Early Transcriptional Responses After Dengue Vaccination Mirror the Response to Natural Infection and Predict Neutralizing Antibody Titers

Abstract

Background: Several promising live attenuated dengue vaccines are in development, but information about innate immune responses and early correlates of protection is lacking.

Methods: We characterized human genome-wide transcripts in whole blood from 10 volunteers at 11 time points after immunization with the dengue virus type 3 (DENV-3) component of the National Institutes of Health dengue vaccine candidate TV003 and from 30 hospitalized children with acute primary DENV-3 infection. We compared day-specific gene expression patterns with subsequent neutralizing antibody (NAb) titers.

Results: The transcriptional response to vaccination was largely confined to days 5-20 and was dominated by an interferon-associated signature and a cell cycle signature that peaked on days 8 and 14, respectively. Changes in transcript abundance were much greater in magnitude and scope in symptomatic natural infection than following vaccination (maximum fold-change >200 vs 21 postvaccination; 3210 vs 286 transcripts with significant fold-change), but shared gene modules were induced in the same sequence. The abundances of 131 transcripts on days 8 and 9 postvaccination were strongly correlated with NAb titers measured 6 weeks postvaccination.

Conclusions: Live attenuated dengue vaccination elicits early transcriptional responses that mirror those found in symptomatic natural infection and provide candidate early markers of protection against DENV infection.

Clinical trials registration: NCT00831012.

Figures

Figure 1.

Significant differences in transcript abundance postvaccination (false discovery rate

Figure 2.

Changes in transcript abundances over time in vaccinees. A, Hierarchical clustering of the 286 transcripts whose abundance was significantly different from baseline on >1 day. Lines and numbers to the right of the heat map mark sets of coexpressed genes (average cluster, r > 0.5). B, Change over time in abundance for each transcript in each gene cluster. Heavy line indicates median expression of all genes in each cluster. C, Gene ontologies associated with gene clusters described in (A) and (B). There were no significant gene ontologies for cluster 3.

Figure 3.

Comparison of postvaccination and postinfection transcript abundance changes. A, Transcripts with significant changes on day 2, 3, 4, or 5 of fever in patients with primary dengue virus type 3 infection (blue circle) and on any day postvaccination (green circle). Numbers indicate transcripts unique to vaccination, infection, or shared (overlap, n = 246). B, Maximum fold-change in transcript abundance following vaccination (red circles) or during infection (blue diamonds). C, Maximum fold-change in abundance for transcripts with significant changes postvaccination or during infection. Dotted diagonal line at equal fold-change included for reference.

Figure 4.

Gene modules affected by dengue virus vaccination and natural infection. A, Blood transcript modules with transcripts that were significantly up- or down-regulated on at least 1 day (false discovery rate <1%) were hierarchically clustered. Vertical lines on right denote module clusters described in the text. B, Hierarchical clustering of each day postvaccination or postinfection using the normalized enrichment score from (A). Days in bold italics represent days of fever for infected patients; days preceded by “v” represent days postvaccination. Abbreviations: Ag, antigen; IFN, interferon; NES, normalized enrichment score.

Figure 5.

Correlation of transcript abundance and the 60% plaque reduction neutralization titer (PRNT60) at day 42 among vaccine recipients. A, Average fold-change in abundance by day for all transcripts with significant differences from baseline postvaccination. Transcripts are ordered and clusters labeled as in Figure 2. Asterisk marks IFI44. B, Spearman correlation of each transcript and day 42 PRNT60 using a moving average of window size 9. Solid lines indicate days postvaccination on which a significant correlation was identified (P < .01, indicated by vertical dotted gray line).

Figure 6.

Gene modules correlated with subsequent neutralizing antibody response. A, Blood transcript modules that were significantly enriched for transcripts positively correlated with 60% plaque reduction neutralization titer at day 42 (vaccinees) or 50% neutralization titer at convalescence (patients) on at least 1 day (false discovery rate <1%) were hierarchically clustered. Vertical lines delineate module clusters described in the text. B, Significant modules (false discovery rate <1%) are marked in red. Modules and samples are organized as in (A). C, Hierarchical clustering of gene module expression from each day postvaccination or postinfection using the normalized enrichment score from (A). Day labels in bold italics represent fever day for infected patients; day labels preceded by “v” represent days postvaccination. Abbreviations: NES, normalized enrichment score; NK, natural killer.