H. Zhang, P. Wang, Y. Zhao, L. Yang, T. Xue, L. Liu, Y. Zhao, Z. Zhang, J. Ma, B. Zeng, P. Zhang, C. Wang, D. Pan, Z. Gao, Z. Liu, Z. Zeng
Spatial transcriptomics offers a glimpse into the immunology of tissues. However, limitations in spatial transcriptomics preclude the detection of highly diverse, low-abundance, and previously unknown sequences, including immune repertoires and microbiota. Here, we introduce Archimap, a spatial transcriptomic platform that simultaneously profiles spatial transcriptomes, immune repertoires, and microbiota from formalin-fixed paraffin-embedded (FFPE) tissues. Using Archimap, we profile the spatial localization of TCRs, BCRs, and the microbiota landscape in archived clinical tissues at single-cell resolution. Through comprehensive benchmarking, we validate Archimap's performance and fidelity. Archimap in situ assembles the immune complex and reconstructs the clonal evolution of antibodies. Together, Archimap shows the power of in situ discovery of functional immune repertoires for their antitumor immunity.