Spectral biophysical cytometry with smart nanosensors for monitoring biophysical remodeling of immune cells in atherosclerosis

It contains data sets from the publication, with the details for citation provided in the README file. Please cite this item as: Cenk O. Gurdap, Dunya Aydos, Luca A. Andronico, Gábor Tóth, Tugce Ceker, John Cowgill, Irem Muge Akbulut Koyuncu, Neslihan Basak, Jaromir Mikes, Andrey S. Klymchenko, Federico Pietrocola, Petter Brodin, Ingela Lanekoff, Verda Bitirim, Erdinc Sezgin DOI: 10.17044/scilifelab.30406327 It contains raw microscopy images, figures, Prism files, and excel sheets of the data. Abstract Biophysical properties of cells determine cellular physiology. Leveraging these properties for biomedical applications demands the ability to measure multiple parameters simultaneously across millions of cells and diverse cell types. However, current technologies are limited by throughput and low dimensionality. Here, we introduce spectral biophysical cytometry (SBC), a high-throughput platform that integrates environment-sensitive nanosensors with spectral flow cytometry to resolve multi-parametric biophysical properties of immune cells at single-cell resolution. By employing fluorescent nanosensors that report membrane order, mitochondrial potential, and membrane potential, SBC enables simultaneous quantification of key cellular physical states across diverse immune cell populations. When applied to peripheral blood mononuclear cells, SBC reveals cell-type–specific biophysical heterogeneity and identifies distinct remodeling signatures associated with atherosclerosis. In particular, T cell subsets exhibit significant alterations in membrane order and mitochondrial depolarization, reflecting coordinated changes in lipid composition and metabolic pathways. Integration with lipidomics and transcriptomics demonstrates that nanosensors enable detection of biophysical shifts that correlate with dysregulated lipid metabolism and mitochondrial function, providing mechanistic insight into immune dysfunction in disease. Importantly, SBC achieves rapid, label-efficient profiling using commercially available instrumentation, enabling scalable biomarker discovery directly from blood samples and establishing a powerful strategy for linking biophysical phenotypes to immune cell function. Data usage Researchers are welcome to use the data contained in the dataset for any projects. Please cite this item upon use or when published. We encourage reuse using the same CC BY 4.0 License. Data Content Excel files and Prism files for graphs fastq.gz files for omics Software to open files .xlsx or .cvs - Microsoft excel .pzfx or .prism – GraphPad Prism (https://www.graphpad.com/features) .fastq.gz – 10x Genomics Cloud