Cinnirella, G. | Search bioRxiv

bioRxiv2025

An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products

BRIEF ABSTRACTWe built a CAR-T cell functional atlas from over one million cells across 13 studies, integrating data from patients and healthy donors. The atlas captures 11 phenotypes, links infusion product composition with clinical response, and reveals sex- and age-dependent effects, metabolic signatures, and rare ICANS-associated cells. This open-access resource provides a foundation to understand CAR-T cell function and guide the design of next-generation therapies.

bioinformatics↗

bioRxiv2025

scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics

Spatial transcriptomics provides a significant advance over studies of dissociated cells in that it reveals the environment in which cells reside, thus opening the way for a more complete description of their state and function. However, most current methods for embedding and discovery of cell states rely only on the cells own gene expression profile, thus raising the need for ways to account for the neighboring cells as well. Here, we introduce scVIVA, a deep generative model that leverages both cell-intrinsic and neighboring gene expression profiles to output stochastic embeddings of cell states as well as normalized gene expression profiles. We demonstrate that scVIVA produces informative fine-grained partitions of cells that reflect both their internal state and the surrounding tissue and that its generative model facilitates the testing of hypotheses of differential expression between tissue niches. We leverage these properties of scVIVA to uncover a spatially-restricted tumor-promoting endothelial population in breast cancer and niche-associated T cell states that are shared across multiple cancers. scVIVA is available as open source software within scvi-tools.org.

bioinformatics↗