Gene expression profiling as a tool to evaluate immune responses

The human immune system is a very complex defense mechanism, consisting of different levels of interacting cells and molecules, to keep out and eliminate pathogens and foreign particles. The immune system can be divided into three main categories: 1) the physical barriers, 2) the innate immune system that creates immediately non-pathogen-specific immune responses, and 3) the adaptive immune system that can activate pathogen-specific immune responses, admittedly after recognition of the pathogenic antigen, differentiation processes and clonal expansion. The adaptive immune system can further be subdivided in the cell-mediated immunity (T-lymphocytes) and the humoral immunity (B-lymphocytes). It is also the key player to build up and maintain protection against a specific pathogen for years, by producing long-lived memory cells and antibodies. A natural infection can be mimicked through vaccination: stimulation of the immune system to build up protection without carrying over the disease itself. To study the activity of immune cells present in blood and monitor the overall immune responses, we use differential gene expression. Using RNA sequencing, we can determine a gene expression profile which contains all present mRNA transcripts and the amount of each transcript (counts), including all immune-relevant ones. By applying differential gene expression, we study the significant differences in gene expression between 2 conditions. The combination of specific down- or/and upregulated gene transcripts can indicate changes in certain pathways. To confirm the performance and efficiency of this method, three proof of concept studies were designed. In part I we determined the influence of two vaccines on the immune system of healthy volunteers: A) de novo Engerix-B vaccine dose and B) an additional Priorix vaccine dose To pinpoint differentially expressed genes, we compared each post-vaccination gene expression profile to the pre-vaccination profile at day 0. Significant alterations in gene expression levels could imply that immune-related pathways are activated by the vaccination. Determination of differentially expressed genes is also applicable in infectious diseases. For part II we applied our method to children, diagnosed with acute meningitis, caused by viruses or bacteria. Differentially expressed genes were studied by comparing the acute gene expression profiles with the profile of the corresponding control sample. Further, we looked into differences in gene expression profiles between bacterial and viral cases to create a predictive model. To conclude, gene expression profiling can be used to monitor immune responses after vaccination or even during an infection.

Jaar van publicatie:2020

Trefwoorden:Doctoral thesis

Toegankelijkheid:Open