CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair [scATAC-seq]

Cell plasticity theoretically extends to all possible cell types, but naturally decreases as cells differentiate, whereas injury-repair re-engages the developmental plasticity. Here we show that the lung alveolar type 2 (AT2)-specific transcription factor (TF), CEBPA, restricts AT2 cell plasticity in the mouse lung. AT2 cells undergo transcriptional and epigenetic maturation postnatally. Without CEBPA, both neonatal and mature AT2 cells reduce the AT2 program, but only the former reactivate the SOX9 progenitor program. Sendai virus infection bestows mature AT2 cells with neonatal plasticity where Cebpa mutant, but not wild type, AT2 cells express SOX9, as well as more readily proliferate and form KRT8/CLDN4+ transitional cells. CEBPA promotes the AT2 program by recruiting the lung lineage TF NKX2-1. The temporal change in CEBPA-dependent plasticity reflects AT2 cell developmental history. The ontogeny of AT2 cell plasticity and its transcriptional and epigenetic mechanisms have implications in lung regeneration and cancer. Overall design: FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed using the 3' Library and Gel Bead Kit following the manufacturer's users guide (v2 rev D) on the Chromium Single-Cell Gene Expression Solution Platform (10X Genomics).

细胞可塑性理论上可覆盖所有潜在细胞类型，但随细胞分化进程自然降低，而损伤修复过程可重新激活发育性细胞可塑性。本研究证实，肺肺泡Ⅱ型（alveolar type 2, AT2）特异性转录因子（transcription factor, TF）CEBPA可限制小鼠肺内AT2细胞的可塑性。AT2细胞在出生后会经历转录组与表观组层面的成熟过程。在缺失CEBPA的情况下，新生期与成熟AT2细胞均会下调AT2特征基因程序，但仅新生期AT2细胞可重新激活SOX9祖细胞程序。仙台病毒感染可赋予成熟AT2细胞新生期可塑性：此时Cebpa突变型而非野生型AT2细胞会表达SOX9，且增殖能力更强，更易形成KRT8/CLDN4+过渡态细胞。CEBPA通过招募肺谱系转录因子NKX2-1来促进AT2特征基因程序的执行。CEBPA依赖性可塑性的时序变化，反映了AT2细胞的发育历程。AT2细胞可塑性的个体发育机制及其转录与表观调控机制，对肺再生与肿瘤研究具有重要参考价值。整体实验设计：通过荧光激活细胞分选术（fluorescence-activated cell sorting, FACS）纯化的肺上皮细胞、免疫细胞、内皮细胞及间充质细胞，均依照制造商用户指南（v2 rev D），使用3'文库与磁珠试剂盒在Chromium单细胞基因表达解决方案平台（10X Genomics）上完成建库与测序流程。