Proteome-wide analysis of a malaria vaccine study reveals personalized humoral immune profiles in Tanzanian adults
- Swiss Tropical and Public Health Institute, Switzerland
- University of Basel, Switzerland
- Antigen Discovery Inc, United States
- Sanaria, United States
- Ifakara Health Institute, United Republic of Tanzania
Figures
Figure 1
Sampling and volunteer information for proteome microarray studies.
Three arms of a randomized, double-blind Phase 1 trial of PfSPZ Vaccine were selected for antibody profiling on Pf whole proteome microarrays: normal saline controls, a lower dose (group 2, 1.35 × …
Figure 2
Antibody immune profile of Tanzanian healthy male adult volunteers is personalized.
The heatmap of the normalized signal intensities of each sample per subject is shown in (a), with the signal intensity of each protein or fragment (rows) displayed for the samples before and after …
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Figure 2—source data 1
Data frame of the normalized signal intensities of the protein microarray.
This table includes log2 signal intensities of each of the 7’455 protein spots for all samples. Serum draw, immunization dose, protection after CHMI, and description of each protein fragment are specified.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig2-data1-v2.xlsx
Figure 3
Breadth of Pf-specific humoral immunity upon PfSPZ vaccination.
Breadth of Pf-specific antibody responses per volunteer (a) before and (b) after PfSPZ vaccination, stratified according to intervention and ordered according to their respective number of …
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Figure 3—source data 1
Breadth of Pf-specific humoral immunity in each sample.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig3-data1-v2.csv
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Figure 3—source data 2
Summary statitistics on breadth per group and protection level.
An estimated effect of immunization on breadth and corresponding p-value performing the inverted beta-binomial test for paired count data using sample at basdeline and after immunization are shown in A, together with the mean and median breadth for each group at baseline and after immunization, and for the protected and unprotected group. (B) indicates the estimated regression coefficient and corresponding p values of the negative binomial regression to test differences in breadth between two groups at either baseline or after immunization.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig3-data2-v2.xlsx
Figure 4 with 3 supplements
Increase in antigen recognition from baseline to after PfSPZ vaccination is moderate.
The three volcano plots in the upper row show (a) the mean fold change in the control group (n = 8), (b) in group 2 (1.35 × 105 PfSPZ Vaccine/dose) (n = 18), and (c) in group 3 (2.7 × 105 PfSPZ …
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Figure 4—source data 1
Source data for plot a.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-data1-v2.csv
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Figure 4—source data 2
Source data for plot b.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-data2-v2.csv
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Figure 4—source data 3
Source data for plot c.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-data3-v2.csv
Figure 4—figure supplement 1
Effect size for the increase in antigen recognition from baseline to after PfSPZ vaccination.
Upper row: The three volcano plots in the upper row show (a) the mean fold change in the control group (n = 8), (b) in group 2 (n = 18), and (c) in group 3 (n = 20). In all groups, the samples …
Figure 4—figure supplement 2
Differential antigen reactivity between control and immunization groups is moderate.
The three volcano plots illustrate (a) the mean fold change of the differential antigen reactivity before and 2 weeks after immunization between controls (n = 8) and group 2 (n = 18), (b) between …
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Figure 4—figure supplement 2—source data 1
Source data for plot a.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-figsupp2-data1-v2.csv
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Figure 4—figure supplement 2—source data 2
Source data for plot b.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-figsupp2-data2-v2.csv
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Figure 4—figure supplement 2—source data 3
Source data for plot c.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig4-figsupp2-data3-v2.csv
Figure 4—figure supplement 3
Variance and mean of the log2 signal intensities.
Mean (x-axis) and variance (y-axis) of the normalized log2 signal intensities of each of the 2804 reactive antigens across (a) all samples at baseline (n = 46), (b) samples 2 weeks after …
Figure 5 with 3 supplements
The five volunteers protected against homologous CHMI showed higher recognition of four distinct proteins after immunization.
The mean fold change between antigen reactivity in the protected (n = 5) and the non-protected (n = 33) individuals from groups 2 and 3 are represented in volcano plots (a) for baseline and (b) …
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Figure 5—source data 1
Source data for plot a.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig5-data1-v2.csv
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Figure 5—source data 2
Source data for plot b.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig5-data2-v2.csv
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Figure 5—source data 3
Source data for plot c.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig5-data3-v2.csv
Figure 5—figure supplement 1
The increased recognition of four distinct proteins in the protected group show small effect size.
The volcano plot in (a) shows the mean fold change in the protected group (n = 5) compared to the unprotected group (n = 33) two weeks past last vaccination were compared. The dashed line represents …
Figure 5—figure supplement 2
No antigens show a significant differential antigen reactivity between the protected and unprotected group.
The volcano plot shows the mean fold change of the differential antigen reactivity before and 2 weeks after immunization between the protected group (n = 5) and unprotected group (n = 33). The …
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Figure 5—figure supplement 2—source data 1
Source data for plot.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig5-figsupp2-data1-v2.csv
Figure 5—figure supplement 3
Multiple sequence alignment of four PfEMP1 protein fragments.
