Changes in the Pulmonary and Systemic Transcriptome in Critically Ill COVID-19 Patients Treated With V-V ECMO

Introduction: Severe respiratory failure is a hallmark manifestation of COVID-19 infection. Veno-venous extracorporeal membrane oxygenation (ECMO) is a critical therapeutic intervention for COVID-19 patients failing standard management. However, the molecular mechanisms by which ECMO alters the inflammatory immune response remains poorly understood. We hypothesized that in COVID-19 patients, ECMO will impart distinct patterns of inflammation within the serum and lower airway host transcriptome. Methods: Patients with confirmed COVID-19 infection were enrolled upon ICU admission at two NYC medical centers between April 2020 and March 2022. Paired blood and bronchoalveolar lavage or tracheal aspirate specimens were acquired at designated time points during the three weeks following intubation and/or ECMO cannulation. RNA sequencing was performed on all samples. Differential expression analysis (DEA) was completed using edgeR. Gene Set Enrichment Analysis (GSEA) was used to identify differentially enriched genes. Propensity matching was done using an optimal matching method. Results: Seventy-seven patients were included in this study. Forty-two patients underwent ECMO cannulation and thirty-five received standard care. At baseline, the earliest time point after intubation and prior to ECMO cannulation, there were no significant differences in the systemic or lower airway host transcriptomes between the two groups. Within one week following ECMO cannulation, differentially expressed genes began to emerge within the lower airway by DEA (Fig 1A). By week two, differentially expressed genes were also found within the systemic transcriptome (Fig 1B). These findings persisted through the third week of follow-up. GSEA demonstrated that pathways related to immune response, including TNFa, interferon gamma, and IL6 signaling, were downregulated after ECMO initiation within the systemic circulation (Fig 1C). Additionally, several immune pathways were downregulated within the lower airway of the ECMO cohort during the first week following cannulation including TNFa signaling via NF-kB and IL6 signaling. By week 3 this pattern reversed with increased lower airway inflammatory expression observed amongst ECMO patients (Fig 1C). Conclusion: ECMO alters the lower airway host transcriptome of critically ill COVID-19 patients within days of cannulation, with longitudinal changes observed in both the lower airways and systemic circulation at two and three weeks. Specifically, inflammatory pathways are differentially enriched and this may play a role in the subsequent phenotype of disease and long-term outcomes. Larger longitudinal studies are needed to fully understand the impacts of ECMO on transcriptome expression and its role on disease course.