Artificial Intelligence for Liquid Biopsy: FTIR Spectroscopy and Autoencoder-Based Detection of Cancer Biomarkers in Extracellular Vesicles

Extracellular vesicles (EVs) are increasingly recognized as promising non-invasive biomarkers for cancer and other diseases, but their clinical translation remains limited by the lack of comprehensive characterization strategies. Spectroscopic approaches such as Fourier-transform infrared (FTIR) spectroscopy can provide a global biochemical fingerprint of intact EVs, but their interpretation requires advanced analytical tools. In this study, we applied an autoencoder-based framework to attenuated total reflection FTIR (ATR-FTIR) spectra of blood-derived components, including plasma, red blood cells (RBCs), RBC-ghosts, and EVs, comprising 278 samples collected from 135 patients, to obtain latent features capable of capturing biologically meaningful variability. The autoencoder compressed spectra into 12 latent features while preserving spectral information with low reconstruction error. Unsupervised UMAP projection of the latent features separated the blood components into different clusters, supporting their biological relevance. The model was then applied to EV spectra from patients with hepatocellular carcinoma (HCC) and cirrhotic controls. Four features significantly differed between the two groups, and an elastic-net regularized logistic model evaluated with a leave-one-out cross-validation framework retained a single latent feature, achieving an out-of-fold ROC AUC of 0.785 (95% CI 0.602-0.967), with performance broadly comparable to that typically reported for AFP, the most commonly used biomarker for HCC. This study provides the first proof-of-concept that an autoencoder can be applied to FTIR spectra of EVs, extracting biologically relevant latent features with potential application in cancer detection.