Transcriptomic analysis of lung mesenchymal cells with lung-mesenchyme specific deletion of Sin3a

Congenital diaphragmatic hernia (CDH) is a common and severe congential malformation characterized by defects in diaphragm, lung, and pulmonary vascular developent. Despite the frequency and severity of CDH, the underlying developmental mechanisms are not understood. We identified SIN3A loss of function sequence variants in two patients with CDH. To understand the genetic and developmental mechanisms of CDH, we generated Sin3a conditional knockout mice that lack Sin3a expression in the lung mesenchyme. SIN3A has been shown to play a critcal role during development, directing cell lineage specification and cell cycling. We found mesenchymal progenitor cells in Sin3a CKO mice have altered expression of cell cycle progression genes from bulk lung transcriptomic analysis. To investigate changes in gene expression that occur specifically in lung mesenchymal cells, we performed fluorescent activated cell sorting (FACS) to isolate cells that underwent recombination of Sin3a. We then performed transcriptomic analysis on sorted mesenchymal cells from embryonic day 16 (E16) Sin3a CKO and control lungs. In this dataset are expression data from FACS-isolated recombined lung mesenchymal cells of Sin3a CKO and control mice. Sin3a CKO mice have conditional deletion of Sin3a in the lung mesenchyme directed by Tbx4rtta; tetocre (Tbx4rtta; tetocre; Sin3a flox/flox CKO). Control mice are heterozygous for Sin3a in the lung mesenchyme (Tbx4rtta; tetocre; Sin3a flox/WT). These data were used to identify transcriptional changes due to loss of Sin3a in the lung mesenchyme. Overall design: 4 controls and 4 Sin3a CKO lungs were collected at E16. We generated comparisons in differential gene expression between control and Sin3a CKO samples at this stage. contributor: University of Wisconsin-Madison Gene Expression Center contributor: University of Wisconsin-Madison Gene Bioinformatics Center

先天性膈疝（Congenital diaphragmatic hernia, CDH）是一类常见且危重的先天性畸形，以膈肌、肺及肺血管发育缺陷为核心特征。尽管CDH发病率较高且病情严重，其潜在的发育调控机制至今仍未阐明。我们在两例CDH患者体内鉴定出SIN3A功能丧失性序列变异。为解析CDH的遗传与发育机制，我们构建了肺间质中Sin3a表达缺失的Sin3a条件性敲除（conditional knockout, CKO）小鼠模型。既往研究已证实，SIN3A在发育过程中发挥关键调控作用，可指导细胞谱系特化与细胞周期进程。通过整体肺转录组分析，我们发现Sin3a CKO小鼠的间质祖细胞中，细胞周期进程相关基因的表达谱发生显著改变。为进一步探究肺间质细胞特异性的基因表达变化，我们采用荧光激活细胞分选术（fluorescent activated cell sorting, FACS）分离出发生Sin3a基因重组的细胞。随后，我们对胚胎第16天（embryonic day 16, E16）Sin3a CKO小鼠与对照小鼠肺脏的分选间质细胞开展转录组分析。本数据集包含Sin3a CKO小鼠与对照小鼠经FACS分离的重组肺间质细胞的基因表达数据。Sin3a CKO小鼠是通过Tbx4rtta;tetocre（Tbx4rtta; tetocre; Sin3a flox/flox CKO）系统介导的肺间质特异性Sin3a条件性敲除构建而成。对照小鼠的肺间质中Sin3a基因处于杂合状态（Tbx4rtta; tetocre; Sin3a flox/WT）。本数据集被用于鉴定肺间质中Sin3a缺失所引发的转录组变化。总体实验设计：于E16时期收集4例对照与4例Sin3a CKO肺脏样本，在该发育阶段开展对照与Sin3a CKO样本间的差异基因表达比较分析。贡献单位：威斯康星大学麦迪逊分校基因表达中心、威斯康星大学麦迪逊分校基因生物信息学中心