Profiling Plasma Extracellular Vesicle Metabotypes and miRNAs: An Unobserved Clue for Predicting Relapse in Patients with Early-Stage NSCLC

Vivi Bafiti; Eleni Thanou; Sotiris Ouzounis; Athanasios Kotsakis; Vasilis Georgoulias; Evi Lianidou; Theodora Katsila; Athina Markou

doi:10.3390/cancers16223729

Profiling Plasma Extracellular Vesicle Metabotypes and miRNAs: An Unobserved Clue for Predicting Relapse in Patients with Early-Stage NSCLC

Cancers (Basel). 2024 Nov 5;16(22):3729. doi: 10.3390/cancers16223729.

Authors

Vivi Bafiti¹, Eleni Thanou², Sotiris Ouzounis¹, Athanasios Kotsakis³, Vasilis Georgoulias⁴, Evi Lianidou², Theodora Katsila¹, Athina Markou²

Affiliations

¹ Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
² Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece.
³ Department of Medical Oncology, University General Hospital of Larissa, 41334 Larissa, Greece.
⁴ First Department of Medical Oncology, Metropolitan General Hospital of Athens, 15562 Cholargos, Greece.

Abstract

Background and objective: Lung cancer, the second most prevalent cancer globally, poses significant challenges in early detection and prognostic assessment. Despite advancements in targeted therapies and immunotherapy, the timely identification of relapse remains elusive. Blood-based liquid biopsy biomarkers, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating-free RNAs (cfRNAs), and extracellular vesicles (EVs)/exosomes, offer promise for non-invasive monitoring.

Methods: We employ a comprehensive approach integrating miRNA/lncRNA/metabolomic datasets, following a mixed-methods content analysis, to identify candidate biomarkers in NSCLC. NSCLC-associated miRNA/gene/lncRNA associations were linked to in silico-derived molecular pathways.

Results: For data validation, mass spectrometry-based untargeted metabolomics of plasma EVs highlighted miRNA/lncRNA/metabotypes, linking "glycerophospholipid metabolism" to lncRNA H19 and "alanine, aspartate and glutamate metabolism" to miR-29a-3p. Prognostic significance was established for miR-29a-3p, showing lower expression in NSCLC patients with disease progression compared to stable disease (p = 0.004). Kaplan-Meier survival analysis indicated that patients with miR-29a-3p under-expression had significantly shorter overall survival (OS) (p = 0.038). Despite the expression of lncRNA H19 in plasma EVs being undetected, its expression in plasma cfRNAs correlated significantly with disease progression (p = 0.035).

Conclusions: Herein, we showcase the potential of plasma EV-derived miR-29a-3p as a prognostic biomarker and underscore the intricate interplay of miRNAs, lncRNAs, and metabolites in NSCLC biology. Our findings offer new insights and avenues for further exploration, contributing to the ongoing quest for effective biomarkers in early-stage NSCLC.

Keywords: NSCLC; extracellular vesicles; liquid biopsy; metabotypes; miRNAs; multi-omics.

Grants and funding

This research is partly supported by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH–CREATE–INNOVATE (project code: T2EDK-03153). We acknowledge PRACE for awarding access to the Fenix Infrastructure resources at CINECA and Jülich hosting sites, which are partially funded by the European Union’s Horizon 2020 research and innovation program through the ICEI project under grant agreement no. 800858.