Characterization of dynamic gene networks in response to thoracotomy, ischemia-reperfusion in mouse heart

Introduction Myocardial infarction is an irreversible death of cardiac cells in response to prolonged ischemia and ischemia-reperfusion injury. Experimental designs and analytical pipelines used in time-series ischemia-reperfusion (IR) transcriptomic studies represent major challenges in the understanding of progression of such multifactorial diseases. Objectives In this study, we aim to provide a pipeline for the analysis of kinetical transcriptomics, characterize the change in gene expression profiles in response to surgical preparations prior IR and measure the dynamic gene regulation during IR in the left ventricle of mouse heart. Methods Eight to twelve- weeks old C57BL/6 mice were anesthetized, undergone surgical preparations with and without IR and sacrificed at different time points (8 animals per time point) of the IR sequence. RNA-seq data from sham myocardium, ischemic and non-ischemic myocardium of IR mice are analyzed, clustered and functionally characterized. Results Gene expression analysis by DESeq2 yielded a total of 1006, 446 and 3878 differentially expressed genes in response to surgical interventions, remote and ischemia-reperfusion effect. Temporal clustering by weighted gene co-expression network analysis (WGCNA) and gene ontology analysis have shown that surgical preparations prior IR initiates inflammatory response mediated mainly by the phenotypic shift between the different macrophages’ subtypes and the infiltration of neutrophils to the heart few hours post-surgery. Conclusion This study not only provides a comprehensive framework for kinetical transcriptomic studies, but also sheds light on the importance of considering the change of gene expression profiles driven by the thoracotomy effect.