Regulation of lung progenitor plasticity and repair by fatty acid oxidation [scRNA-seq]

Idiopathic pulmonary fibrosis (IPF) is an age-related interstitial lung disease, characterized by inadequate alveolar regeneration and ectopic bronchiolization. While some molecular pathways regulating lung progenitor cells have been described, the role of metabolic pathways in alveolar regeneration is poorly understood. We report that expression of fatty acid oxidation (FAO) genes significantly diminishes in alveolar epithelial cells of IPF lungs by single-cell RNA sequencing and tissue staining. Genetic and pharmacological inhibition in AT2 cells of carnitine palmitoyltransferase 1a (CPT1a), the rate-limiting enzyme of FAO, promoted mitochondrial dysfunction and acquisition of aberrant intermediate states expressing basaloid, and airway secretory cell markers SCGB1A1, and SCGB3A2. Further, mice with deficiency of CPT1a in AT2 cells show enhanced susceptibility to developing lung fibrosis with an accumulation of epithelial cells expressing markers of intermediate cells, airway secretory cells, and senescence. We found that deficiency of CPT1a causes a decrease in SMAD7 protein levels and TGF-β signaling pathway activation. These findings suggest that the mitochondrial FAO metabolic pathway contributes to the regulation of lung progenitor cell repair responses and deficiency of FAO contributes to aberrant lung repair and the development of lung fibrosis. To investigate the FAO pathway in AT2 cells, we collected IPF lung explants from patients diagnosed with IPF and undergoing transplantation. In parallel, we collected lung tissue from aged non-IPF individuals. Tissues were formalin-fixed and paraffin-embedded (FFPE) for preservation and used as input material for scRNA-Seq.

特发性肺纤维化（Idiopathic Pulmonary Fibrosis, IPF）是一种年龄相关性间质性肺疾病，以肺泡再生不足与异位细支气管化生为核心特征。尽管已有研究阐明了部分调控肺祖细胞的分子通路，但代谢通路在肺泡再生中的作用仍有待深入解析。本研究通过单细胞RNA测序与组织染色发现，IPF患者肺组织的肺泡上皮细胞中，脂肪酸氧化（Fatty Acid Oxidation, FAO）相关基因的表达水平显著下调。研究人员对脂肪酸氧化的限速酶——肉碱棕榈酰转移酶1a（Carnitine Palmitoyltransferase 1a, CPT1a）在AT2细胞中开展了遗传与药理学抑制实验，结果显示该操作可诱发线粒体功能障碍，并使细胞获得异常中间表型，表达基底样细胞与气道分泌细胞的标志物SCGB1A1及SCGB3A2。进一步的动物实验表明，AT2细胞中CPT1a缺陷的小鼠对肺纤维化的易感性显著升高，且体内会积累表达中间细胞、气道分泌细胞及衰老标志物的上皮细胞。研究发现，CPT1a缺陷会导致SMAD7蛋白水平下调，并激活转化生长因子-β（TGF-β）信号通路。上述结果证实，线粒体脂肪酸氧化代谢通路参与调控肺祖细胞的修复应答，而脂肪酸氧化功能缺陷会促成异常肺修复与肺纤维化的发生发展。为探究AT2细胞中的脂肪酸氧化通路，本团队收集了经确诊并接受肺移植的IPF患者的肺切除标本；同时采集了老年非IPF个体的肺组织。所有组织均经福尔马林固定石蜡包埋（FFPE）保存，用作单细胞RNA测序（scRNA-Seq）的实验材料。