In The FEBS journal
Investigations of spatial cellular composition of tissue architectures revealed by multiplexed in situ RNA detection often rely on inaccurate cell segmentation or prior biological knowledge from complementary single cell sequencing experiments. Here we present spage2vec, an unsupervised segmentation free approach for decrypting the spatial transcriptomic heterogeneity of complex tissues at subcellular resolution. Spage2vec represents the spatial transcriptomic landscape of tissue samples as a graph and leverages a powerful machine learning graph representation technique to create a lower dimensional representation of local spatial gene expression. We apply spage2vec to mouse brain data from three different in situ transcriptomic assays and to a spatial gene expression dataset consisting of hundreds of individual cells. We show that learned representations encode meaningful biological spatial information of re-occuring localized gene expression signatures involved in cellular and subcellular processes.
Partel Gabriele, Wählby Carolina
RNA profiling, Spatial transcriptomics, gene expression, graph representation learning, tissue analysis