Table 1.
Overall HSCT cohort characteristics.
Fig 1.
A. Study Design. B. SARS-CoV-2 Spike antibody titers were assessed using the Roche Elecsys anti-SARS-CoV-2 Spike immunoassay pre-vaccination and after each subsequent dose.
C. Proportion of patients in each cohort who achieved a good, poor, and no antibody response. Mann-Whitney test continuous variables with Bonferroni correction for multiple comparisons were performed, with two-sided p-values ≤ 0.05 considered statistically significant with p ≤ 0.01 = ** and p ≤ 0.0001 = ****. D. Flow Cytometry analysis was performed on PBMCs taken pre-vaccination and following 2nd vaccine dose (5 controls, 4 autoSCTs and 16 alloSCTs). Percent of spike reactive CD4 cells pre and post dose 2 of the vaccine over vehicle stimulated cells by markers TNFα and CD154. E. Same as D, except for CD8 cells and markers IFNγ and TNFα. F. Proportion of patients in each cohort who achieved a spike-specific T cell response. Wilcoxon signed-rank tests were performed, with a p-values ≤ 0.05 considered statistically significant.
Fig 2.
Forest Plots demonstrating clinical variables of interest and their odds ratios of developing a positive T cell response (panel A) or a good (>210 AU/mL) antibody titer (panel C) among allogeneic stem cell recipients.
Gehan-Breslow-Wilcoxon tests were performed to test if having a SARS-CoV-2 specific T cell (panel B) or a significant antibody (panel D) response resulted in a difference in probability of COVID infection and mortality. IS stands for immunosuppression.
Fig 3.
A. CYTOF results showing cell types presented as percentage of lymphocytes separated by transplant type.
B. Clinical pre-vaccination immunodeficiency flow panel results separated based on antibody response of allogeneic patients. C. Clinical pre-vaccination immunodeficiency flow panel results separated based on SARS-CoV-2 specific T cell stimulation assay response in allogeneic patients. D. Clinical pre-vaccination immunodeficiency flow panel results separated based on cGVHD in allogeneic patients. Mann-Whitney test for continuous variables were performed, with two-sided p-values ≤ 0.05 considered statistically significant. Reference ranges for the variables that have them are indicated by the dotted lines.
Fig 4.
Single cell RNA sequencing of patient samples and TCR clonotype analysis.
A. Seurat clustering annotated by reference annotation “MonacoImmuneData”, subpanels on the right (top) cells in teal are positive for having a T cell clonotype, and cells colored in red do not have a T cell clonotype attributed from the T cell sequencing, (bottom) same as top, except for B cell clonotypes. Cells with high mitochondrial reads or low or extremely high RNA counts were filtered out. B. Data was filtered to include only T cell clusters and excluded two post-COVID-19 infection samples. UMAP projection of the T cells re-clustered and re-annotated as before with markers CD4, and CD8. C. Cells from the UMAP projection in D were split by T cell response and colored by cluster annotation. D. Quantitation of C, where the percentage of each individual’s cells in each cluster was calculated (Healthy n = 3, Good n = 2, Poor n = 2) and plotted on a bar graph. E. TCR repertoire diversity using the Chao1 estimator, the calculated value is plotted as a bar graph displaying the calculated 95% confidence interval. Healthy donors are colored in purple, good responders are in pink and poor responders are in orange and in D. F. A bar graph displaying the number of unique clonotypes in each sample sequenced, colored as in D and E. G. Summary proportion of clonotypes with specific frequencies by sample. The sample labels follow the color scheme from E. H. Top clonotypes found to be unique to post vaccination when compared to pre vaccination for each individual were mapped back to the cells in the T cell UMAP both in aggregate (left) and the UMAP with cells divided by T cell response in the antigen specific T cell assay cohort (right).