Whole-Cell Scale Dynamic Organization of Lysosomes Revealed by Spatial Statistical Analysis

In eukaryotic cells, lysosomes are distributed in the cytoplasm as individual membrane-bound compartments to degrade macromolecules and to control cellular metabolism. A fundamental yet unanswered question is whether and, if so, how individual lysosomes are organized spatially to coordinate and integrate their functions. To address this question, we analyzed their collective behavior in cultured cells using spatial statistical techniques. We found that in single cells, lysosomes maintain non-random, stable, yet distinct spatial distributions mediated by the cytoskeleton, the endoplasmic reticulum (ER), and lysosomal biogenesis. Throughout the intracellular space, lysosomes form dynamic clusters that significantly increase their interactions with endosomes. Cluster formation is associated with local increases in ER spatial density but does not depend on fusion with endosomes or spatial exclusion by mitochondria. Taken together, our findings reveal whole-cell scale spatial organization of lysosomes and provide insights into how organelle interactions are mediated and regulated across the entire intracellular space. [Display omitted] •Lysosomes maintain non-random, stable, yet distinct spatial distributions•Cytoskeleton, ER, and biogenesis jointly mediate lysosomal spatial distributions•Lysosomes form dynamic clusters that increase their interactions with endosomes•Lysosomal clustering is associated with local increases in ER spatial density Ba et al. use spatial statistical analysis to map the whole-cell scale dynamic organization of lysosomes. Lysosomes form dynamic clusters that significantly increase their interactions with endosomes. The formation of lysosomal clusters is associated with local increases in ER spatial density but does not depend on fusion with endosomes.