Two-dimensional blood-brain barrier models assessed by gene, protein, and label-free spectroscopic descriptors. A new insight into cell-cell communication between the key cells of the barrier.

This dataset comprises multimodal Raman, Fourier-Transform Infrared (FTIR), and Optical Photothermal Infrared (O-PTIR) spectroscopic measurements collected from a 2D in vitro blood–brain barrier (BBB) model composed of human astrocytes, pericytes, and brain microvascular endothelial cells (HBEC-5i). The data capture cellular and molecular responses under hypoxic (1% O₂) and cytotoxic (HgCl₂) stress conditions and are complemented by molecular and functional assays, including RNA isolation and RT-qPCR, Western blotting, flow cytometry, apoptosis analysis, cell-cycle profiling, and live fluorescence imaging of mitochondria. Together, these datasets offer a comprehensive view of stress-induced alterations in gene expression, protein regulation, mitochondrial dynamics, and intercellular communication. By integrating vibrational spectroscopy with biochemical and imaging methods, the dataset enables detailed examination of molecular fingerprints, stress-response pathways, and cell–cell interactions within the BBB model. All raw and processed data, metadata, and analysis scripts required to reproduce the results of the associated publication are included, providing a robust resource for investigating BBB dysfunction and adaptive mechanisms. This research was funded by the National Science Centre NCN (DEC-2021/41/B/ST4/02000) granted to KM and RZ, and a grant from the Faculty of Chemistry under the Strategic Programme Excellence Initiative at Jagiellonian University – YL-4: “Tracking of the blood-brain barrier by infrared and Raman microscopy” granted to AA. The research was conducted using equipment supported by grants No. 5/491340/SPUB/SN/2021 (Military Institute of Medicine – National Research Institute) and 35/598515/SPUB/SP/2024 (Jagiellonian University in Krakow) from the Ministry of Science and Higher Education in Poland.