Parsa Roham, Assis Helder, de Castro Tiago B R, Dos Reis Gabriella Lima, Hartweger Harald, Bilate Angelina, Mucida Daniel
Immune Cell Dynamics and Function, Chan Zuckerberg Biohub New York, New York, NY 10032, USA.
Laboratory of Mucosal Immunology, Rockefeller University, New York, NY 10063, USA.
bioRxiv. 2025 Aug 28:2025.08.25.672130. doi: 10.1101/2025.08.25.672130.
Pathogen-specific CD4 T cells undergo dynamic expansion and contraction during infection, ultimately generating memory clones that shape the subsequent immune responses. However, the influence of distinct tissue environments on the differentiation and clonal selection of polyclonal T cells remains unclear, primarily because of the technical challenges in tracking these cells in vivo. To address this question, we generated Tracking Recently Activated Cell Kinetics (TRACK) mice, a dual-recombinase fate-mapping system that enables precise spatial and temporal labeling of recently activated CD4 T cells. Using TRACK mice during influenza infection, we observed organ-specific clonal selection and transcriptional differentiation in the lungs, mediastinal lymph nodes (medLNs), and spleen. T cell receptor (TCR) sequencing revealed that local antigenic landscapes and clonal identity shape repertoire diversity, resulting in a low clonal overlap between tissues during acute infection. During the effector phase, spleen-derived CD4 T cells preferentially adopted a stem-like migratory phenotype, whereas those activated in the medLNs predominantly differentiated into T follicular helper (Tfh) cells. Memory formation was associated with increased clonal overlap between lung and medLN-derived cells, whereas splenic clones retained a distinct repertoire. Additionally, memory CD4 T cells displayed converging antigen specificity across tissues over time. These results highlight the tissue-dependent mechanisms driving clonal selection and functional specialization during infection and underscore how memory development facilitates clonal redistribution and functional convergence.
病原体特异性CD4 T细胞在感染过程中经历动态扩增和收缩，最终产生塑造后续免疫反应的记忆克隆。然而，不同组织环境对多克隆T细胞分化和克隆选择的影响仍不清楚，主要是因为在体内追踪这些细胞存在技术挑战。为了解决这个问题，我们构建了追踪近期活化细胞动力学（TRACK）小鼠，这是一种双重组酶命运图谱系统，能够对近期活化的CD4 T细胞进行精确的空间和时间标记。在流感感染期间使用TRACK小鼠，我们观察到肺、纵隔淋巴结（medLNs）和脾脏中存在器官特异性的克隆选择和转录分化。T细胞受体（TCR）测序显示，局部抗原格局和克隆身份塑造了库多样性，导致急性感染期间不同组织之间的克隆重叠率较低。在效应期，脾脏来源的CD4 T细胞优先采用一种类似干细胞的迁移表型，而在medLNs中活化的细胞则主要分化为滤泡辅助性T（Tfh）细胞。记忆形成与肺和medLN来源的细胞之间克隆重叠增加有关，而脾脏克隆则保留了独特的库。此外，随着时间的推移，记忆性CD4 T细胞在不同组织中表现出趋同的抗原特异性。这些结果突出了感染期间驱动克隆选择和功能特化的组织依赖性机制，并强调了记忆发育如何促进克隆重新分布和功能趋同。
