Integrated B and T Cell Repertoire Analysis Reveals Organized but Heterogeneous Adaptive Immunity in Chronic Experimental Stroke

Ischemic stroke drives prolonged accumulation of lymphocytes within the injured brain, and we recently showed that the T-cell compartment of the chronic infarct is not a random infiltrate but a reproducibly organized oligoclonal repertoire. Whether this organization is a broader property of the post-stroke adaptive immune response, extending to B cells and coordinated across lymphocyte lineages, has remained unknown. Here we performed immunoglobulin heavy-chain (IGH) repertoire sequencing of chronic infarct tissue across different cohorts spanning age, sex, experimental stroke models, and independent study centers, and integrated these data with T-cell receptor β (TRB) repertoires from the same lesions. Chronic infarcts exhibited increased B-cell receptor clonality relative to matched splenic repertoires, a pattern reproducible across age, sex, models, and centers, yet heterogeneous among individual lesions owing to variable expansion of dominant clonotypes. Dominant B-cell clonotypes showed recurrent V(D)J gene usage across animals, and a subset of recurrent receptor frameworks contained public CDR3 amino-acid sequences despite substantial overall sequence diversity. Integrated analysis revealed that B- and T-cell repertoire concentration was positively associated within individual infarcts while remaining heterogeneous in its relative organization across lesions, and complementary immunoglobulin light-chain analyses supported the overall pattern of localized B-cell remodeling. Together, these findings show that persistent adaptive immunity after stroke is organized across multiple hierarchical levels, from clonal concentration to recurrent receptor architecture and paired B- and T-cell repertoire organization, yet remains biologically heterogeneous across individuals. This organizational framework, together with the publicly deposited repertoire dataset, provides a foundation for future studies of the antigenic drivers and functional consequences of chronic post-stroke adaptive immunity.