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Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response.

Matsumiya M, Harris SA, Satti I, Stockdale L, Tanner R, O'Shea MK, Tameris M, Mahomed H, Hatherill M, Scriba TJ, Hanekom WA, McShane H, Fletcher HA - BMC Infect. Dis. (2014)

Bottom Line: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples.Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination.The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, UK. magali.matsumiya@ndm.ox.ac.uk.

ABSTRACT

Background: Tuberculosis (TB) remains a global health problem, with vaccination likely to be a necessary part of a successful control strategy. Results of the first Phase 2b efficacy trial of a candidate vaccine, MVA85A, evaluated in BCG-vaccinated infants were published last year. Although no improvement in efficacy above BCG alone was seen, cryopreserved samples from this trial provide an opportunity to study the immune response to vaccination in this population.

Methods: We investigated blood samples taken before vaccination (baseline) and one and 28 days post-vaccination with MVA85A or placebo (Candin). The IFN-γ ELISpot assay was performed at baseline and on day 28 to quantify the adaptive response to Ag85A peptides. Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis.

Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination. By contrast, previous work done in UK adults shows early inflammation in this population is not associated with a strong T cell response but that induction of regulatory pathways inversely correlates with the magnitude of the T cell response. This may be indicative of important mechanistic differences in how T cell responses develop in these two populations following vaccination with MVA85A.

Conclusion: The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults. Understanding differences in immune response to vaccination between populations is likely to be an important aspect of developing successful vaccines and vaccination strategies.

Trial registration: ClinicalTrials.gov number NCT00953927.

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Related in: MedlinePlus

Heatmaps of BTMs associated with a higher response to vaccination. Heatmaps show expression of genes for MVA85A-vaccinated infants in unstimulated PBMC taken pre-vaccination (a) or whole blood taken one day post-vaccination (b). The colour coding along the top of the heatmap shows responder (blue) and non-responder (black) infants as measured by IFN-γ ELISpot. Genes are arranged by module (right).
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Figure 4: Heatmaps of BTMs associated with a higher response to vaccination. Heatmaps show expression of genes for MVA85A-vaccinated infants in unstimulated PBMC taken pre-vaccination (a) or whole blood taken one day post-vaccination (b). The colour coding along the top of the heatmap shows responder (blue) and non-responder (black) infants as measured by IFN-γ ELISpot. Genes are arranged by module (right).

Mentions: The following analyses were performed using only samples from infants vaccinated with MVA85A, to further investigate the mechanisms underlying the immune response to this vaccine. The R package Significance Analysis of Microarrays (SAMR) was used to identify genes whose expression correlated with the Ag85A-specific T cell frequencies measured 28 days post-vaccination by IFN-γ ELISpot assay. SAM identifies genes significantly correlating with a continuous response variable, in this case the IFN-γ ELISpot, and outputs a positive and negative set of genes based on the strength of the correlation of each gene with higher (positive) or lower (negative) values of the response phenotype[29,35]. Since the IFN-γ ELISpot responses in this study were very low, we have subsequently defined infants as responders or non-responders. An ELISpot response was deemed positive if the average count in the positive control wells was at least twice that in the negative control wells and at least 5 spots more than the negative control wells[36]. Sets of correlating genes pre-vaccination and one day post-vaccination were generated and ranked according to their significance score (Figure 3a). This ranked list of genes was then analysed using the Broad Institute Gene Set Enrichment Analysis PreRanked function, using the Blood Transcription Modules defined by Li et al. as a reference gene set[33]. Pre-vaccination, responder infants have an over-representation of genes enriched in monocytes, activated dendritic cells and neutrophils as well chemokines and inflammatory pathways (Figure 3b). One day post-vaccination, there is a negative association between lymphoid cells and the subsequent development of an ELISpot response (Figure 3c). Moreover, there is positive enrichment of gene sets associated with myeloid cells, inflammation and an antiviral response. The expression pattern of these clusters and their relationship to the ELISpot response is shown in heatmaps in Figure 4. Higher expression of genes associated myeloid cells and inflammation pre- and 1 day post-vaccination are both associated with the development of an antigen-specific T cell response to vaccination with MVA85A, suggesting the ability of MVA to induce a strong innate response is key to its function as a vaccine vector in this population. Additionally, higher expression of genes associated with activation of lymphoid cells such as NK cells and cytotoxic T cells one day post-vaccination is associated with an absent ELISpot response 28 days later.


Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response.

