Fig. 4: scCLEAN identifies 2 lineages of VSMCs corresponding with the artery of origin.

a Schematic figure of experimental workflow. A total of ~50,000 VSMCs were isolated from 4 donors and 2 tissue locations: coronary and pulmonary artery. b Normalized density of cells along the force directed layout (FLE) according to their artery of origin comparing 10x-V3 (top) with scCLEAN (bottom). c RNA velocity stream plots along pseudotime (CytoTRACE) mapped onto the FLE embedding. All detected genes are utilized to automatically calculate early pseudotime (black) to late pseudotime (yellow) according to the number of genes expressed. Black arrows indicate direction of transcriptional transition. d The total number of terminal states identified using CellRank comparing 10x-V3 (left) and scCLEAN (right). Number of lineages are shown. Optimal terminal states were found using Schur decomposition (gap in the real portion of eigenvalues) and then refined according to stationary distance of the coarse-grained Markov transition matrix (non-zero distance). e Only scCLEAN is shown (>1 lineage). Absorption probability of each cell belonging to each lineage and thus differentiating along pseudotime into either of the 2 terminal states, corresponding with lineage 1 (top) and lineage 2 (bottom). Yellow represents a 100% probability of that cell belonging to that lineage. f (left) Lineage absorption probability (lineage 1 = top, lineage 2 = bottom) plotted as a function of each cell’s position along the differentiation trajectory (ct pseudotime). Colors reflect tissue origin: coronary (red) or pulmonary (gray) artery. (right) Violin plots of absorption probabilities across coronary and pulmonary arteries for each lineage. g Heat matrix illustrating the relationship between the quantified absorption probability of each cell belonging to each lineage compared to the ground truth arterial identity of that cell. h Receiver operating characteristic (ROC) depicting the classification performance of identifying each artery to each lineage (both pulmonary and coronary lineage AUC = 0.99). Created in BioRender. Pandey, A. (2025) https://BioRender.com/r94y754.