SuperResNET: Single molecule network analysis detects changes to clathrin structure by small molecule inhibitors.

Here, we apply SuperResNET network analysis of dSTORM single-molecule localization microscopy (SMLM) to determine how the clathrin endocytosis inhibitors pitstop 2, dynasore and Latrunculin A alter the morphology of clathrin-coated pits. SuperResNET analysis of HeLa and Cos7 cells identifies: small oligomers (Class I); pits and vesicles (Class II); and larger clusters corresponding to fused pits or clathrin plaques (Class III). Pitstop 2 and dynasore induce distinct homogeneous populations of Class II structures in HeLa cells suggesting that they arrest endocytosis at different stages. Inhibition is not via actin depolymerization, as the actin-depolymerizing agent latrunculin A (LatA) induces large, heterogeneous clathrin structures. Ternary analysis of SuperResNET shape features presents a distinct more planar profile for pitstop 2 blobs that align with clathrin pits identified with high-resolution MINFLUX, while control structures resemble MINFLUX clathrin vesicles. SuperResNET analysis therefore shows that pitstop 2 arrests clathrin pit maturation at early stages of pit formation, representing an approach to detect the effect of small molecules on target structures in situ in the cell from SMLM data sets.