{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:58:49Z","timestamp":1782280729543,"version":"3.54.5"},"posted":{"date-parts":[[2025,2,6]]},"group-title":"Immunology","reference-count":55,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T00:00:00Z","timestamp":1738800000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,2,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-\u03b3) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.<\/jats:p>","DOI":"10.1101\/2025.01.31.635509","type":"posted-content","created":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T05:20:17Z","timestamp":1738819217000},"source":"Crossref","is-referenced-by-count":3,"title":["A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8934-0161","authenticated-orcid":false,"given":"Shaowen","family":"Jiang","sequence":"first","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"},{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9844-7852","authenticated-orcid":false,"given":"Madhav","family":"Mantri","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"},{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1575-3510","authenticated-orcid":false,"given":"Viviana","family":"Maymi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott A.","family":"Leddon","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7013","authenticated-orcid":false,"given":"Peter","family":"Schweitzer","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7120-7429","authenticated-orcid":false,"given":"Subash","family":"Bhandari","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"},{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3359-5592","authenticated-orcid":false,"given":"Chase","family":"Holdener","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"},{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4157-1665","authenticated-orcid":false,"given":"Ioannis","family":"Ntekas","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Vollmers","sequence":"additional","affiliation":[{"name":"Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8722-479X","authenticated-orcid":false,"given":"Andrew I.","family":"Flyak","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7093-4448","authenticated-orcid":false,"given":"Deborah J.","family":"Fowell","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9742-8358","authenticated-orcid":false,"given":"Brian D.","family":"Rudd","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6085-7311","authenticated-orcid":false,"given":"Iwijn","family":"De Vlaminck","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041023580529000_2025.01.31.635509v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-387664-5.00004-2"},{"key":"2026041023580529000_2025.01.31.635509v1.2","doi-asserted-by":"crossref","unstructured":"Roth, D. 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