Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning

Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael

Abstract: Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns. We address this issue by deriving a topographic map of a tissue slice—analogous to a map of elevation in a landscape—using a novel quantity called the isodepth. Contours of constant isodepth enclose spatial domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in gene expression. We develop GASTON, an unsupervised and interpretable deep learning algorithm that simultaneously learns the isodepth, spatial gene expression gradients, and piecewise linear functions of the isodepth. GASTON models both continuous gradients and discontinuous spatial variation in the expression of individual genes. We show that GASTON accurately identifies spatial domains and marker genes in multiple SRT datasets.