Plasma-Derived Extracellular Vesicles Convey Protein Signatures That Reflect Pathophysiology in Lung and Pancreatic Adenocarcinomas

Abstract

Using a combination of mass-spectrometry and aptamer array-based proteomics, we characterized the protein features of circulating extracellular vesicles (EVs) in the context of lung (LUAD) and pancreatic ductal (PDAC) adenocarcinomas. We profiled EVs isolated from conditioned media of LUAD and PDAC cell lines to identify EV-associated protein cargoes released by these cancer cell types. Analysis of the resulting data identified LUAD and PDAC specific and pan-adenocarcinoma EV protein signatures. Bioinformatic analyses confirmed enrichment of proteins annotated to vesicle-associated processes and intracellular compartments, as well as representation of cancer hallmark functions and processes. Analysis of upstream regulator networks indicated significant enrichment of TP53, MYC, TGFB1 and KRAS-driven network effectors (p = 1.69 × 10−77–2.93 × 10−49) manifest in the adenocarcinoma sEV protein cargoes. We extended these findings by profiling the proteome of EVs isolated from lung (N = 15) and pancreatic ductal (N = 6) adenocarcinoma patient plasmas obtained at time of diagnosis, along with EVs derived from matched healthy controls (N = 21). Exploration of these proteomic data revealed abundant protein features in the plasma EVs with capacity to distinguish LUAD and PDAC cases from controls, including features yielding higher performance in the plasma EV isolates relative to unfractionated plasmas.

Detection of Tumor-Associated Membrane Receptors on Extracellular Vesicles from Non-Small Cell Lung Cancer Patients via Immuno-PCR

“…sEVs are secreted from all cell types and present in all body fluids. Because sEVs are higher in number and with diameters below 200 nm smaller in size than CTCs, they are easier to separate from blood cells, and their membrane protects their cargo, allowing for reproducible analysis after storage [ 8 , 9 ].…”

Proteomic Approach for Searching for Universal, Tissue-Specific, and Line-Specific Markers of Extracellular Vesicles in Lung and Colorectal Adenocarcinoma Cell Lines

“…Our experimental dataset included proteins that were determined as LC and CRC markers: TSPAN1, LGALS3BP, SLC1A5, and GPRC5A were determined in HT29 and HCT116 line-derived EVs [23], YWHAZ was revealed in HTC116-derived vesicles [32], and ICAM1, PTGFRN, DMBT1, and FN1 were identified in NCI-H23-derived EVs [33], as well as the diagnostically valuable KRAS and EGFR.…”

Proteomic profiling in extracellular vesicles for cancer detection and monitoring

“…[110]. In clinical applications, protein marker screening in plasma-derived EVs from pancreatic and lung adenocarcinoma using an aptamer array showed that a 6-protein marker panel including platelet derived growth factor subunit A, vascular endothelial growth factor C, secreted frizzled related protein 1, beta-2-microglobulin, nidogen 2, and proteasome 26S subunit 7, which is useful for cancer diagnosis and also representative in cancer hallmark functions and processes [111]. subunit alpha (PSMA) 3 and PSMA6 were further validated by western blotting as potential cancer diagnostic markers [116].…”

“…introduced a global‐scale protein array with proteome epitope tag antibody library including 62,208 antibodies that detected 15,199 peptides in proteomics [110]. In clinical applications, protein marker screening in plasma‐derived EVs from pancreatic and lung adenocarcinoma using an aptamer array showed that a 6‐protein marker panel including platelet derived growth factor subunit A, vascular endothelial growth factor C, secreted frizzled related protein 1, beta‐2‐microglobulin, nidogen 2, and proteasome 26S subunit 7, which is useful for cancer diagnosis and also representative in cancer hallmark functions and processes [111]. For protein‐binding DNA array, it solves the difficulty of protein immobilization.…”