Fig. 6: Single-cell analysis of morphology and gene expression using the morphome.

a, b Predicted response of a pre-osteoblast and fibroblast co-culture to nanotopography. Contour plots show the sum of predicted a osteogenic (RUNX2, SP7, BGLAP, SPP1) and b fibrotic (TGFB1I1, COL3, ELN) gene expression for individual cells on FLAT, SQ, NSQ, and HEX topographies. Pre-osteoblast and fibroblast cells were co-cultured on FLAT, SQ, NSQ, and HEX nanotopographies for 2 days, and their morphome obtained from the entire nanotopography surface. The newly collected morphome was then used as input in the linear regression model (shown in Fig. 5a) to predict gene expression. x and y axes of each contour plot shows are spatial coordinates on the nanotopogrpahy substrate, while the color of the contour represents the level of summed gene expression. Scale bar = 100 µm. c, d Morphology and gene expression at the single-cell level is provided by the morphome. Each dot in the scatterplot denotes a single-cell. Nanotopographies are color coded, with FLAT denoted in pink, SQ denoted in purple, NSQ denoted in blue and HEX denoted in green. e, f Cell–cell interaction altered by nanotopography. The average changes in e cell morphology and f gene expression between two neighboring cells separated by a specified distance was measured and normalized to the maximum observed change. Data are presented as mean ± standard deviation and reported as a function of distance between two cells binned every 125 µm. N ≥ 5000 cells per topography from one independent experiment.