Postdoc University of Chicago Chicago, Illinois, United States
Disclosure(s):
huili wang, PhD: No financial relationships to disclose
Introduction/Rationale: Spatial profiling of proteins and protein interactions is essential for understanding immune responses, yet existing methods cannot simultaneously measure protein complexes in situ. We developed Spatial Proximity-Sequencing (Sprox-seq), a multi-omic technique that simultaneously profiles proteins, protein complexes, and mRNAs with spatial resolution in intact tissues.
Methods: Sprox-seq integrates proximity ligation assay with spatial transcriptomics on the 10x Visium platform. Antibody-oligonucleotide conjugate pairs targeting 32 proteins were applied to human tonsil sections. Upon spatial proximity, probes ligate to generate PLA products captured alongside mRNAs via spatial barcodes. Fisher's Exact Test and fractional overlap analysis were used to identify and quantify protein complexes.
Results: We profiled 32 proteins, 528 pairwise interactions, and thousands of mRNAs across human tonsil germinal centers. Protein interaction networks revealed higher complexity in the Light zone compared to Dark zone, consistent with B cell selection dynamics. Trajectories inferred from protein interactions uncovered a B cell state transition distinct from that inferred by RNA. We identified spatially enriched complexes including CD19-CD21, CD21-CD35, and directly captured VLA-4–VCAM1 mediated B cell-FDC interactions in the Light zone.
Conclusion: Sprox-seq enables simultaneous spatial profiling of transcriptomes, proteomes, and interactomes, revealing protein interaction dynamics during B cell state transition that cannot be inferred from RNA or protein expression alone. This technology provides new insights into cell-cell communication in immune tissues.