PfEMP1 sequence named NF54_SpzPfEMP1 or PF3D7_0809100 (Zanghì et al., 2018) is compared to the sequences of the three PfEMP1 protein fragments found to be associated with protection in this study …
Figure 6
Breadth and magnitude of Pf-specific humoral immunity in protected and unprotected individuals.
(a) Breadth counts of all PfSPZ vaccinees grouped by protection status following CHMI, with protected group in green and non-protected volunteers depicted in white, before and after immunization. …
Figure 7 with 1 supplement
Protected individuals showed higher numbers of reactive antigens compared to the non protected group.
The number of antigens that were reactive in at least 80% of the individual in each group are represented for (a) baseline for the protected group (green, n = 5) and the unprotected group (grey, n = …
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Figure 7—source data 1
Table of commonly recognized antigens .
List of the antigens that increased in reactivity following immunization, or that were reactive after immunization in at least 50% (highlighted in blue) of a given group are listed, including the ID, gene ID, Description, and the number of volunteers for which the antigen was reactive or had increased reactivity following immunization.
- https://cdn.elifesciences.org/articles/53080/elife-53080-fig7-data1-v2.xlsx
Figure 7—figure supplement 1
The number of commonly recognized antigens, per threshold.
The number of antigens that were reactive in at least 60% (upper row), 80% (middle row), and 100% (lower row) of the individual in each group are represented for (a) baseline for the protected group …
Tables
Table 1
Intracellular proteins are the most abundant reactive proteins.
The frequencies of reactive antigens allocated into the different subcellular localization categories (rows) for each group (columns), tested using 2-propotions Z-test and p-values adjusted using …
| Subcellular localization | N reactive proteins | Baseline reactivity | Post-Immz reactivity | Baseline reactivity (protected) | Post-Immz reactivity (protected) | Baseline reactivity (unprotected) | Post-Immz reactivity (unprotected) | |
|---|---|---|---|---|---|---|---|---|
| Extracellular | 53 | 3 (6%) | 3 (6%) | 10 (19%) | 12 (23%) | 3 (6%) | 3 (6%) | |
| Cell membrane | 208 | 11 (5%) | 8 (4%) | 63 (30%) | 70 (34%) | 10 (5%) | 5 (2%) | |
| Intracellular (N = 1978) | Cytoplasm | 661 | 14 (2%) | 16 (2%) | 73 (11%) | 79 (12%) | 12 (2%) | 14 (2%) |
| Endoplasmic reticulum | 429 | 12 (3%) | 11 (3%) | 53 (12%) | 60 (14%) | 11 (3%) | 10 (2%) | |
| Golgi apparatus | 76 | 2 (3%) | 2 (3%) | 13 (17%) | 15 (20%) | 2 (3%) | 2 (3%) | |
| Lysosome/Vacuole | 32 | 1 (3%) | 1 (3%) | 3 (9%) | 2 (6%) | 1 (3%) | 1 (3%) | |
| Mitochondrion | 150 | 3 (2%) | 3 (2%) | 11 (7%) | 14 (9%) | 3 (2%) | 3 (2%) | |
| Nucleus | 624 | 24 (4%) | 20 (3%) | 107 (17%) | 115 (18%) | 17 (3%) | 18 (3%) | |
| Peroxisome | 3 | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | |
| Plastid | 3 | 2 (67%) | 2 (67%) | 2 (67%) | 2 (67%) | 2 (67%) | 2 (67%) | |
| Total | 2239 | 72 (3%) | 66 (3%) | 335 (15%) | 369 (16%) | 61 (3%) | 58 (3%) |
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Table 1—source data 1
The full list of reactive antigens and DeepLoc subcellular localization predictions.
- https://cdn.elifesciences.org/articles/53080/elife-53080-table1-data1-v2.xlsx
Additional files
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Source data 1
Gene Ontology prediction for the molecular function of the Pf genes.
- https://cdn.elifesciences.org/articles/53080/elife-53080-data1-v2.csv
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Source data 2
Gene Ontology prediction for the cellular component of the Pf genes.
- https://cdn.elifesciences.org/articles/53080/elife-53080-data2-v2.csv
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Source data 3
Gene Ontology prediction for the biological process of the Pf genes.
- https://cdn.elifesciences.org/articles/53080/elife-53080-data3-v2.csv
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Source data 4
Pfam database for the prediction of protein families.
- https://cdn.elifesciences.org/articles/53080/elife-53080-data4-v2.csv
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Supplementary file 1
Gene and protein families present in the protected versus non protected groups.
This table lists Pfam protein family prediction (El-Gebali et al., 2019), and gene ontology prediction available on Plasmodb.org (Huntley et al., 2015) and identified protein characteristics and distinct functional categories which were identified as being reactive in at least 80% of the protected or non protected group before and after immunization. Reactive proteins were associated to each group using the Fisher’s exact test, and p value correct using the Benjamini-Hochberg method (BH) (Benjamini and Hochberg, 1995). Pfam and GO description were found in https://www.ebi.ac.uk/QuickGO/ and https://biocyc.org/ and https://www.ebi.ac.uk/QuickGO/ and https://biocyc.org/, respectively. See also Source datas 1–4.
- https://cdn.elifesciences.org/articles/53080/elife-53080-supp1-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/53080/elife-53080-transrepform-v2.docx
