Abstract：
The thymus is a sophisticated primary lymphoid organ in jawed vertebrates, but knowledge on teleost thymus remains scarce. In this study, for the first time in the European sea bass, laser capture microdissection was leveraged to collect two thymic regions based on histological features, namely the cortex and the medulla. The two regions were then processed by RNAseq and in-depth functional transcriptome analyses with the aim of revealing differential gene expression patterns and gene sets enrichments, ultimately unraveling unique microenvironments imperative for the development of functional T cells. The sea bass cortex emerged as a hub of T cell commitment, somatic recombination, chromatin remodeling, cell cycle regulation, and presentation of self antigens from autophagy-, proteasome- or proteases-processed proteins. The cortex therefore accommodated extensive thymocyte proliferation and differentiation up to the checkpoint of positive selection. The medulla instead appeared as the center stage in autoimmune regulation by negative selection and deletion of autoreactive T cells, central tolerance mechanisms and extracellular matrix organization. Region-specific canonical markers of T and non-T lineage cells as well as signals for migration to/from, and trafficking within, the thymus were identified, shedding light on the highly coordinated and exquisitely complex bi-directional interactions among thymocytes and stromal components. Markers ascribable to thymic nurse cells and poorly characterized post-aire mTEC populations were found in the cortex and medulla, respectively. An in-depth data mining also exposed previously un-annotated genomic resources with differential signatures. Overall, our findings contribute to a broader understanding of the relationship between regional organization and function in the European sea bass thymus, and provide essential insights into the molecular mechanisms underlying T-cell mediated adaptive immune responses in teleosts.
摘要：
胸腺是颌骨脊椎动物中复杂的初级淋巴器官，但是关于硬骨鱼胸腺的知识仍然很少。在这项研究中,第一次在欧洲鲈鱼上，激光捕获显微切割被用来收集基于组织学特征的两个胸腺区域，即皮质和髓质。然后通过RNAseq和深度功能转录组分析对这两个区域进行处理，以揭示差异基因表达模式和基因集富集，最终解开独特的微环境对于功能性T细胞的发展至关重要。鲈鱼皮层成为T细胞承诺的枢纽，体细胞重组，染色质重塑，细胞周期调节，和自噬自身抗原的呈递-，蛋白酶或蛋白酶加工的蛋白质。因此，皮质容纳了广泛的胸腺细胞增殖和分化，直至阳性选择的检查点。相反，髓质通过阴性选择和自身反应性T细胞的缺失而成为自身免疫调节的中心阶段，中枢耐受机制和细胞外基质组织。T和非T谱系细胞的区域特异性规范标记以及向/从，以及内部贩运，确定了胸腺,在胸腺细胞和基质成分之间高度协调且复杂的双向相互作用上发光。在皮质和髓质中发现了可归因于胸腺护士细胞和特征不佳的后mTEC群体的标志物，分别。深入的数据挖掘还暴露了具有差异签名的先前未注释的基因组资源。总的来说,我们的发现有助于更广泛地理解欧洲鲈鱼胸腺的区域组织和功能之间的关系，并为硬骨鱼中T细胞介导的适应性免疫反应的分子机制提供必要的见解。
