DataSheet2_Complex Involvement of the Extracellular Matrix, Immune Effect, and Lipid Metabolism in the Development of Idiopathic Pulmonary Fibrosis.PDF

Background and objective: Idiopathic pulmonary fibrosis (IPF) is an aggressive fibrotic pulmonary disease with spatially and temporally heterogeneous alveolar lesions. There are no early diagnostic biomarkers, limiting our understanding of IPF pathogenesis.
Methods: Lung tissue from surgical lung biopsy of patients with early-stage IPF (n = 7), transplant-stage IPF (n = 2), and healthy controls (n = 6) were subjected to mRNA sequencing and verified by real-time quantitative PCR (RT-qPCR), immunohistochemistry, Western blot, and single-cell RNA sequencing (scRNA-Seq).
Results: Three hundred eighty differentially expressed transcripts (DETs) were identified in IPF that were principally involved in extracellular matrix (ECM) remodeling, lipid metabolism, and immune effect. Of these DETs, 21 (DMD, MMP7, POSTN, ECM2, MMP13, FASN, FADS1, SDR16C5, ACAT2, ACSL1, CYP1A1, UGT1A6, CXCL13, CXCL5, CXCL14, IL5RA, TNFRSF19, CSF3R, S100A9, S100A8, and S100A12) were selected and verified by RT-qPCR. Differences in DMD, FASN, and MMP7 were also confirmed at a protein level. Analysis of scRNA-Seq was used to trace their cellular origin to determine which lung cells regulated them. The principal cell sources of DMD were ciliated cells, alveolar type I/II epithelial cells (AT cells), club cells, and alveolar macrophages (AMs); MMP7 derives from AT cells, club cells, and AMs, while FASN originates from AT cells, ciliated cells, and AMs.
Conclusion: Our data revealed a comprehensive transcriptional mRNA profile of IPF and demonstrated that ECM remodeling, lipid metabolism, and immune effect were collaboratively involved in the early development of IPF.

背景与目的：特发性肺纤维化（Idiopathic pulmonary fibrosis, IPF）是一种侵袭性纤维化肺部疾病，其病变呈时空异质性肺泡损伤。目前尚无早期诊断生物标志物，这限制了我们对IPF发病机制的认知。
研究方法：收集早期IPF患者（n=7）、移植阶段IPF患者（n=2）及健康对照者（n=6）的外科肺活检肺组织，进行mRNA测序，并通过实时定量聚合酶链反应（real-time quantitative PCR, RT-qPCR）、免疫组织化学、蛋白质印迹法（Western blot）以及单细胞RNA测序（single-cell RNA sequencing, scRNA-Seq）进行验证。
研究结果：本研究在IPF样本中共鉴定出380个差异表达转录本（differentially expressed transcripts, DETs），其主要参与细胞外基质（extracellular matrix, ECM）重塑、脂质代谢及免疫效应过程。其中21个差异表达转录本（DMD、MMP7、POSTN、ECM2、MMP13、FASN、FADS1、SDR16C5、ACAT2、ACSL1、CYP1A1、UGT1A6、CXCL13、CXCL5、CXCL14、IL5RA、TNFRSF19、CSF3R、S100A9、S100A8及S100A12）通过RT-qPCR进行了验证。DMD、FASN及MMP7的表达差异在蛋白层面也得到了证实。通过单细胞RNA测序数据分析，本研究追踪了这些差异转录本的细胞来源，以明确调控其表达的肺脏细胞类型：DMD的主要细胞来源为纤毛细胞、I/II型肺泡上皮细胞（alveolar type I/II epithelial cells, AT cells）、棒状细胞及肺泡巨噬细胞（alveolar macrophages, AMs）；MMP7来源于AT细胞、棒状细胞及AMs，而FASN则来源于AT细胞、纤毛细胞及AMs。
研究结论：本研究揭示了IPF全面的转录组mRNA表达谱，并证实细胞外基质重塑、脂质代谢及免疫效应共同参与了IPF的早期发生发展过程。