Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile.
Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.
Sci Rep. 2024 May 8;14(1):10553. doi: 10.1038/s41598-024-61158-4.
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions of the gastrointestinal tract associated with multiple pathogenic factors, including dysregulation of the immune response. Effector CD4 T cells and regulatory CD4 T cells (Treg) are central players in maintaining the balance between tolerance and inflammation. Interestingly, genetic modifications in these cells have been implicated in regulating the commitment of specific phenotypes and immune functions. However, the transcriptional program controlling the pathogenic behavior of T helper cells in IBD progression is still unknown. In this study, we aimed to find master transcription regulators controlling the pathogenic behavior of effector CD4 T cells upon gut inflammation. To achieve this goal, we used an animal model of IBD induced by the transfer of naïve CD4 T cells into recombination-activating gene 1 (Rag1) deficient mice, which are devoid of lymphocytes. As a control, a group of Rag1 mice received the transfer of the whole CD4 T cells population, which includes both effector T cells and Treg. When gut inflammation progressed, we isolated CD4 T cells from the colonic lamina propria and spleen tissue, and performed bulk RNA-seq. We identified differentially up- and down-regulated genes by comparing samples from both experimental groups. We found 532 differentially expressed genes (DEGs) in the colon and 30 DEGs in the spleen, mostly related to Th1 response, leukocyte migration, and response to cytokines in lamina propria T-cells. We integrated these data into Gene Regulatory Networks to identify Master Regulators, identifying four up-regulated master gene regulators (Lef1, Dnmt1, Mybl2, and Jup) and only one down-regulated master regulator (Foxo3). The altered expression of master regulators observed in the transcriptomic analysis was confirmed by qRT-PCR analysis and found an up-regulation of Lef1 and Mybl2, but without differences on Dnmt1, Jup, and Foxo3. These two master regulators have been involved in T cells function and cell cycle progression, respectively. We identified two master regulator genes associated with the pathogenic behavior of effector CD4 T cells in an animal model of IBD. These findings provide two new potential molecular targets for treating IBD.
炎症性肠病（IBD）是一组与多种致病因素相关的胃肠道慢性炎症性疾病，包括免疫反应失调。效应 CD4 T 细胞和调节性 CD4 T 细胞（Treg）是维持耐受和炎症之间平衡的核心参与者。有趣的是，这些细胞中的遗传修饰已被牵连到调节特定表型和免疫功能的特异性。然而，控制 IBD 进展中辅助性 T 细胞致病行为的转录程序仍然未知。在这项研究中，我们旨在寻找控制效应 CD4 T 细胞在肠道炎症时致病行为的主转录调控因子。为了实现这一目标，我们使用了一种通过将幼稚 CD4 T 细胞转移到重组激活基因 1（Rag1）缺陷型小鼠中诱导的 IBD 动物模型，该模型缺乏淋巴细胞。作为对照，一组 Rag1 小鼠接受了整个 CD4 T 细胞群体的转移，其中包括效应 T 细胞和 Treg。当肠道炎症进展时，我们从结肠固有层和脾脏组织中分离 CD4 T 细胞，并进行批量 RNA-seq。我们通过比较两组实验样本，确定了差异上调和下调的基因。我们在结肠中发现了 532 个差异表达基因（DEGs），在脾脏中发现了 30 个 DEGs，这些基因主要与 Th1 反应、白细胞迁移和固有层 T 细胞中的细胞因子反应有关。我们将这些数据整合到基因调控网络中，以识别主调控因子，确定了四个上调的主调控基因（Lef1、Dnmt1、Mybl2 和 Jup）和一个下调的主调控基因（Foxo3）。通过 qRT-PCR 分析证实了转录组分析中观察到的主调控因子的改变表达，并发现 Lef1 和 Mybl2 的上调，但 Dnmt1、Jup 和 Foxo3 没有差异。这两个主调控因子分别参与 T 细胞功能和细胞周期进程。我们在 IBD 的动物模型中鉴定出与效应 CD4 T 细胞致病行为相关的两个主调控基因。这些发现为治疗 IBD 提供了两个新的潜在分子靶点。
