Super-resolution microscopy reveals the nanoscale organization of the DEK protein cancer biomarker

The chromatin architectural factor DEK is involved in regulating the chromatin organization and is highly overexpressed in numerous forms of cancer. DEK is traditionally described as uniformly distributed within the nucleus by diffraction-limited microscopy studies, but super-resolution advent highlighted the formation of cluster-like DEK structures. Still, a characterization of the DEK protein cellular distribution and its role in cancer and cell proliferation is missing. In this work, we used single-molecule localization microscopy (SMLM) to investigate the nanoscale characteristics of DEK organization in normal-like and aggressive types of breast cancer cell lines, characterizing the number of localizations per cluster, as well as areas and density of clusters. We show how the cluster features correlate with the breast cell type and how the chromatin decompaction influences the DEK clusters in both cell lines. Our results suggest that the DEK density and nano-organization are preserved and are not influenced by protein overexpression itself or by chromatin compaction changes.