Marcus Woodworth, Tristan Mcdonnell, and Melike Lakadamyali. BPS2025 – Visualizing chromatin states in native contexts using expansion microscopy. Biophysical Journal (2025). DOI: https://doi.org/10.1016/j.bpj.2024.11.080.

Abstract

The nanoscale arrangement of chromatin within the nuclei of cells has been implicated in the establishment of cell identity during development and disease progression. As such, much research has been dedicated to studying this architecture in bulk cell studies, where state heterogeneity is lost, or in isolated cells that are devoid of their tissue context features. This is because there are few strategies available to visualizing nanoscale chromatin architecture within the native tissue, particularly those with dense extracellular matrices (ECMs), or at length scales relevant to gene activation. For example, although we have demonstrated that the chromatin organization of isolated tendon cells depend on surface stiffness, and isolated tendon cells from tendinosis patient show remarkable changes in nanoscale chromatin organization compared to cells from healthy patients, we have yet to see how each cells micro-environment relates to their chromatin state. To address this need, we have adapted the novel method fluorescent labeling of abundant reactive entities (FLARE) along with expansion microscopy (ExM) to visualize chromatin features of cells within their native and dense ECM environment. FLARE provides details of both ECM matrix uniformity and composition for multiple tissue types and species (e.g., mouse and bovine tendons). We also show our method is compatible with histone mark staining and capable of revealing relationships between ECM matrix heterogeneity and chromatin state distributions for multiple cell types. We anticipate the application of these novel methods will uncover the epigenetic changes in healthy and diseased cells within tissue, such as for tendinopathy progression, while creating the possibility for future therapeutics that target epigenetic states for better patient outcomes in multiple tissue modalities.