Longitudinal transcriptomic analysis reveals persistent enrichment of iron homeostasis and erythrocyte function pathways in severe COVID-19 ARDS

• Published in: Frontiers in immunology Vol. 15; p. 1397629
• Main Authors: Eltobgy, Moemen, Johns, Finny, Farkas, Daniela, Leuenberger, Laura, Cohen, Sarah P, Ho, Kevin, Karow, Sarah, Swoope, Gabrielle, Pannu, Sonal, Horowitz, Jeffrey C, Mallampalli, Rama K, Englert, Joshua A, Bednash, Joseph S
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 05-08-2024
• Subjects: Aged; ARDS (acute respiratory disease syndrome); COVID - 19; COVID-19 - blood; COVID-19 - genetics; Erythrocytes - metabolism; Female; Gene Expression Profiling; Homeostasis; Humans; Immunology; Iron - metabolism; longitudinal analysis; Longitudinal Studies; Male; Middle Aged; Respiratory Distress Syndrome - blood; Respiratory Distress Syndrome - genetics; RNA seq analysis; SARS-CoV-2; SARS-CoV-2 - physiology; Transcriptome; longitudinal analysis; COVID - 19; SARS-CoV-2; ARDS (acute respiratory disease syndrome); RNA seq analysis
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2024.1397629

The acute respiratory distress syndrome (ARDS) is a common complication of severe COVID-19 and contributes to patient morbidity and mortality. ARDS is a heterogeneous syndrome caused by various insults, and results in acute hypoxemic respiratory failure. Patients with ARDS from COVID-19 may represent a subgroup of ARDS patients with distinct molecular profiles that drive disease outcomes. Here, we hypothesized that longitudinal transcriptomic analysis may identify distinct dynamic pathobiological pathways during COVID-19 ARDS.
We identified a patient cohort from an existing ICU biorepository and established three groups for comparison: 1) patients with COVID-19 ARDS that survived hospitalization (COVID survivors, n = 4), 2) patients with COVID-19 ARDS that did not survive hospitalization (COVID non-survivors, n = 5), and 3) patients with ARDS from other causes as a control group (ARDS controls, n = 4). RNA was isolated from peripheral blood mononuclear cells (PBMCs) at 4 time points (Days 1, 3, 7, and 10 following ICU admission) and analyzed by bulk RNA sequencing.
We first compared transcriptomes between groups at individual timepoints and observed significant heterogeneity in differentially expressed genes (DEGs). Next, we utilized the likelihood ratio test to identify genes that exhibit different patterns of change over time between the 3 groups and identified 341 DEGs across time, including hemoglobin subunit alpha 2 (
), hemoglobin subunit beta (
), von Willebrand factor C and EGF domains (
), and carbonic anhydrase 1 (
), which all demonstrated persistent upregulation in the COVID non-survivors compared to COVID survivors. Of the 341 DEGs, 314 demonstrated a similar pattern of persistent increased gene expression in COVID non-survivors compared to survivors, associated with canonical pathways of iron homeostasis signaling, erythrocyte interaction with oxygen and carbon dioxide, erythropoietin signaling, heme biosynthesis, metabolism of porphyrins, and iron uptake and transport.
These findings describe significant differences in gene regulation during patient ICU course between survivors and non-survivors of COVID-19 ARDS. We identified multiple pathways that suggest heme and red blood cell metabolism contribute to disease outcomes. This approach is generalizable to larger cohorts and supports an approach of longitudinal sampling in ARDS molecular profiling studies, which may identify novel targetable pathways of injury and resolution.