Persia, E. | Search bioRxiv

bioRxiv2025

Organ-specific isolation of hepatocyte extracellular vesicles from human plasma enables tissue-resolved proteomic and miRNA profiling

Tissue-specific resolution remains a key limitation in liquid biopsy to achieve the highest accuracy for precision medicine. To address this limitation, we developed NEXPLOR (Novel EXtracellular vesicle PopuLation and Omics Revealer), a magnetic bead-based platform enabling selective immuno-isolation of tissue-derived EVs. Focusing on hepatocyte-derived EVs (h-EVs), we demonstrate NEXPLORs specificity and sensitivity in capturing rare EV subpopulations directly from human plasma. Using in silico tissue marker discovery, we identified and validated a TOP4 capture antibody panel (ASGR1, ASGR2, TFR2, SLCO1B1) for h-EV isolation through an ultrasensitive orthogonal method (O-NEXOS). Applied to liver disease using clinical plasma samples, NEXPLOR enabled deeper and more reproducible proteomic profiling compared to matched bulk EVs, revealing liver-specific and disease-relevant pathways, including ferroptosis, HIF-1 signaling, and central carbon metabolism in cancer. Moreover, small RNA sequencing uncovered a reduced but highly informative set of miRNAs, including miR-124-3p and miR-23b-3p, differentially expressed in hepatocellular carcinoma (HCC) compared to cirrhosis, and undetectable in bulk EVs. These molecular signatures suggest disease state based on real-time hepatocyte biology. Our findings establish NEXPLOR as a robust platform for tissue-specific EV capture, enabling tissue-resolved, multi-omic biomarker discovery. This opens new frontiers in early disease detection, longitudinal monitoring, and AI-powered biomarker discovery for precision medicine.

molecular biology↗

bioRxiv2022

An electro-optical bead-nanochip technology for the ultrasensitive and multi-dimensional detection of small extracellular vesicles and their markers

Small extracellular vesicles (sEVs), including exosomes, are enriched in multiomics information mirroring their parental cells. They have been investigated in health and disease and utilised in several applications from drug discovery to diagnostics. In disease diagnostics, sEVs can be sampled via a blood draw, enabling the convenient liquid biopsy of the tissue they originate from. However, few applications with sEVs have been translated into clinical practice. We developed a Nanoparticle EXOsome Sensing (NEXOS) technology, for the ultrasensitive and multi-dimensional detection of sEVs. NEXOS comprises two methods: a novel nanoelectronics method, E-NEXOS, and a high-throughput optical detection method, O-NEXOS. Both methods share the same steps for the immunocapture and antibody-labelling of sEVs and can be combined to derive differentiated detection parameters. As a proof of concept, we show the analytical detection and sensitivity of these methods in detecting pre-prepared cancer cell-derived CD9+CD81+ and CD9+HER2+ sEVs. Both sEV populations were diluted in PBS and spiked in processed plasma. We also provide a novel approach for the determination of target sEVs (TEVs), target epitopes in sEVs (TEPs), and epitopes per target sEV, as yet unseen from current and emerging technologies. Further, we demonstrate the higher sensitivity of O-NEXOS compared to the gold standard techniques, as well as demonstrating that E-NEXOS possesses commensurate sensitivity whilst only being powered by 36 nanogap-based sensors per nanochip. Finally, this manuscript lays the groundwork for a scalable electronics miniaturization of E-NEXOS nanochip with millions of nanogap-based sensors for the translation of NEXOS into standard clinical practice.

molecular biology↗