Spatially Constrained Monte Carlo Permutation Test Reveals Diffusion Changes Near Stress Granules

Intracellular diffusion exhibits significant variability, but single-particle tracking (SPT) studies typically report cell-wide averages that may mask localized alterations. To address this issue, researchers have developed SPaCe-MC (Spatially Constrained Monte Carlo permutation test), a statistical approach that generates cell-specific null models to determine if diffusion near certain cellular structures, such as stress granules (SG), differs from that in the surrounding heterogeneous cytoplasm.

Three different conditions that induce stress granule formation were investigated, including oxidative stress, DDX3 inhibition, and a combined treatment. Global cytoplasmic analyses showed diverse responses, ranging from increased nanoparticle mobility to increased subdiffusive behavior. However, SPaCe-MC consistently identified a localized diffusion constraint in regions associated with SG, relative to the treatment-matched cytoplasmic background.

This finding suggests a conserved local diffusion effect, despite the varied global cytoplasmic responses.

By establishing SPaCe-MC as a framework for identifying compartment-specific diffusion changes in heterogeneous cellular environments, this research highlights the importance of considering the spatial context when analyzing intracellular diffusion patterns.