Figure 6.

Severity-associated EN-RAGE gene set is associated with poor outcome and decreased by IL-6 blockade in COVID-19 patients (COVACTA cohort)

(A) Heatmap of EN-RAGE gene set associations with NIH ordinal scale severity at baseline (Severity NIH), need for new mechanical ventilation in patients not ventilated at baseline (Mech Vent), 28-day mortality (Death), treatment with tocilizumab or placebo at day 3 or day 7 relative to baseline, and tocilizumab (TCZ) vs. placebo at day 7 relative to baseline.

(B−E) Gene set enrichment analyses (GSEA) for gene sets associated with the myeloid cell programs EN-RAGE, MS1,¹⁰ and MDSC⁶¹ and T cells (CIBERSORT⁴⁸). Normalized enrichment scores are shown, with red shading for FDR<0.05. TCZ = tocilizumab. For (C) and (D), analyses were adjusted for baseline severity by incorporating baseline ordinal score as a covariate in our model. F. Kaplan-Meier curve showing differences between high and low risk patients for 28-day mortality. The cut point used to determine high- vs. low-risk patients was determined using Youden’s J index on the ROC curve of a linear predictor defined using a combined risk score incorporating EN-RAGE expression, age, treatment arm, and baseline ordinal severity score. Significance was determined using the log rank test.

(G and H) Tocilizumab treatment normalizes EN-RAGE and CD8⁺ T cell gene expression to healthy levels more rapidly than placebo in survivors. Only patients with measurements for all three time points are included. Lines represent the mean expression value for the gene set signature score across tocilizumab- or placebo-treated subjects. Error bars represent the 95% confidence interval around the mean. Patients are split into those that were discharged before 28, those that remained hospitalized, or subjects that died by day 28. Average signature scores are shown across the first 7 days of treatment. CTRL = healthy controls, SOC = standard of care drug therapy; significance testing was performed using t-test comparing each day to baseline, split by study arm ∗ = p < 0.05, ∗∗ = p < 0.01, ∗∗∗ = p < 0.001, ∗∗∗∗ = p < 0.0001.