Genome-wide expression of the residual lung reacting to experimental Pneumonectomy

Abstract

Background 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). Results 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− 3) and “Response to insulin” (FDR q = 7.60 × 10− 3) genes, along with an enrichment of genes involved as “Negative regulators of DDX58/IFIH1 signaling” (FDR q = 7.50 × 10− 4) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections. Conclusion 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.

Whole‐genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype

“…The animals were raised at the experimental station of the INIA (the Peruvian National Institute for Agronomic Innovation) located in Quimsachata, Peru. Sampling of the animals and genomic analysis were performed as reported in Pallotti et al (2023). Briefly, genomic DNA extracted from skin biopsies underwent whole‐genome sequencing on an Illumina NovaSeq 6000 System, with a 150 × 2 bp mode and an average sequencing depth of 30×.…”

FLRT3 and TGF‐β/SMAD4 signalling: Impacts on apoptosis, autophagy and ion channels in supraventricular tachycardia

“…Within this realm, it functions as a cell adhesion molecule, facilitating neuronal connectivity 26 . While its prominence in neural contexts is recognized, contemporary studies have broadened its significance beyond the neural landscape 27,28 . Emerging evidence elucidates its involvement in diverse cellular processes encompassing tissue development, immune modulation and even cancer progression 29,30 .…”

“… 26 While its prominence in neural contexts is recognized, contemporary studies have broadened its significance beyond the neural landscape. 27 , 28 Emerging evidence elucidates its involvement in diverse cellular processes encompassing tissue development, immune modulation and even cancer progression. 29 , 30 Intriguingly, before our study, the role of FLRT3 in cardiac physiology and, specifically, within the backdrop of SVT, remained relatively uncharted.…”

RNA-sequencing comparison of pneumonectomy and bleomycin reveals anti-fibrotic mechanisms of lung fibroblasts

“…To our knowledge, this is the rst report identifying a role for ITPKC in the lung. Analysis of supplementary data from a porcine study using whole-lung RNA-sequencing found Itpkc to be upregulated 60 days following PNX [32], and this was predicted to occur via AT2 cells using the machine learning algorithm CIBERSORTx [33]. The authors also noted that broblasts made up only a small portion of cells used for their RNA-sequencing analysis [32].…”

“…Analysis of supplementary data from a porcine study using whole-lung RNA-sequencing found Itpkc to be upregulated 60 days following PNX [32], and this was predicted to occur via AT2 cells using the machine learning algorithm CIBERSORTx [33]. The authors also noted that broblasts made up only a small portion of cells used for their RNA-sequencing analysis [32]. Taken in the context of our results, this could indicate that ITPKC does not necessarily have a cell-type-speci c role, and rather functions to regulate processes that could otherwise cause brotic changes.…”