背景:单核细胞来源的肺泡巨噬细胞(Mo_AMs)越来越被认为是特发性肺纤维化(IPF)的潜在致病因素。虽然scRNAseq分析在Mo_AMs的转录组分析中被证明是有价值的,多组学的整合分析可能为理解这些细胞群体提供更多维度.
方法:我们对116个scRNAseq,119份来自IPF的bulkseq和5份scATACseq肺组织样本。Webuiltalarge-scIPFscRNAseqatlasandconductedtheMonocle2/3aswellastheCellchattoexplorethedevelopmentpathandintercellularcommunicationonMo_AMs.Wealsoreportedthedifferenceinmetabolisms,Mo_AMs和组织驻留的肺泡巨噬细胞(TRMs)之间的组织修复和吞噬作用。为了确定Mo_AMs是否影响肺功能,我们将来自bulkseq数据集的临床表型(FVC%pred)预测到scRNAseq图谱上。最后,我们使用scATATCseq来揭示上游调控机制并确定Mo_AMs的关键驱动因素。
结果:我们确定了三个Mo_AMs集群,轨迹分析进一步验证了这些集群的起源。此外,通过Cellchat分析,发现CXCL12/CXCR4轴通过激活Mo_AMs中的ERK途径参与Mo_AMs与成纤维细胞之间的相互作用的分子基础。SPP1_RecMacs(RecMacs,招募的巨噬细胞)在低FVC组高于高FVC组。具体来说,与TRM相比,Mo_AMs的脂质和能量代谢以及组织修复功能高于TRMs。但是,TRMs可能比TRMs具有更高的吞噬水平。SPIB(PU.1),JUNB,JUND,BACH2,FOSL2和SMARCC1与Mo_AM的开放染色质比TRMs更强。在SPP1_RecMacs和TRMs中均观察到APOE的显着上调表达和深染色质可及性。
结论:通过轨迹分析,证实SPP1_RecMacs来源于单核细胞。此外,Mo_AMs可能通过与成纤维细胞的通讯影响FVC%pred并加重肺纤维化。此外,Mo_AMs和TRMs之间独特的转录调节因子暗示它们可能依赖于不同的上游调节机制。总的来说,这项工作提供了Mo_AMs如何管理IPF的全球概述,也有助于确定更好的方法和干预疗法。
BACKGROUND: Monocyte-derived alveolar macrophages (Mo_AMs) are increasingly recognised as potential pathogenic factors for idiopathic pulmonary fibrosis (IPF). While scRNAseq analysis has proven valuable in the transcriptome profiling of Mo_AMs, the integration analysis of multi-omics may provide additional dimensions of understanding of these cellular populations.
METHODS: We performed multi-omics analysis on 116 scRNAseq, 119 bulkseq and five scATACseq lung tissue samples from IPF. We built a large-scale IPF scRNAseq atlas and conducted the Monocle 2/3 as well as the Cellchat to explore the developmental path and intercellular communication on Mo_AMs. We also reported the difference in metabolisms, tissue repair and phagocytosis between Mo_AMs and tissue-resident alveolar macrophages (TRMs). To determine whether Mo_AMs affected pulmonary function, we projected clinical phenotypes (FVC%pred) from the bulkseq dataset onto the scRNAseq atlas. Finally, we used scATATCseq to uncover the upstream regulatory mechanisms and determine key drivers in Mo_AMs.
RESULTS: We identified three Mo_AMs clusters and the trajectory analysis further validated the origin of these clusters. Moreover, via the Cellchat analysis, the CXCL12/CXCR4 axis was found to be involved in the molecular basis of reciprocal interactions between Mo_AMs and fibroblasts through the activation of the ERK pathway in Mo_AMs. SPP1_RecMacs (RecMacs, recruited macrophages) were higher in the low-FVC group than in the high-FVC group. Specifically, compared with TRMs, the functions of lipid and energetic metabolism as well as tissue repair were higher in Mo_AMs than TRMs. But, TRMs may have higher level of phagocytosis than TRMs. SPIB (PU.1), JUNB, JUND, BACH2, FOSL2, and SMARCC1 showed stronger association with open chromatin of Mo_AMs than TRMs. Significant upregulated expression and deep chromatin accessibility of APOE were observed in both SPP1_RecMacs and TRMs.
CONCLUSIONS: Through trajectory analysis, it was confirmed that SPP1_RecMacs derived from Monocytes. Besides, Mo_AMs may influence FVC% pred and aggravate pulmonary fibrosis through the communication with fibroblasts. Furthermore, distinctive transcriptional regulators between Mo_AMs and TRMs implied that they may depend on different upstream regulatory mechanisms. Overall, this work provides a global overview of how Mo_AMs govern IPF and also helps determine better approaches and intervention therapies.