Transcriptional profiling technology for studying vaccine responses: An untapped goldmine

•We still do not understand how vaccines work to induce protective immunity.•Several high throughput methods can analyse the whole human transcription profile.•Transcription profiling has been used to predict vaccine immunogenicity and efficacy.•‘Systems vaccinology’ is the application of systems biology to study vaccines.•‘Systems vaccinology’ is poised to provide major advances in vaccine research.

There is much that we do not understand about the immune mechanisms whereby vaccines exert their specific and non-specific effects. Most studies take the reductionist approach of examining vaccine responses at the humoral or cellular level. Whole human transcriptional profiling is becoming more accessible, and provides a picture of the entire immune response to vaccination in a single ‘snapshot’. The potential uses of such information are enormous, and the data mining tools are becoming more sophisticated to handle the complex data generated. We now face the exciting prospect of gaining in depth knowledge as to exactly what vaccines do to the immune system as a whole, and identifying molecular signatures and biomarkers that can predict immediate and long term outcomes of vaccination. The challenge now is to carry out the studies and generate the much needed data.