Figure 3. Clustering LMNA variant morphological profiles yields rich, interpretable phenotypes.
(A) Center: UMAP of LMNA variant profiles (Figure 2H) colored by Louvain128-derived clusters. Periphery: images of variants and description of nuclear morphology, lamin A abundance and lamin A localization associated with each cluster. Silver dashed lines depict the borders of cells, blue=DAPI, green=lamin A-mEGFP. Scale bar indicates 5 μm. Graphical representations of each cluster indicate nuclear envelope morphology (black), lamin A localization and abundance (green) and nuclear circularization (red arrows). UMAP point and text color indicate cluster identity, depicted in (B).
(B) Heatmap of landmark feature medians and EMDs for each cluster, colored by z-score versus the synonymous variant distribution. The nuclear mEGFP-lamin A intensity feature measures the average lamin A pixel intensity in the nucleus, the boundary mEGFP-lamin A intensity feature measures the average lamin A pixel intensity within two pixels of the nuclear boundary. The nuclear mEGFP-lamin A granularity 1 feature is related to the presence of lamin A aggregates, with high values indicating aggregates. The nuclear circularity feature is the normalized ratio of nuclear perimeter squared to nuclear area, with high values indicating a circular nucleus.
(C) Plot of the mEGFP-lamin A total intensity in radial deciles of distance from the centroid of the nucleus, normalized to the DAPI total intensity in each decile. Bin 1 corresponds to the innermost radial decile and bin 10 to the outermost (see diagram below plot). mEGFP-laminA/DAPI median intensity for clusters 1, 3, 4, and 8 z-scored versus the synonymous variant distribution are shown. The remaining clusters are shown in Figure S4C.