Fig 1: Circulating cytokine and chemokine signatures of COVID-19(A) Violin plots of measured cytokines in mild (green), moderate (blue), and severe (magenta) samples, including all samples. Stars indicate significance for the comparison of severe against mild and moderate as follows: ∗ adjusted p <0.05, ∗∗ adjusted p <0.01, ∗∗∗ adjusted p <0.005.(B) As in A, but analysis includes only first available samples per patient.(C) As in A, but for circulating chemokines.(D) As in C, but analysis includes only first available samples per patient.(E) Heatmaps showing Spearman correlation between cytokines and chemokines for mild, moderate, and severe groups separately. The average value over all available measurements for each patient was used in the calculation of correlations.(F) Plots of IFNγ against CCL20 levels in mild (green), moderate (blue), and severe (magenta) patients. Correlation coefficients (c.c.) are shown above each scatter plot.
Fig 2: Integration of miRNA, and cytokine and chemokine signatures(A) Score plots for the first two latent variables from PLSR obtained using cytokine and chemokine data together with DE miRNA measurements. The plot on the left was obtained using all three severity levels (mild, moderate, and severe), whereas that on the right was obtained using only two classes (severe and mild/moderate).(B) Results from PLSR with patients considered in two groups for different datasets with continuous output values assigned to the nearest discrete class number. Accuracies shown were obtained using leave-one-patient-out cross validation, using only cytokine and chemokine (CC) values, all miRNA values, only DE miRNAs values, or combining all CC values with DE miRNAs.(C) Example scatterplots showing strong, severity group-specific correlations in mild (green), moderate (blue), or severe (magenta) patients.(D) Number of miRNAs (Y axis) in the top 5 strongest correlations with 1, 2, 3, 4, 5, 6, or over 6 cytokines/chemokines per severity group. See Table S4(E) Spearman correlation coefficients for top 5 correlated miRNAs with IL6 and CCL20 in mild (green), moderate (blue), and severe (magenta) groups.(F) As in E, but for CCL17, CXCL10, and CCL5.(G) Canonical correlation analysis (CCA) to relate the miRNAs associated with cell death in the severe group (Figure 1E) with cytokines and chemokines. Cytokines/chemokines with individual absolute correlation greater than 0.4 (for the severe group) with any of these miRNAs were included in the analysis. The canonical scores plot shows data (from individual samples) for the12 patients used to determine the canonical covariates (c.c. = 0.8, p = 4.8 × 10−6) in black. The coefficients obtained are shown in the table and are used to obtain the canonical scores for 5 randomly chosen patients reserved as an independent test set (plotted in red).
Fig 3: miRNA/CC correlates of fatal COVID-19 identified in a leftover blood sample cohort(A) Violin plots of measured cytokines in mild (green), moderate (blue), and severe (magenta) samples, in the leftover blood sample cohort. Stars indicate significance for the comparison of severe against mild and moderate as follows: ∗ adjusted p <0.05, ∗∗ adjusted p <0.01, ∗∗∗ adjusted p <0.005.(B) As in A, but for chemokine levels.(C) As in A, but for miRNA levels.(D) Violin plots of measured cytokines in samples from discharged (white) and deceased (gray) patients, in the leftover blood sample cohort. Stars indicate significance for the comparison of severe against mild and moderate as follows: ∗ adjusted p <0.05, ∗∗ adjusted p <0.01, ∗∗∗ adjusted p <0.005.(E) As in D, but for chemokine levels.(F) As in D, but for miRNA levels.(G) Results of forward regression models including accuracy for deceased and discharged patients, residual deviance, and AIC. Results are shown for the CCL20-only model, the CCL20/IL6/IL10/miR-451a model, and the 3 miRNAs/11 CC models (see Table S11).(H) Balloon plots for the parameters included in the 3 miRNAs/11 CC model. The size of each dot reflects the number of patients in the deceased or discharged group with high (left panel), or low (right panel) levels of the shown CCs and miRNAs. Gray blocks indicate the proportion of the total counts (high or low) each variable accounts for. See STAR methods for definition of high and low values.
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