Identification of potential biomarkers of vaccine inflammation in mice

  1. Paul F McKay  Is a corresponding author
  2. Deniz Cizmeci
  3. Yoann Aldon
  4. Jeroen Maertzdorf
  5. January Weiner
  6. Stefan HE Kaufmann
  7. David JM Lewis
  8. Robert A van den Berg
  9. Giuseppe Del Giudice
  10. Robin J Shattock  Is a corresponding author
  1. Imperial College London, United Kingdom
  2. Max Planck Institute for Infection Biology, Germany
  3. Imperial College Healthcare NHS Trust, Hammersmith Hospital, United Kingdom
  4. GSK, United States
  5. GSK, Italy
6 figures, 2 tables and 1 additional file

Figures

Overview of the transcriptomic responses to the injected vaccines and TLR agonists in the injected muscle, the draining lymph nodes (MLN), and the blood.

The width of each violin is scaled to the number of genes that are differentially expressed at each given time point (BH-adjusted p-value <0.01). Differentially expressed genes were defined as those …

https://doi.org/10.7554/eLife.46149.004
Figure 2 with 3 supplements
Gene-set enrichment analysis reveals distinct mechanisms of transcriptional response to the injected vaccines and TLR agonists.

Tissue data sets are presented as three coloured segments along the perimeter for the injected muscle (purple), the draining lymph nodes (green), and the blood compartment (red). An ordered list of …

https://doi.org/10.7554/eLife.46149.005
Figure 2—figure supplement 1
Gene-set enrichment analysis in the muscle data set.

Enrichment scores were calculated for blood transcriptional modules defined by Li et al. (2014) using R package tmod (version 0.34) (US National Library of Medicine, 2004). The modules (in rows) are …

https://doi.org/10.7554/eLife.46149.006
Figure 2—figure supplement 2
Gene-set enrichment analysis in the draining lymph nodes data set.

Enrichment scores were calculated for blood transcriptional modules defined by Li et al. (2014) using R package tmod (version 0.34) (US National Library of Medicine, 2004). The modules (in rows) are …

https://doi.org/10.7554/eLife.46149.007
Figure 2—figure supplement 3
Gene-set enrichment analysis in blood data set.

Enrichment scores were calculated for blood transcriptional modules defined by Li et al. (2014) using R package tmod (version 0.34) (US National Library of Medicine, 2004). The modules (in rows) are …

https://doi.org/10.7554/eLife.46149.008
Figure 3 with 1 supplement
Heatmap representing the transcript overlap between WGCNA modules and the reference modules.

Reference modules are the blood transcriptional modules defined by Li et al. (2014). These modules are shown in rows and are annotated within a higher functional group. Only WGCNA modules that …

https://doi.org/10.7554/eLife.46149.009
Figure 3—figure supplement 1
Weighted gene co-expression network analysis of module–trait relationships.

Modules extracted by co-expression analyses in the injected muscle (A), draining lymph nodes (B), and blood (C) datasets are in rows labelled with a colour for each treatment and an identificaton …

https://doi.org/10.7554/eLife.46149.010
Circular map representing the differentially expressed genes and reporting the observed correlations between each tissue.

The three tissues analysed are organised as in Figure 2 and are indicated on the outer part of the circular map. Each outer tile has a different colour to denote which injection they received: Fluad …

https://doi.org/10.7554/eLife.46149.011
Figure 5 with 1 supplement
Serum chemokine and cytokine expression.

Serum chemokines and cytokines were measured using a Luminex bead 9-plex assay, and serum amyloid A3 was measured by quantitative ELISA. (A) Each panel shows the longitudinal expression of an individ…

https://doi.org/10.7554/eLife.46149.012
Figure 5—figure supplement 1
Comparison of gene expression levels measured by microarray and protein levels of chemokines and cytokines measured by Luminex bead 9-plex assay and quantitative ELISA.

Differential expression of transcripts and proteins induced by the LPS immunisation are shown. Each panel shows the fold changes (transcripts – green line; proteins – orange line) of individual …

https://doi.org/10.7554/eLife.46149.013
Comparison of gene expression levels measured by microarray with the protein levels of chemokines and cytokines measured by Luminex bead 9-plex assay and quantitative ELISA.

The correlations between fold changes in transcript and protein levels are presented in this heatmap. All measured chemokine and cytokines are in rows (left axis legend). Columns represent different …

https://doi.org/10.7554/eLife.46149.014

Tables

Table 1
Vaccines and inflammatory agents.

The vaccines, TLR agonists, adjuvant and saline used in the present study are detailed. Vaccines were administered by injection of 1/10th the human dose in a 50 µL volume. TLR agonists, IFA and …

https://doi.org/10.7554/eLife.46149.003
Vaccine/TLRComponentsAbbreviationManufacturer
Pentavac SDDiphtheria, tetanus, pertussis (whole cell), hepatitis B (rDNA) and haemophilus type b conjugate vaccinePentavacSerum Institute India
AgrippalTrivalent flu subunits – H3N2, H1N1 and influenza BTri-FluSeqirus
FluadTrivalent flu subunits – H3N2, H1N1 and influenza B + MF59Tri-Flu + MF59Seqirus
Engerix BRecombinant hepatitis B sAg absorbed on alumGlaxoSmithKline
IFAMontanide ISA 51 VGSeppic
LPSLPS-EB UltrapureInvivogen
Poly I:CPolyinosinic:polycytidylic acidSigma
Key resources table
Reagent type
(species) or resource
DesignationSource or
reference
IdentifiersAdditional information
Strain, strain
background)
M. musculus, Female)
CB6F1/Crl;
Strain Code 176
Charles River
Commercial
assay or kit
RNAprotect
animal blood
tubes
QiagenCat number: 76544
Commercial
assay or kit
miRNeasy mini
kit
QiagenCat number: 217004
Commercial
assay or kit
QIAzol lysis
reagent
QiagenCat number: 79306
Commercial
assay or kit
9-plex LuminexBio-TechneCat number: LXSAMS-09
Chemical
compound, drug
Pentavac SDSerum Institute
India
Chemical
compound, drug
AgrippalSeqirus
Chemical
compound, drug
FluadSeqirus
Chemical
compound, drug
Engerix BGlaxoSmithKline
Chemical
compound, drug
IFA - Montanide
ISA 51 VG
SeppicNSC#737063
Chemical
compound, drug
LPS-EB UltrapureInvivogenCat number: tlrl-3pelps
Chemical
compound, drug
Poly I:CSigmaCat number: P1530

Additional files

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