Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)

Data-sets
RNAseq_CountTable.tsv: Raw count table from RNA-seq experiments
WGBS_MethylationTable.tsv: Total read coverage and number of methylated sites at CpG positions  (reference genome: hg19) 
Abstract
Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barrier integrity and impaired lung regeneration. We hypothesized that alveolar type 2 (AT2) cells, as alveolar epithelial progenitors, will carry molecular alterations that compromise alveolar regeneration in COPD. Sorted AT2 cells from ex-smokers with and without COPD at different disease stages were subjected to RNA sequencing and whole-genome bisulfite sequencing to generate unbiased transcriptome and DNA methylation maps of alveolar progenitors in the lung. Our analysis revealed genome-wide epigenetic changes in AT2 cells during COPD that were associated with global gene expression changes. Integrative data analysis uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that dysregulation of COPD-associated pathways in AT2 cells may be regulated by DNA methylation. Interferon (IFN) signaling was the top-upregulated pathway associated with the concomitant loss of promoter DNA methylation. Epigenetic regulation of the IFN pathway was validated in both global and targeted DNA demethylation assays in A549 cells. Notably, targeted DNA demethylation of IRF9 triggered upregulation of IFN signaling, mimicking the effects observed in COPD AT2 cells in the profiling data. Our findings suggest that COPD-triggered epigenetic alterations in AT2 cells impair internal regeneration programs in human lung parenchyma.

数据集
RNAseq_CountTable.tsv：RNA测序实验获得的原始计数表
WGBS_MethylationTable.tsv：CpG位点的总测序读段覆盖度与甲基化位点数量（参考基因组：hg19）
摘要
慢性肺部疾病（包括慢性阻塞性肺疾病（COPD））影响全球超过5亿人群，是全球主要致死病因之一。急慢性肺部疾病的共同特征为呼吸屏障完整性改变与肺再生能力受损。我们提出假说：作为肺泡上皮祖细胞的肺泡2型（alveolar type 2, AT2）细胞，会携带损害COPD患者肺泡再生能力的分子改变。我们对来自不同疾病阶段的有、无COPD的既往吸烟者的分选AT2细胞开展RNA测序与全基因组亚硫酸氢盐测序，以绘制肺部肺泡祖细胞的无偏倚转录组与DNA甲基化图谱。本研究分析显示，COPD患者的AT2细胞中存在全基因组范围的表观遗传改变，且该改变与整体基因表达变化相关。整合数据分析揭示了基因表达与启动子甲基化之间存在显著负相关，这提示AT2细胞中COPD相关通路的失调可能受DNA甲基化调控。干扰素（IFN）信号通路是与启动子DNA甲基化同步缺失相关的上调幅度最高的通路。干扰素通路的表观遗传调控在A549细胞的全基因组与靶向DNA去甲基化实验中得到了验证。值得注意的是，对IRF9开展靶向DNA去甲基化可触发干扰素信号通路的上调，模拟了测序分析数据中COPD患者AT2细胞所呈现的效应。本研究结果表明，COPD诱导的AT2细胞表观遗传改变会损害人类肺实质的内源性再生程序。