Dataset Information

Proteomic analysis of serum extracellular vesicles from biliary tract infection patients to identify novel biomarkers

ABSTRACT: Biliary tract infection (BTI) is a common abdominal disease and without proper management can even lead to bacteremia and further death. Although studies have focused on the initiation and mechanisms of this disease, diagnostic biomarkers for BTI are still lacking. Extracellular vesicles (EVs) are a kind of biological noano-particles that released from multiple types of cells reflected different physiological or pathological conditions. In the past decades, the development of EV-based diagnostic methods for many diseases is emerging. However, the utilization of EV-directed approaches for BTI diagnosis has not been well-investigated. To explore effective protein biomarkers for patients with BTI, we applied a label-free quantitative proteomic method, which is unbiased and high through-put, on the EVs from serum of control healthy donors or patients with BTI in this study. After analyzing the results, 62 novel proteins were unique in the BTI samples from the healthy controls. Moreover, 192 differentially expressed proteins were identified in EVs from patients with BTI when compared with those from healthy controls. To gain an overview on the functions of these proteins and the biological processes/pathways that the proteins are involved in, we performed GO and KEGG analysis by using this set of proteins an input. Importantly, some key pathways involved in fat acid processing were enriched as key pathways. Here we first idenfified biomarkers, Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) and Crumbs homolog 3 (CRB3) presented significant different between BTI patients and healthy individuals. Clinical validation from plasma derived EVs samples that demonstrated its specificity to BTI. Our work applied an unbiased proteomic tool to identify CEACAM1 and CRB3 protein biomarkers in serum EVs may facilitate the development of diagnostic systems to identify patients with BTI.

ORGANISM(S): Homo Sapiens

SUBMITTER: Chih-Jung Chang

PROVIDER: PXD045960 | iProX | Sat Oct 07 00:00:00 BST 2023

REPOSITORIES: iProX

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Proteomic analysis of serum extracellular vesicles from biliary tract infection patients to identify novel biomarkers.

Chang Chih-Jung CJ Huang Yung-Ning YN Lu Yang-Bor YB Zhang Yi Y Wu Ping-Hua PH Huang Jian-Shan JS Yang Wei W Chiang Tung-Ying TY Hsieh Hui-Shan HS Chung Wen-Hung WH Weng Yu-Chieh YC

Scientific reports 20240308 1

Biliary tract infection (BTI), a commonly occurring abdominal disease, despite being extensively studied for its initiation and underlying mechanisms, continues to pose a challenge in the quest for identifying specific diagnostic biomarkers. Extracellular vesicles (EVs), which emanate from diverse cell types, serve as minute biological entities that mirror unique physiological or pathological conditions. Despite their potential, there has been a relatively restricted exploration of EV-oriented m ...[more]

PMID: 38459197

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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.

Dataset Information

Proteomic analysis of serum extracellular vesicles from biliary tract infection patients to identify novel biomarkers

Publications

Proteomic analysis of serum extracellular vesicles from biliary tract infection patients to identify novel biomarkers.

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