RNA-seq profiling of thymic epithelial cells from Mcl1 knockout and wildtype mice

T cell differentiation is governed by interactions with thymic epithelial cells (TECs) and defects in this process undermine immune function and tolerance. To uncover new strategies to restore thymic function and adaptive immunity in immunodeficiency, we sought to determine the molecular mechanisms that control life and death decisions in TEC. We created a mouse model which specifically deleted the pro-survival gene Mcl1 in TEC. We found that while BCL-2 and BCL-XL were dispensable for TEC homeostasis, MCL-1 deficiency impacted on TEC as early as E15.5, resulting in early thymic atrophy and T cell lymphopenia, with near complete loss of thymic tissue by 2 months of age. MCL-1 was not necessary for TEC differentiation but was continually required for the survival of medullary TEC, including autoimmune regulator (AIRE) expressing TECs and the maintenance of overall thymic architecture. To understand the molecular mechanisms in more detail, RNA-seq profiling was undertaken of cortical and medullary thymic epithelial cells (cTECs and mTECs) from wildtype and knockout mice. The number of biological replicates was n=4 for WT cTECs, n=2 for WT mTECs, n=1 for KO cTECs and n=1 for KO mTECs.T细胞分化受与胸腺上皮细胞（thymic epithelial cells, TECs）的相互作用调控，该过程中的缺陷会损害免疫功能与免疫耐受。为探索在免疫缺陷状态下恢复胸腺功能及适应性免疫的新策略，我们旨在阐明调控胸腺上皮细胞生死抉择的分子机制。我们构建了一种可在胸腺上皮细胞中特异性敲除促存活基因Mcl1的小鼠模型。研究发现，尽管BCL-2与BCL-XL对胸腺上皮细胞稳态并非必需，但MCL-1缺陷早在胚胎期15.5天（E15.5）便对胸腺上皮细胞造成影响，引发早期胸腺萎缩与T细胞淋巴细胞减少症，至小鼠2月龄时胸腺组织几乎完全丧失。MCL-1并非胸腺上皮细胞分化所必需，却是持续维持髓质胸腺上皮细胞（包括表达自身免疫调节因子（autoimmune regulator, AIRE）的胸腺上皮细胞）存活以及整体胸腺结构稳定的关键因子。为更深入地解析其分子机制，我们对野生型与敲除型小鼠的皮质胸腺上皮细胞（cortical thymic epithelial cells, cTECs）及髓质胸腺上皮细胞（medullary thymic epithelial cells, mTECs）开展了RNA测序（RNA-seq）分析。各组生物学重复数分别为：野生型皮质胸腺上皮细胞n=4，野生型髓质胸腺上皮细胞n=2，敲除型皮质胸腺上皮细胞与髓质胸腺上皮细胞均为n=1。