Figure 5. Morphological profiles of >1,200 PTEN variants in iPS cells and NGN2-induced neuron-like cells.
(A) Image of PTEN library at positions 112–172 expressed in human PTEN-KO iPS cells carrying dox-inducible NGN2 (left) and neuron-like cells 7 days after induction of NGN2 (right). MAP2=anti-MAP2 antibody, ConA=concanavalin A. Scale bar indicates 10 μm.
(B) UMAP visualization of 1,228 PTEN variant morphological profiles collected in iPS cells (left) and NGN2-induced neurons (right). Point color indicates variant type: synonymous (green), missense (grey), 3-nt deletions (blue), nonsense (red), and frameshift (purple).
(C,E,G) Missense variant effect maps for iPS cell PTEN landmark features (grey boxes=missing variants, black dots=synonymous substitutions). Blue to red coloring indicates feature z-score versus the synonymous variant distribution. Linker or coil subdomains are shown directly above the heatmap. Position-averaged scores are below and amino acid substitution marginal feature z-score distributions are on the right (points depict variants; black lines depict medians).
(D,F,H) UMAPs of PTEN variant morphological profiles in iPS cells (left) and NGN2-induced neurons (right) colored by landmark features. Blue indicates low and red indicates high z-score versus the synonymous variant distribution, as in (C,E,G).
(I) Barplot of fraction of variants that perturb landmark features in iPS cells and NGN2-induced neurons. For each variant, a feature was considered perturbed if |z-score|>2.5 and KS-test Bonferroni-corrected p<0.01. *** indicates χ2 p<0.001.
(J) Graphic depicting the relationship between PTEN localization (cell membrane, cytoplasm, or nucleus), activity and protein abundance, annotated with changes to landmark features.