Genomic and Molecular Epidemiology (GAME) Lab., School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
Independent Researcher, Montefalco, Italy.
BMC Genomics. 2021 Dec 6;22(1):881. doi: 10.1186/s12864-021-08171-3.
Acute or chronic irreversible respiratory failure may occur in patients undergoing pneumonectomy. Aim of this study was to determine transcriptome expression changes after experimental pneumonectomy in swine model. Experimental left pneumonectomy was performed in five pigs under general anaesthesia. Both the resected and the remaining lung, after 60 post-operative completely uneventful days, underwent genome-wide bulk RNA-Sequencing (RNA-Seq).
Histological analysis showed dilation of air spaces and rupture of interalveolar septa. In addition, mild inflammation, no fibrosis, radial stretch of the bronchus, strong enlargement of airspaces and thinning of the blood supply were observed. Bioinformatic analyses of bulk RNA-Seq data identified 553 Differentially Expressed Genes (DEGs) at adjusted P-value below 0.001, between pre- and post-pneumonectomy. The top 10 up-regulated DEGs were Edn1, Areg, Havcr2, Gadd45g, Depp1, Cldn4, Atf3, Myc, Gadd45b, Socs3; the top 10 down-regulated DEGs were Obscn, Cdkn2b, ENSSSCG00000015738, Prrt2, Amer1, Flrt3, Efnb2, Tox3, Znf793, Znf365. Leveraging digital cytometry tools, no difference in cellular abundance was found between the two experimental groups, while the analysis of cell type-specific gene expression patterns highlighted a striking predominance of macrophage-specific genes among the DEGs. DAVID-based gene ontology analysis showed a significant enrichment of "Extrinsic apoptotic signaling pathway" (FDR q = 7.60 × 10) and "Response to insulin" (FDR q = 7.60 × 10) genes, along with an enrichment of genes involved as "Negative regulators of DDX58/IFIH1 signaling" (FDR q = 7.50 × 10) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections.
This translational genomics study highlighted the existence both of individual genes, mostly dysregulated in certain cellular populations (e.g., macrophages), and gene-networks involved in pulmonary reaction after left pneumonectomy. Their involvement in lung homeostasis is largely supported by previous studies, carried out both in humans and in other animal models (under homeostatic or disease-related conditions), that adopted candidate-gene approaches. Overall, the present findings represent a preliminary assessment for future, more focused, studies on compensatory lung adaptation, pulmonary regeneration and functional reload.
在接受肺切除术的患者中可能会出现急性或慢性不可逆转的呼吸衰竭。本研究的目的是确定实验性猪肺切除术后的转录组表达变化。在全麻下对 5 头猪进行了左侧肺切除术。在术后 60 天完全无并发症的情况下，对切除的肺和剩余的肺进行了全基因组批量 RNA 测序（RNA-Seq）。
组织学分析显示肺泡空间扩张和肺泡间隔破裂。此外，还观察到轻度炎症、无纤维化、支气管放射状伸展、肺泡腔明显增大和血液供应变薄。对批量 RNA-Seq 数据的生物信息学分析确定了 553 个差异表达基因（DEG），在调整后的 P 值低于 0.001 时，在术前和术后之间。上调的前 10 个 DEG 是 Edn1、Areg、Havcr2、Gadd45g、Depp1、Cldn4、Atf3、Myc、Gadd45b、Socs3；下调的前 10 个 DEG 是 Obscn、Cdkn2b、ENSSSCG00000015738、Prrt2、Amer1、Flrt3、Efnb2、Tox3、Znf793、Znf365。利用数字细胞计数工具，在两个实验组之间未发现细胞丰度的差异，而细胞类型特异性基因表达模式的分析突出显示了 DEG 中巨噬细胞特异性基因的显著优势。基于 DAVID 的基因本体分析显示，“细胞外凋亡信号通路”（FDR q=7.60×10）和“对胰岛素的反应”（FDR q=7.60×10）基因显著富集，同时还发现了与查询反应组途径数据库中的“DDX58/IFIH1 信号的负调节因子”（FDR q=7.50×10）相关的基因富集。基因网络分析表明基因相互连接普遍失调。
这项转化基因组学研究强调了个体基因的存在，这些基因主要在某些细胞群体中失调（例如巨噬细胞），以及肺切除后参与肺反应的基因网络。它们在肺稳态中的作用在很大程度上得到了先前研究的支持，这些研究在人类和其他动物模型（在稳态或疾病相关条件下）中都采用了候选基因方法。总的来说，目前的发现代表了未来更集中研究补偿性肺适应、肺再生和功能恢复的初步评估。
