Multiomic analysis reveals decidual-specific transcriptional programing of MAIT cells

Problem: Mucosal-Associated Invariant T (MAIT) cells have been recently identified at the maternal-fetal interface. However, transcriptional programming of decidual MAIT cells in pregnancy remains poorly understood. Method of Study: We employed a multiomic approach to address this question. Mononuclear cells from the decidua basalis and parietalis, and control PBMCs, were analyzed via flow cytometry to investigate MAIT cells in the decidua and assess their transcription factor expression. In a separate study, both decidual and matched peripheral MAIT cells were analyzed using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) coupled with gene expression analysis. Lastly, decidual MAIT cells were stimulated with E. coli and expression of MR1 by antigen presenting cells was measured to evaluate decidual MAIT cell function. Results: First, we identified MAIT cells in both the decidua basalis and parietalis. CITE-seq, coupled with scRNAseq gene expression analysis, highlighted transcriptional programming differences between decidual and matched peripheral MAIT cells at a single cell resolution. Transcription factor expression analysis further highlighted transcriptional differences between decidual MAIT cells and non-matched peripheral MAIT cells. Functionally, MAIT cells are skewed towards IFNg and TNFa production upon stimulation, with E. coli leading to IFNg production. Lastly, we demonstrate that MR1, the antigen presenting molecule restricting MAIT cells, is expressed by decidual APCs. Conclusion: MAIT cells are present in the decidua basalis and obtain a unique gene expression profile. The presence of MR1 on APCs coupled with in vitro activation by E. coli suggests that MAIT cells might be involved in tissue-repair mechanisms at the maternal-fetal interface. CD3+ T cells were obtained from matched decidua basalis and peripheral blood samples from three individuals and submitted for single cell RNA and antibody capture sequencing. Unsupervised clustering analysis identified a cluster that was determined to be MAIT cells based on the surface protein expression of CD161 and TCR-Va7.2.

# 研究问题
黏膜相关恒定T细胞（Mucosal-Associated Invariant T, MAIT）近期已在母胎界面被鉴定，但妊娠期间蜕膜MAIT细胞的转录编程机制仍未被充分阐明。
# 研究方法
本研究采用多组学策略解答该科学问题：首先通过流式细胞术分析基蜕膜、壁蜕膜及对照外周血单个核细胞（Peripheral Blood Mononuclear Cells, PBMC）中的蜕膜MAIT细胞，并评估其转录因子表达水平；在另一独立实验中，利用转录组与表位细胞索引测序（Cellular Indexing of Transcriptomes and Epitopes by Sequencing, CITE-seq）结合基因表达分析，对蜕膜MAIT细胞及配对外周血MAIT细胞进行检测；最后以大肠杆菌（Escherichia coli, E. coli）刺激蜕膜MAIT细胞，并检测抗原呈递细胞（antigen presenting cells, APCs）表面MR1的表达水平，以评估蜕膜MAIT细胞的功能活性。
# 研究结果
本研究首先在基蜕膜与壁蜕膜中均鉴定出MAIT细胞。结合单细胞RNA测序的CITE-seq分析结果显示，单细胞分辨率下蜕膜MAIT细胞与配对外周血MAIT细胞存在转录编程差异；转录因子表达分析进一步证实，蜕膜MAIT细胞与非配对外周血MAIT细胞之间存在转录谱差异。功能实验表明，MAIT细胞受刺激后倾向于分泌干扰素-γ（Interferon-gamma, IFN-γ）与肿瘤坏死因子-α（Tumor Necrosis Factor-alpha, TNF-α），其中大肠杆菌刺激可诱导MAIT细胞产生IFN-γ；此外本研究证实，蜕膜APCs可表达限制MAIT细胞活性的抗原呈递分子MR1。
# 研究结论
MAIT细胞存在于基蜕膜中，并具有独特的基因表达谱。蜕膜APCs表达MR1，结合大肠杆菌体外激活实验结果，提示MAIT细胞可能参与母胎界面的组织修复过程。
本研究从3名个体的配对基蜕膜与外周血样本中分离获取CD3阳性T细胞（CD3+ T cells），进行单细胞RNA测序与抗体捕获测序；通过无监督聚类分析，依据CD161与TCR-Vα7.2的表面蛋白表达特征，成功鉴定出一个MAIT细胞亚群簇。