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Spatially resolved measurement of proteins, protein complexes and mRNAs in immune tissues by proximity sequencing

ABSTRACT: Spatially resolved measurement of proteins, protein complexes and mRNAs in immune tissues by proximity sequencing

PROVIDER: PRJNA1302449 | ENA |

REPOSITORIES: ENA

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Spatial Proximity Sequencing Maps Developmental Dynamics in the Germinal Center

Project description:Spatial profiling of proteins and protein interactions with mRNAs is essential for studies understanding cellular signaling. However, technologies capable of integrating these modalities remain limited. Here, we present Spatial Proximity-Sequencing (Sprox-seq), a method that combines proximity ligation assay with spatial transcriptomics to simultaneously profile mRNAs, surface proteins, and their interactions in intact tissues. Applied to human tonsil tissue, Sprox-seq profiled 32 proteins and their pairwise interactions alongside thousands of mRNAs. We developed a robust computational framework for analyzing protein proximity data, enabling both the statistical identification and interaction strength measurements of protein complexes. Clustering based on protein interaction strength recapitulated RNA-defined tissue architecture. Interaction networks constructed from protein complexes revealed significantly higher interaction complexity in Light zone. Trajectory inference based on protein interaction strength uncovered a maturation path distinct from that inferred by RNA data, and spatially enriched protein complexes were associated with functional gene-expression pathways. Moreover, Sprox-seq also captured cell–cell interactions mediated by protein complex ITGA4–VCAM1 in Light zone. Overall, Sprox-seq provides a spatially resolved, multi-modal view of cell states, offering a powerful tool for studying immune responses, tissue development, and disease progression.

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