Systems vaccinology and big data in the vaccine development chain

Raeven, René H. M.; van Riet, Elly; Meiring, Hugo D.; Metz, Bernard; Kersten, Gideon F. A.

In the context of systems vaccinology, conventional assays that are neither high throughput, nor unbiased, remain necessary to confirm hypotheses. Histology is still the common method to confirm the influx and the location of immune cells in tissues as a result of an infection or immunization. However, visualization of cells in tissue sections continually improves by better immunoimaging techniques 48 such as confocal microscopy. Ex vivo, assays such as ELISA and flow cytometry are applied to identify and quantify specific cell subsets as well as their activation state and function (such as cytokine production or proliferation). These immunological techniques for studying these responses have also become more powerful. Flow cytometry equipment has improved, for example, by combining the measurement of the amount of proteins per cell (flow cytometry), with visualization of their localization within the cells (microscopy), so-called imaging flow cytometry. 49 Also, more fluorescent labels have become available, increasing the number of markers that can be investigated simultaneously. Multi-parameter flow cytometry enables the identification of these specialized, often rare, subsets of cells. 50 For example, innate cells that play a crucial role in pathogen recognition and in influencing the magnitude and direction of adaptive immunity, such as specific subtypes of antigen-presenting cells and innate lymphoid cells. With respect to adaptive immune responses, the ability to identify rare subsets mainly focuses on antigen-specific B-cells 51 and T-cells, 52 both circulating and tissue-resident cells, and precursors as well as effector and memory cells. 7, 8 Cytometry by Time-of-Flight mass spectrometry (CyTOF) 53 uses raremetal isotopes instead of fluorescent labels for labeling, thereby almost abolishing the spectral overlap seen with fluorescent dyes and expanding the number markers that can be measured simultaneously even further. For example, Van Unen et al. 54 identified 142 immune subsets in the human mucosal immune system.