Spatiotemporal dynamics of the lymph adaptive immune repertoire in response to viral infection

The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we investigated the spatial and temporal changes in the adaptive immune repertoire (AIR) in the draining lymph node after footpad infection with Vaccinia virus (VACV) in mice. To achieve this, we integrated high-resolution spatial transcriptomics with high-fidelity long-read adaptive immune receptor sequencing of T and B cell receptors. This approach enables simultaneous analysis of whole transcriptomes and AIR in their spatial context. We mapped the spatial distribution and temporal dynamics of immune phenotypes and AIRs at 3, 7, 10, 14, and 21 days post-infection. Our analysis revealed heterogeneous activation niches characterized by Interferon-gamma (IFN-?) during the early stages of infection. We observed sub-anatomical structures within the germinal center (GC) and provided direct evidence that antibody-producing plasma cells differentiate and exit the GC from the dark zone. Furthermore, we traced the spatial lineage trajectory of B cell clones and found evidence of B cell maturation across multiple GCs. Overall, this method offers valuable insights into the spatial dynamics of immune responses within lymphoid organs, with relevance for spatiotemporal studies of the immune system response to an infectious agent. Overall design: Six popliteal lymph nodes were collected from 6 individual mice with different conditions including one mock sample as control. We performed spatial transcriptomics on these lymph nodes by using the Curio Seeker platform and followed their protocol to get the complimentary cDNA library from it. Each cDNA library was split into short read (SR) for unbiased spatial trancriptomics or long read (LR) for TCR/BCR transcripts enrichment. So in total we have 12 samples library.