Dataset Information

In-depth proteome profiling of small extracellular vesicles isolated from cancer cell lines and patient serum

ABSTRACT: Extracellular Vesicle (EV) secretion has been observed from most types of normal and tumor cells. These EVs contain a variety of distinctive cargo where tumor-derived serum proteins in EVs secreted into the bloodstream can be used to provide a minimally invasive method for clinical monitoring. We have therefore undertaken a comprehensive study of the protein content of the EVs from several cancer cell lines using direct Data Independent Analysis (DIA). Several thousand proteins were detected including many of the classic EV markers such as CD9, CD81, CD63, TSG101 and Syndecan-1 among others. Many distinctive cancer related proteins were detected and some of them are known to be potential markers of cancer detection and monitoring of cancer progression. We have further studied the protein content of EVs from patient serum for both normal controls and pancreatic (PC) and Hepatocellular Carcinoma (HCC) cancers. The EVs for these studies have been isolated by various methods for comparison including ultracentrifugation (UC) and CD9 immunoaffinity column (CD9-IC). Typically, 500-1,000 proteins were identified where most of them overlapped with the EV proteins identified from the cell lines studied. Many of the EV protein markers were identified in these serum EVs and large numbers of proteins related to pancreatic and HCC cancers were identified.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Tujin Shi

PROVIDER: PXD045198 | JPOST Repository | Sun Sep 08 00:00:00 BST 2024

REPOSITORIES: jPOST

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 20

Publications

In-Depth Proteome Profiling of Small Extracellular Vesicles Isolated from Cancer Cell Lines and Patient Serum.

Abhange Komal K Kitata Reta Birhanu RB Zhang Jie J Wang Yi-Ting YT Gaffrey Matthew J MJ Liu Tao T Gunchick Valerie V Khaykin Valerie V Sahai Vaibhav V Cuneo Kyle C KC Parikh Neehar D ND Shi Tujin T Lubman David M DM

Journal of proteome research 20231219 1

Extracellular vesicle (EV) secretion has been observed in many types of both normal and tumor cells. EVs contain a variety of distinctive cargoes, allowing tumor-derived serum proteins in EVs to act as a minimally invasive method for clinical monitoring. We have undertaken a comprehensive study of the protein content of the EVs from several cancer cell lines using direct data-independent analysis. Several thousand proteins were detected, including many classic EV markers such as CD9, CD81, CD63, ...[more]

PMID: 38113368

Similar Datasets

Project description:Background & Aims: Extracellular vesicles (EVs) play a pivotal role in connecting tumor cells and their local and distant microenvironment. Here, we aimed to understand the role and molecular basis of patient-derived EVs in modulating cancer stemness and tumorigenesis in the context of hepatocellular carcinoma (HCC). Methods: EVs were isolated, quantified and characterized from patients’ sera. EVs were tested vigorously, both in vitro and in vivo, by various functional assays. Proteomic analysis was performed to identify the functional components of EVs. The expression level of polymeric immunoglobulin receptor (pIgR) in circulating EVs, tumor and non-tumorous tissues of HCC patients was determined by ELISA, immunoblotting, immunohistochemistry and quantitative PCR. The functional role and underlying mechanism of EVs with an enhanced pIgR expression was elucidated. Blockage of EV-pIgR with neutralizing antibody was performed in nude mice implanted with patient-derived tumor xenograft (PDTX). Results: Circulating EVs of late-stage HCC (L-HCC) patient had significantly elevated pIgR expression when compared to the EVs released by control individuals. The augmenting effect of L-HCC patient in cancer stemness and tumorigenesis was hindered by anti-pIgR antibody. EVs enriched with pIgR consistently promoted cancer stemness and cancerous phenotypes in the recipient cells. Mechanistically, EV-pIgR-induced cancer aggressiveness was abrogated by Akt and β-catenin inhibitors, ascertaining the role of EV-pIgR through the activation of PDK1/Akt/GSK3β/β-catenin signaling axis. Furthermore, anti-pIgR neutralizing antibody attenuated the tumor growth in mice implanted with PDTX. Conclusion: The study illustrates an unrevealed role of EV-pIgR in regulating cancer stemness and aggressiveness, in which EV-pIgR activates PDK1/Akt/GSK3β/β-catenin signaling cascades. The blockage of intercellular communications mediated by EV-pIgR in the tumor microenvironment may provide a new therapeutic strategy for cancer patients.

Project description:Circulating extracellular vesicles (EVs) contain molecular footprints - lipids, proteins, metabolites, RNA, and DNA - from their cell of origin and may provide non-invasive access for detection, characterization, and monitoring of diseases. Consequently, EV-associated RNA and proteins have gained widespread interest in developing liquid-biopsy assays for cancer. Yet, an integrative proteo-transcriptomic landscape of EVs and a direct comparison with their cell of origin remains relatively unexplored. Here, we report that EVs enrich for distinct molecular cargo and their proteo-transcriptome does not linearly correlate with their cell of origin. Our sub-cellular compartment analyses revealed that EV enrich 2-6 times more cytoskeletal and extracellular proteins, while their donor cells cargo 3-10 times more nuclear and mitochondrial proteins. EVs predominantly enrich (40-60%) for small RNA between ~15-200 nucleotides, which include miRNAs, siRNAs, tRNA, 5S rRNAs, and snRNAs, associated with cell differentiation, development, and Wnt signaling signatures. Finally, our integrated proteo-transcriptomic analyses reveal that EVs are enriched with specific small RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, SRSF1/2). These analyses suggest that RNA-protein complexes may constitute a functional interaction network inside EVs to protect and regulate access to EV-RNA. To ensure that our analyses are unbiased and independent of the cell of origin, EV isolation methods, site of experimentation, site of data generation, and methodologies applied for RNAseq and mass spectrometry, we have generated and curated comprehensive datasets of proteomics and transcriptomics from a total of 12 cancer cell lines, their EVs, and prostate cancer patientsÕ serum EVs (A detailed description is provided in Fig. 1). These combined analyses demonstrated that irrespective of the cell of origin and other aforementioned conditions, EVs enrich for distinct RNA and protein signatures that do not linearly correlate with their cell of origin.

			Action	DRS
	2478_Lubman_mv_01.raw	Raw
	2478_Lubman_mv_02.raw	Raw
	2478_Lubman_mv_03.raw	Raw
	2478_Lubman_mv_04.raw	Raw
	EVs_Asc_N_HCC.sne	Other