Quentin Blampey

Abstract Understanding the composition of the tumor microenvironment is critical for cancer research. Spatial transcriptomics profiles gene expressions in spatial context, revealing tissue architecture and cellular heterogeneity, but its cost and technical complexity limit adoption. To address this issue, we introduce a pipeline to build STHELAR, a large-scale dataset that integrates spatial transcriptomics with Hematoxylin and Eosin (H&E) whole-slide images for cell type annotation.

Abstract Spatial transcriptomics is advancing molecular biology by providing high-resolution insights into gene expression within the spatial context of tissues. This context is essential for identifying spatial domains, enabling the understanding of microenvironment organizations and their implications for tissue function and disease progression.

Discussion In this paper, we described for the first time how an immune response against common viral infections might be used to predict the response to cancer immunotherapy. Our data suggests that patients whose serum antibodies are capable of recognizing a higher number of unique viral peptides have an improved prognosis when treated with ICBs. When going to the species level, this correlation was especially seen with more common viruses, such as rhinovirus, coxsackievirus and enterovirus.