Through the lens of spatial transcriptomics and associated tools, novel immune niche constituents can now be resolved. Drawing on gut and tumor contexts, we propose a framework to define immune niches and integrate clonal dynamics, aiming to advance niche-directed therapies toward precise, context-specific immune modulation.
ABSTRACT
Spatial transcriptomics allows for the investigation of complex cellular ecosystems directly in their native tissues and enables the dissection of immune niches as spatially organized and functionally diverse microenvironments across homeostatic, inflammatory, and malignant settings. In this review, we examine how spatial transcriptomics tools have been applied to interrogate the cellular and molecular architecture of immune niches, including the emerging studies of B and T cell clonal niches. We focus on immune niches in intestinal and tumor tissues due to their importance to both health and pathology, discuss pressing immunological questions these technologies may help to address, and highlight future developments in the field.