Dissection of tumoral niches using spatial transcriptomics and deep learning

This study introduces TG-ME, an innovative computational framework that integrates transformer with graph variational autoencoder (GraphVAE) models for dissection of tumoral niches using spatial transcriptomics data and morphological images. TG-ME effectively identifies and characterizes niches in bench datasets and a high resolution NSCLC dataset. The pipeline consists in different stages that include normalization, spatial information integration, morphological feature extraction, gene expression quantification, single cell expression characterization, and tumor niche characterization. For this, TG-ME leverages advanced deep learning techniques that achieve robust clustering and profiling of niches across cancer stages. TG-ME can potentially provide insights into the spatial organization of tumor microenvironments (TME), highlighting specific niche compositions and their molecular changes along cancer progression. TG-ME is a promising tool for guiding personalized treatment strategies by uncovering microenvironmental signatures associated with disease prognosis and therapeutic outcomes.