Surfaceome profiling enables isolation of cancer-specific exosomal cargo in liquid biopsies from pancreatic cancer patients

Abstract

Exosomes provide unique opportunities in the context of liquid biopsies for enrichment of tumor-specific material in circulation. We present a comprehensive surfaceome characterization of PDAC exosomes which allows for capture and molecular profiling of tumor-derived DNA.

Surfaceome of Exosomes Secreted from the Colorectal Cancer Cell Line SW480: Peripheral and Integral Membrane Proteins Analyzed by Proteolysis and TX114

“…There is a growing interest in exosome surface proteins due to their potential as diagnostic disease targets and therapeutic interventions. Although membrane proteins are predicted to constitute a third of the human genome, their identification using traditional mass spectrometry approaches is still technically challenging; for a review of membrane protein isolation methods, see ref.…”

“…Because circulating cancer‐derived exosomes are most likely extensively diluted by nontumor‐derived exosomes as well as platelet‐derived microvesicles, their low concentration may confound interpretation of blood‐based exosome‐based diagnostic biomarker analyses . Thus, exosomal surfaceome profiling potentially would provide a means to separate and enrich specific cancer‐cell exosomes from noncancer‐derived exosomes using immunocapture bead technology, thereby improving specificity and sensitivity of exosome‐based cancer diagnostics …”

Urinary exosomal proteins as (pan‐)cancer biomarkers: insights from the proteome

“…Biotin‐tagging of enzymatically cleaved surface peptides or intact surface proteins may also be performed to obtain a verified surface fraction. A combination of both approaches was employed in in vitro MS studies that predicted over 1000 proteins to be located on the surface of exosomes . Importantly, the potential exosome surface proteome was shown to be highly enriched for DNA and RNA‐binding proteins, and nuclear proteins such as histones when compared to the global exosome proteome .…”

“…A combination of both approaches was employed in in vitro MS studies that predicted over 1000 proteins to be located on the surface of exosomes . Importantly, the potential exosome surface proteome was shown to be highly enriched for DNA and RNA‐binding proteins, and nuclear proteins such as histones when compared to the global exosome proteome . Moreover, topology analyses revealed some proteins to have an inside‐out orientation, that is opposite to their conventional orientation on the cell membrane with their cytoplasmic domains facing outwards on the exosome membrane .…”

Opportunities and Resistance to Signal-targeted Therapies in Pancreatic Cancer: What Can We Learn from Proteomic Studies?

“…These cells being possibly at the origin of tumor relapse under chemotherapy, discovering specific targets of this pool of cells could improve the current treatments. Recent data show that surface proteome of circulating exosomes provides unique opportunities to analyze the heterogeneity of the metastatic disease though the easy-to-access liquid biopsies [55]. Proteomics studies bring insight in metastatic PDAC biology, leading to the discovery of novel targets.…”