Identifying label-free and untargeted biomarkers of SH-SY5Y cell fate in ATRA-induced differentiation through FTIR spectroscopy and integrated omics

SH-SY5Y cells are widely used as an in vitro model to investigate the neurotoxic effects of environmental pollutants and various neurological conditions linked to neurodegenerative diseases. Elucidating the molecular pathways underlying SH-SY5Y differentiation and identifying readily detectable markers are crucial for advancing these applications. In this study, we characterized intact SH-SY5Y cells undergoing all trans retinoic acid (ATRA)-induced differentiation using Fourier Transform Infrared (FTIR) microspectroscopy. Our results demonstrate that this technique can effectively distinguish between undifferentiated and differentiated cells by directly identifying characteristic marker bands in the acquired spectra. Multivariate analysis of the spectral data revealed significant changes in global protein phosphorylation that coincided with variations in glycogen content, alongside alterations reflecting lipid physicochemical modifications. Complementary biochemical, metabolic, lipidomics, and proteomics analyses enabled us to correlate these spectroscopic markers with specific molecular events occurring during SH-SY5Y differentiation. Overall, FTIR (micro-)spectroscopy emerges as a powerful in situ approach to detect and monitor in an untargeted and unbiased way the key marker factors that play a role in determining the fate of SH-SY5Y cells during ATRA-induced differentiation.