A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.

ABSTRACT: The tonsil is a highly compartmentalized organ in which different microanatomical structures orchestrate designated (immune) functions. We use this already well-studied tissue to survey imaging-based spatial transcriptomics data for studying immune responses in native tissue context, and, to demonstrate its advantages for faithfully recapitulating cellular composition in direct comparison with single-cell RNA sequencing. While these data still pose many analytical challenges and lack standardization, we established a versatile analysis pipeline focused on their profitable particularities: considering organization (microenvironment), interactions (signaling), and function (higher order structures) across scales. Specifically, we resolve ∼$\sim$ 2M cells into 52 subpopulations across immune

SUBMITTER: Crowell HL 

PROVIDER: S-EPMC12790319 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature