicular and intra-cellular signals. Results: Plasma ACS-derived EVs showed a significant up-regulation of DNA methyltransferases (DNMTs) gene expression levels as compared to HS (P<0.001). Specifically, de novo methylation transcripts, as DNMT3A and DNMT3B were significantly increased in plasma ACS-EVs. DNA methylation analysis of PBMCs from volunteer donors treated with HS- and ACS-derived EVs showed that RNF166 and CCND3 genes resulted the most hyper- and hypo-methylated, respectively, after by ACS-EV treatment. In addition, PPI network analysis specifically evidenced the subnetwork with SRC, as a hub gene, connecting it to NOTCH1, FOXO3, CDC42, IKBKG, RXRA, DGKG, known as important genes already involved in the onset of CVDs. Surprising, other novel genes, BAIAP2, SYP, CHL1, and SHB, which were hypomethylated, were found significantly overexpressed in PBMCs (P<0.005), underlying the fundamental modulating properties of EV cargo in atherosclerosis. Conclusions: These findings support the significant role of ACS plasma-derived EVs, inducing de novo DNA methylation signals, and modulating specific signaling pathways in target cells.

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