Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Protein Spike-in Controls
2.3. Shared Protein Sequence Database and Protein Families
2.4. LC-MS/MS Proteomics Experiment and Data Processing
2.5. 2D-DIGE/MS Proteomics Experiment and Data Processing
2.6. Statistical Analysis
2.6.1. Normalization
- (1)
- for each sample, the median of the log2 protein signal distribution was determined.
- (2)
- the global median of all 30 sample medians calculated in (1) was obtained.
- (3)
- a sample specific scaling factor was then calculated as the difference (log2 scale) between the global median obtained in (2) and the sample-specific median obtained in (1).
- (4)
- the log2 protein signal distribution for each sample was then median normalized by adding the scaling factor (log2 scale), determined in (4).
2.6.2. Missing Value Imputation and Log Fold Change from Baseline Calculation
2.6.3. Identification of Differentially Abundant Proteins
2.6.4. Pathway Enrichment Analysis
2.6.5. Identification of Protein Responses that Best Predicted Humoral and Cellular Responses
2.7. Transcriptomics Data
3. Results
3.1. Technical Assessments and Method Comparisons
3.2. DA Proteins and Enriched Pathways
3.3. Identification of Protein Responses that Best Predicted Humoral and Cellular Responses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Protein ID | Gene Name | Protein Description | 50% Protein Cluster ID (Gene Name) | LC-MS/MSTime Point | 2D-DIGE/MS Time Point | LC/MS/MS Log2 Fold Change | 2D-DIGE Log2 Fold Change |
---|---|---|---|---|---|---|---|
P33176 | KIF5B | Kinesin-1 heavy chain | Q12840 (KIF5A) | Day 7 | Day 7 | 1.11 | 0.33 |
P33176 | KIF5B | Kinesin-1 heavy chain | Q12840 (KIF5A) | Day 7 | Day 14 | 1.11 | 0.35 |
P07900 | HSP90AA1 | Heat shock protein HSP 90-alpha | P07900 (HSP90AA1) | Day 14 | Day 7 | 1.12 | 1.00 |
P60174 | TPI1 | Triosephosphate isomerase | P60174 (TPI1) | Day 14 | Day 7 | 1.12 | 0.58 |
P07900 | HSP90AA1 | Heat shock protein HSP 90-alpha | P07900 (HSP90AA1) | Day 14 | Day 14 | 1.12 | 1.02 |
P52907 | CAPZA1 | F-actin-capping protein subunit alpha-1 | P52907 (CAPZA1) | Day 14 | Day 14 | 0.56 | 0.58 |
Assay | Day | Pathway | Pathway Genes # | Significant Genes (%) [Protein Families] | Genes Up (%) | Genes Down (%) | Jaccard Similarity Coefficient | p | FDR-Adjusted P |
---|---|---|---|---|---|---|---|---|---|
LC-MS/MS | Day 7 | Ribosome | 127 | 5 (3.9) [5] | 5 (3.9) | 0 (0) | 0.036 | <0.0001 | 0.003 |
Day 14 | Ribosome | 127 | 13 (10.2) [14] | 13 (10.2) | 0 (0) | 0.0798 | <0.0001 | <0.0001 | |
Proteasome | 44 | 4 (9.1) [4] | 4 (9.1) | 0 (0) | 0.0449 | 0.0003 | 0.0473 | ||
2-DIGE/MS | Day 7 | Pathogenic Escherichia coli infection | 54 | 3 (5.6) [3] | 3 (5.6) | 0 (0) | 0.2273 | 0.0001 | 0.0287 |
Antigen processing and presentation | 64 | 3 (4.7) [2] | 3 (4.7) | 0 (0) | 0.046 | 0.0002 | 0.0287 | ||
Estrogen signaling pathway | 97 | 3 (3.1) [2] | 3 (3.1) | 0 (0) | 0.0333 | 0.0006 | 0.0653 | ||
Day 14 | Protein processing in endoplasmic reticulum | 159 | 8 (5) [7] | 8 (5) | 0 (0) | 0.0481 | <0.0001 | <0.0001 | |
Antigen processing and presentation | 64 | 5 (7.8) [4] | 5 (7.8) | 0 (0) | 0.0745 | <0.0001 | 0.0002 | ||
Pathogenic Escherichia coli infection | 54 | 4 (7.4) [4] | 4 (7.4) | 0 (0) | 0.2133 | <0.0001 | 0.0023 | ||
Estrogen signaling pathway | 97 | 4 (4.1) [3] | 4 (4.1) | 0 (0) | 0.0388 | 0.0002 | 0.0175 | ||
