Science Spotlight

System vaccinology, providing information for the future

From Vaccine and Infectious Disease Division

Most vaccine design is accomplished by trail and error methods, meaning make something, test it, then make modifications and repeat the process. In this manner many highly effective vaccines have been developed. However, this approach has not always yielded effective vaccines. HIV is an example where trial and error has yet to be successful. It is important that vaccine design is not only based on empirical optimization, but also informed by past vaccines and how they protect. Not every pathogen can be neutralized by the same mechanism but this information can be used to set an immunologic goal for future vaccines to meet. This approach called systems vaccinology is defined as a multi-level understanding of the genetic network changes as well as the immune response induced by vaccination that confers protection. A systems approach was applied to the study of the yellow fever vaccine by researchers in China and at Fred Hutch (Vaccine and Infectious Disease Division) that was recently published in the Journal of Immunology. The yellow fever vaccine (YF-17D) was selected as the vaccine of choice due to the fact that is has been administered for over 75 years in 600 million plus people globally. The vaccine has broad innate and adaptive protective immunity after a single dose and elicits neutralizing antibodies that can last up to 30 years. Hence, YF-17D is a great candidate for the study of protective immunity induced by vaccination and sets a high bar for new vaccines to attain. The goal of this study was to further characterize the YF-17D immune response in order to better understand the molecular and immune mechanisms responsible for the strong long-lived immunity after vaccination.

For the study, 21 sero-negative (meaning never exposed to the virus) participants were selected. Blood was collected before vaccination, 4 hours after a single dose of YF-17D and on days 1, 2, 3, 5, 7, 14, 28, 84, and 168 post vaccination (see figure). Immune cells were isolated and transcriptomes (genome-wide mRNA expression profiles) were. This assay yielded identification of 1001 differentially expressed genes (DEG) which were then compared across the time points looking at transcript kinetics. Results suggested that changes started as early as 4 hours post vaccination and peaked at days 2 and 5 then returned to baseline by day 28. To identify gene networks changed during vaccination the human protein reference database was used. Proteins important for connecting networks and for organizing network pathways were identified and further investigated. Of these there were genes in the transcription factor family, cell cycle proteins, and chemokine/ cytokine genes. Results suggested that YF-17D induced persistent gene regulation and activation for the first month after injection and that this pattern varied with time. Bioinformatic analysis was performed to identify significantly activated or inhibited pathways. Interesting pathways tended to stay either activated or inactivated throughout the study. Some pathways that were upregulated after vaccination were involved in functions such as cellular differentiation, development, antiviral sensors (like RIG-I) and the interferon signaling. Taking a step back, pathways activated early were associated with innate immune responses (RIG-I, IFN, etc), and ones activated later were related to cell division and B cell markers associated with humoral immunity.

Graphical representation of the experimental layout. Blue shading represents aspects of the approach that are expanded and new from previous studies. Image provided by Lindsay Carpp

In addition to the transcriptome analysis cells were stained for cell-type identification and functional analysis. In general, monocytes and natural killer (NK) cells decreased after vaccination and dendritic cells fluctuated throughout the time points. Even though NK cells decreased, the ones remaining still possessed functional capacity. B cells increased after day 14 and lasted for 3 months with memory phenotypes identified.  In contrast, T cells showed decreases in activated cells. However, T cells specific for virus were found and showed signs of activation and function. To further investigate the responses established, the vaccine participants were tested for sero-positivity to other viruses from the same family (Flavivirus). This was done because cross-reactivity between different viruses in this family has been seen before. In this study they found 6 of the 21 participants were sero-positive for another flavivirus (i.e. Dengue virus) and that the innate response did not differ between either group. However, functional NK and T cell responses were primed in sero-positive participants creating a boost like effect. When asked about the importance of pre-screening for cross-reactivity researcher Lindsay Carpp said, “To the extent possible, pre-existing flavivirus serostatus should be considered in the development of vaccines against flaviviruses and when interpreting data from vaccine clinical trials. Vaccines that are appropriate for deployment in one geographical area may not be appropriate in others, based on baseline levels of exposure to various flaviviruses. Epidemiological data and knowledge of flavivirus exposure history of a target population are very valuable in this context.”

In conclusion, this study used a systems approach to follow the immune response after yellow fever vaccination starting as early as 4 hours after vaccination and continuing out to 3 months. The approach found that vaccination induced a broad immunological response with a strong adaptive immune response and that pre-exposure to other flaviviruses can complicate the immune response.

Funding for this study was provided by the National Natural Science Foundation of China and the National Major Projects for Infectious Diseases Control and Prevention.


Hou J, Wang S, Jia M, Li D, Liu Y, Li Z,Zhu H, Xu H, Sun M, Lu L, Zhou Z, Peng H, Zhang Q, Fu S, Liang G, Yao L, Yu X, Carpp LN, Huang Y, McElrath J, Self S, Shao Y. 2017. A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine. J Immunol.