Matsumiya M, Harris SA, Satti I, Stockdale L, Tanner R, O'Shea MK, Tameris M, Mahomed H, Hatherill M, Scriba TJ, Hanekom WA, McShane H, Fletcher HA - BMC Infect. Dis. (2014)

Heatmaps of BTMs associated with a higher response to vaccination. Heatmaps show expression of genes for MVA85A-vaccinated infants in unstimulated PBMC taken pre-vaccination (a) or whole blood taken one day post-vaccination (b). The colour coding along the top of the heatmap shows responder (blue) and non-responder (black) infants as measured by IFN-γ ELISpot. Genes are arranged by module (right).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4061512&req=5

Figure 4: Heatmaps of BTMs associated with a higher response to vaccination. Heatmaps show expression of genes for MVA85A-vaccinated infants in unstimulated PBMC taken pre-vaccination (a) or whole blood taken one day post-vaccination (b). The colour coding along the top of the heatmap shows responder (blue) and non-responder (black) infants as measured by IFN-γ ELISpot. Genes are arranged by module (right).
Mentions: The following analyses were performed using only samples from infants vaccinated with MVA85A, to further investigate the mechanisms underlying the immune response to this vaccine. The R package Significance Analysis of Microarrays (SAMR) was used to identify genes whose expression correlated with the Ag85A-specific T cell frequencies measured 28 days post-vaccination by IFN-γ ELISpot assay. SAM identifies genes significantly correlating with a continuous response variable, in this case the IFN-γ ELISpot, and outputs a positive and negative set of genes based on the strength of the correlation of each gene with higher (positive) or lower (negative) values of the response phenotype[29,35]. Since the IFN-γ ELISpot responses in this study were very low, we have subsequently defined infants as responders or non-responders. An ELISpot response was deemed positive if the average count in the positive control wells was at least twice that in the negative control wells and at least 5 spots more than the negative control wells[36]. Sets of correlating genes pre-vaccination and one day post-vaccination were generated and ranked according to their significance score (Figure 3a). This ranked list of genes was then analysed using the Broad Institute Gene Set Enrichment Analysis PreRanked function, using the Blood Transcription Modules defined by Li et al. as a reference gene set[33]. Pre-vaccination, responder infants have an over-representation of genes enriched in monocytes, activated dendritic cells and neutrophils as well chemokines and inflammatory pathways (Figure 3b). One day post-vaccination, there is a negative association between lymphoid cells and the subsequent development of an ELISpot response (Figure 3c). Moreover, there is positive enrichment of gene sets associated with myeloid cells, inflammation and an antiviral response. The expression pattern of these clusters and their relationship to the ELISpot response is shown in heatmaps in Figure 4. Higher expression of genes associated myeloid cells and inflammation pre- and 1 day post-vaccination are both associated with the development of an antigen-specific T cell response to vaccination with MVA85A, suggesting the ability of MVA to induce a strong innate response is key to its function as a vaccine vector in this population. Additionally, higher expression of genes associated with activation of lymphoid cells such as NK cells and cytotoxic T cells one day post-vaccination is associated with an absent ELISpot response 28 days later.

Bottom Line: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples.Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination.The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, UK. magali.matsumiya@ndm.ox.ac.uk.

ABSTRACT

Background: Tuberculosis (TB) remains a global health problem, with vaccination likely to be a necessary part of a successful control strategy. Results of the first Phase 2b efficacy trial of a candidate vaccine, MVA85A, evaluated in BCG-vaccinated infants were published last year. Although no improvement in efficacy above BCG alone was seen, cryopreserved samples from this trial provide an opportunity to study the immune response to vaccination in this population.

Methods: We investigated blood samples taken before vaccination (baseline) and one and 28 days post-vaccination with MVA85A or placebo (Candin). The IFN-γ ELISpot assay was performed at baseline and on day 28 to quantify the adaptive response to Ag85A peptides. Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis.

Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination. By contrast, previous work done in UK adults shows early inflammation in this population is not associated with a strong T cell response but that induction of regulatory pathways inversely correlates with the magnitude of the T cell response. This may be indicative of important mechanistic differences in how T cell responses develop in these two populations following vaccination with MVA85A.

Conclusion: The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults. Understanding differences in immune response to vaccination between populations is likely to be an important aspect of developing successful vaccines and vaccination strategies.

Trial registration: ClinicalTrials.gov number NCT00953927.

Show MeSH
Related in: MedlinePlus