{"doi":"10.1101/2025.01.31.635509","title":"A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection","abstract":"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-γ) 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":555405,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9005,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":622738,"name":"Madhav Mantri","orcid":"0000-0001-9844-7852","position":1,"is_corresponding":false},{"id":1070819,"name":"Viviana I. Maymí","orcid":"0000-0002-1575-3510","position":2,"is_corresponding":false},{"id":332444,"name":"Scott A. Leddon","orcid":"0000-0002-8226-6042","position":3,"is_corresponding":false},{"id":1453695,"name":"Peter A. Schweitzer","orcid":"0000-0003-4525-7013","position":4,"is_corresponding":false},{"id":1454196,"name":"Subash Bhandari","orcid":null,"position":5,"is_corresponding":false},{"id":1453696,"name":"Chase Holdener","orcid":"0000-0003-3359-5592","position":6,"is_corresponding":false},{"id":1208286,"name":"Ioannis Ntekas","orcid":"0000-0002-4157-1665","position":7,"is_corresponding":false},{"id":322869,"name":"Christopher Vollmers","orcid":"0000-0002-7626-6222","position":8,"is_corresponding":false},{"id":485161,"name":"Andrew I. Flyak","orcid":"0000-0002-8722-479X","position":9,"is_corresponding":false},{"id":326992,"name":"Deborah J. Fowell","orcid":"0000-0001-7093-4448","position":10,"is_corresponding":false},{"id":728209,"name":"Brian D. Rudd","orcid":"0000-0002-9742-8358","position":11,"is_corresponding":false},{"id":94489,"name":"Iwijn De Vlaminck","orcid":"0000-0001-6085-7311","position":12,"is_corresponding":false},{"id":556134,"name":"Shaowen Jiang","orcid":"0000-0002-8934-0161","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-19T02:54:59.329539Z","pmid":"39975238","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}