Characterisation of small RNAs in response to human vaccination and infection

Background
Heterogeneity in host responses plays a role in vaccine failure, vaccine-related adverse events and infection outcomes and undermines efforts to produce universally effective vaccines and treatments. Gene expression analyses have provided insights into the immune response, but a deeper understanding requires a broader view encompassing gene regulation.
MicroRNAs (miRNAs) are small RNAs (sRNAs) that post-transcriptionally regulate protein-coding genes. Small RNA sequencing (sRNA-seq) has revealed the presence of other small RNA molecules ~20 to 30 nucleotides long, which arise from RNAs classes, including tRNAs, small nucleolar RNAs and yRNAs. The action of these so-called sRNA-derived fragments (sRNA-dfs) is poorly understood; they may play a role in gene regulation. Their role in the immune system is not known.
Research questions:
1. Does vaccination and infection alter miRNA expression?
2. Can miRNA expression predict or shape the response to vaccination and/or infection?
3. What is the role of miRNAs in the immune response to infection/vaccination?
Methods
sRNA-seq was run on samples from three studies: an infant vaccine study involving the reactogenic 4CMenB vaccine, a randomised controlled trial of two typhoid vaccines set within a typhoid vaccine-challenge study, and a ChAdOx1 nCoV-19 vaccine study that followed participants through COVID-19 infection.
Results
This thesis found vaccination and infection strongly influence miRNAs and sRNA-df expression in plasma, whole blood and PBMCs. In total, 1846 sRNAs were DE after vaccination or infection in at least one study. These features comprised miRNAs and sRNA-dfs derived from tRNAs, snoRNAs, lncRNAs and protein-coding genes.
Associations were found between aspects of the immune response and sRNA expression. The infant vaccine study revealed an association between vaccine fever and post-vaccination expression of hsa-miR-122-5p at 4 months of age. Integration of miRNA, mRNA expression, and proteomics revealed a possible link between liver-derived miRNAs and the acute phase response to vaccination via the action of IL6 on hepatocytes. An in-vitro model supported this.
The typhoid vaccine-challenge study revealed a divergent pattern of miRNA expression 10 days after vaccination is associated with vaccine-mediated protection from typhoid, and that a hypo-responsiveness to S. Typhi challenge is associated with susceptibility to typhoid fever.
Finally, the COVID-19 study showed downregulation of miRNAs at COVID-19 onset was associated with wide-scale upregulation of pro-inflammatory genes and pathways. Amelioration of COVID-19 disease severity after ChAdOx1 nCoV-19 vaccination was reflected at the sRNA level, with less perturbation occurring compared with COVID-19 infection in unvaccinated individuals.
Conclusion
This thesis reports for the first time that vaccination and infection alter the expression of sRNA fragments derived from snoRNA, lncRNAs and protein-coding genes. This thesis opens up exciting avenues for investigating the role of miRNAs and sRNA-dfs as purveyors of the acute phase response and correlates of vaccine-mediated protection, whose dysregulation may contribute to disease pathogenesis, aspects hitherto overlooked.

Keywords: miRNA
4CMenB
immunology
COVID-19
vaccine
microRNA
epigenetics
proteomics
typhoid
cytokines
ChAdOx
Sars-Cov2
Advisor: Pollard, A
O'connor, D
Mohorianu, I