Nuclear receptor coregulator NRIP1 R448G modulates T cell gut-homing and Teff:Treg balance to control intestinal inflammation [scRNA-seq]

Nuclear receptors (NRs) are crucial to integrate metabolite sensing and immune responses in the gut. Nuclear receptor-interacting protein 1 (NRIP1) is an important coregulator of various NRs that has been implicated in inflammatory bowel disease risk, but mechanistic details of how NRIP1 controls NR activities mediating immune homeostasis and inflammation remain elusive. We unveil pleiotropic functions of NRIP1 in distinct CD4+ T cell subsets during intestinal inflammation. We demonstrate that a coding risk variant, NRIP1 R448G, promotes activated CD4+ T cell gut homing and inflammatory cytokine production but impairs regulatory T cell stability, ultimately leading to exacerbated intestinal inflammation. Mechanistically, NRIP1 acts as a corepressor in retinoic acid signaling by modulating VDR (vitamin D receptor) expression and BATF (Basic leucine zipper transcription factor, ATF-like) activity. Our study reveals the impacts of NRIP1 on CD4+ T cells in immune regulation during intestinal inflammation, providing insights into mechanisms by which an NR coregulator controls immune homeostasis and tissue inflammation. Mouse splenic naïve CD4+ T cells were purified using EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL). Cells were then stimulated by plates coated with 2μg/ml anti-mouse CD3e and 2μg/ml anti-mouse CD28 antibodies, with or without 100nM atRA supplement in full RPMI 1640 medium. Cells were harvested on day 3 and submitted for 10x genomics single-cell multiome sequencing.

核受体（Nuclear receptors, NRs）是整合肠道代谢物感知与免疫应答的关键分子。核受体相互作用蛋白1（Nuclear receptor-interacting protein 1, NRIP1）是多种核受体的重要共调节因子，已被证实与炎症性肠病的发病风险相关，但NRIP1如何调控介导免疫稳态与炎症的核受体活性的具体机制仍不明晰。本研究揭示了NRIP1在肠道炎症过程中不同CD4+ T细胞亚群内的多效性功能。我们证实，编码区风险变异体NRIP1 R448G可促进活化CD4+ T细胞的肠道归巢与炎性细胞因子产生，却损害调节性T细胞的稳定性，最终加剧肠道炎症。机制上，NRIP1通过调节维生素D受体（vitamin D receptor, VDR）的表达以及碱性亮氨酸拉链转录因子ATF样（Basic leucine zipper transcription factor, ATF-like, BATF）的活性，在视黄酸信号通路中发挥共抑制因子的作用。本研究阐明了NRIP1对肠道炎症过程中CD4+ T细胞免疫调控的影响，为核受体共调节因子如何调控免疫稳态与组织炎症的机制提供了新见解。本研究采用EasySep™小鼠初始CD4+ T细胞分离试剂盒（STEMCELL）纯化小鼠脾脏初始CD4+ T细胞。随后将细胞接种于包被有2μg/ml抗小鼠CD3e抗体与2μg/ml抗小鼠CD28抗体的培养板中进行刺激，在完全RPMI 1640培养基中添加或不添加100nM全反式维甲酸（atRA）。于培养第3天收集细胞，进行10x Genomics单细胞多组学测序。