Host transcriptomic responses of chicken embryos during Avian Pathogenic Escherichia coli infection reveal the significant role of the yolk sac in embryonic mortality

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a major disease syndrome in poultry with the yolk sac infection recognized as a leading factor contributing to embryonic mortality. Yolk sac is the initial site of infection, however its contribution in embryonic mortality at molecular level has remained unexplored. To address this critical gap, we conducted RNA sequencing (RNA-seq) to analyze the comprehensive in vivo transcriptomic profiles of yolk sac and embryonic liver from APEC-infected embryos, comparing dead embryos with those that survived and mock-infected controls, to uncover key differences in host responses in multiple scenarios. Our results revealed that dead embryos displayed significant pro-inflammatory cytokine activity and cellular senescence, disrupted lipid and energy metabolism, and compromised antioxidative defenses, particularly in the yolk sac. In contrast, surviving embryos exhibited a regulated inflammatory response, enhanced mitochondrial activity, robust antioxidative responses and tissue repair mechanisms, which likely underpinned its resilience. Notably, yolk sac showed positive correlation (r = 0.531) with the embryonic liver, but demonstrated more severe inflammation and metabolic dysregulation, thereby highlighting its heightened vulnerability. Furthermore, reactive oxygen species (ROS) levels, the balance of the inflammatory response, and yolk sac integrity are crucial determinants of embryonic survival, with mitochondrial dysfunction serving as a key regulator of host immune and metabolic adaptation. The insights provide a deeper understanding of the previously overlooked role of yolk sac compared to liver during APEC infection, offering potential avenues for improving host resilience and mitigating economic losses in poultry. Overall design: RNA-Seq profiling of yolk sac and liver from APEC-infected embryos: A comparative analysis between infected dead, infected surviving, and mock-infected control groups