Legionellosis | 48 | 3 (6.2) [2] | 3 (6.2) | 0 (0) | 0.0366 | 0.0005 | 0.0279 | ||
Phagosome | 142 | 4 (2.8) [4] | 4 (2.8) | 0 (0) | 0.0982 | 0.001 | 0.0498 |
LC-MS/MS | 2D-DIGE/MS | ||||||
---|---|---|---|---|---|---|---|
Category Name | Category Genes | Sig. Genes (%) [Protein Fam.] | Jaccard Similarity Coefficient | FDR | Sig. Genes (%) [Protein Fam] | Jaccard Similarity Coefficient | FDR |
Day 7 | |||||||
GSE41978 KLRG1 HIGH VS LOW EFFECTOR CD8 TCELL DN | 186 | 5 (2.7) [5] | 0.0244 | 0.0101 | 3 (1.6) [3] | 0.0234 | 0.0543 |
GSE41978 ID2 KO VS ID2 KO AND BIM KO KLRG1 LOW EFFECTOR CD8 TCELL DN | 190 | 5 (2.6) [5] | 0.0239 | 0.0101 | 5 (2.6) [5] | 0.0324 | 0.0006 |
GSE2405 0H VS 9H A PHAGOCYTOPHILUM STIM NEUTROPHIL DN | 192 | 5 (2.6) [5] | 0.0237 | 0.0101 | 5 (2.6) [5] | 0.0321 | 0.0006 |
GSE3982 EOSINOPHIL VS MAST CELL DN | 186 | 4 (2.2) [4] | 0.0194 | 0.0999 | 3 (1.6) [3] | 0.0186 | 0.0543 |
GSE2405 0H VS 24H A PHAGOCYTOPHILUM STIM NEUTROPHIL UP | 193 | 4 (2.1) [4] | 0.0188 | 0.0999 | 3 (1.6) [3] | 0.0226 | 0.0543 |
Day 14 | |||||||
GSE2405 0H VS 9H A PHAGOCYTOPHILUM STIM NEUTROPHIL DN | 192 | 20 (10.4) [20] | 0.0813 | <0.0001 | 8 (4.2) [8] | 0.0485 | <0.0001 |
GSE2405 0H VS 24H A PHAGOCYTOPHILUM STIM NEUTROPHIL UP | 193 | 17 (8.8) [17] | 0.068 | <0.0001 | 4 (2.1) [4] | 0.0302 | 0.029 |
GSE41978 ID2 KO VS ID2 KO AND BIM KO KLRG1 LOW EFFECTOR CD8 TCELL DN | 190 | 12 (6.3) [12] | 0.0476 | <0.0001 | 5 (2.6) [5] | 0.0306 | 0.0045 |
GSE22886 NAIVE CD8 TCELL VS DC DN | 187 | 5 (2.7) [5] | 0.0195 | 0.0598 | 4 (2.1) [4] | 0.0264 | 0.029 |
GSE29618 BCELL VS MDC DAY7 FLU VACCINE DN | 191 | 5 (2.6) [5] | 0.0192 | 0.0598 | 5 (2.6) [5] | 0.0304 | 0.0045 |
GSE23114 PERITONEAL CAVITY B1A BCELL VS SPLEEN BCELL DN | 194 | 5 (2.6) [5] | 0.019 | 0.0601 | 4 (2.1) [4] | 0.0213 | 0.029 |
GSE2405_0H_VS_24H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_UP | |||
Assay | Gene | UniProt ID | Day 14 Fold Change |
2D DIGE/MS | ACTB;ACTG1 | P60709 | 2.271;2.004 |
TUBA1A;TUBA1B;TUBA1C;TUBA3D;TUBA3E;TUBA8 | P68363 | 2.046 | |
HSPA8 | P11142 | 1.629 | |
HSPA5 | P11021 | 1.522 | |
LC MS/MS | NPM1 | P06748 | 2.02 |
TKT | P29401 | 1.784 | |
RPS21 | P63220 | 1.702 | |
RPL30 | P62888 | 1.638 | |
RPL4 | P36578 | 1.602 | |
RPL5 | P46777 | 1.559 | |
RPL7 | P18124 | 1.555 | |
RPL22 | P35268 | 1.526 | |
RPS29 | P62273 | 1.503 | |
RPL3 | P39023 | 1.495 | |
RPL17 | P18621 | 1.449 | |
EEF1B2 | P24534 | 1.433 | |
RPS18 | P62269 | 1.428 | |
RPS27 | P42677 | 1.349 | |
RPL6 | Q02878 | 1.327 | |
EIF3I | Q13347 | 1.309 | |
BRK1 | Q8WUW1 | 1.271 | |
GSE2405_0H_VS_9H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_DN | |||
Assay | Gene | UniProt ID | Day 14 Fold Change |
2D DIGE/MS | ACTB;ACTG1 | P60709 | 2.271;2.004 |
TUBA1A;TUBA1B;TUBA1C;TUBA3D;TUBA3E;TUBA8 | P68363 | 2.046 | |
HSP90AA1;HSP90AB1 | P07900 | 2.036 | |
TUBB;TUBB2A;TUBB2B;TUBB3;TUBB4A;TUBB4B | P07437 | 1.857 | |
YWHAZ | P63104 | 1.848 | |
CAPZB;CEP128;PSME1 | P47756 | 1.674 | |
HSPA8 | P11142 | 1.629 | |
VCP | P55072 | 1.498 | |
LC MS/MS | HSP90AA1 | P07900 | 2.183 |
NPM1 | P06748 | 2.02 | |
EIF4A1 | P60842 | 1.838 | |
TKT | P29401 | 1.784 | |
HMGB1 | P09429 | 1.75 | |
RPS21 | P63220 | 1.702 | |
RPL30 | P62888 | 1.638 | |
RPL4 | P36578 | 1.602 | |
RPL5 | P46777 | 1.559 | |
RPL7 | P18124 | 1.555 | |
CHTOP | Q9Y3Y2 | 1.539 | |
RPL22 | P35268 | 1.526 | |
RPS29 | P62273 | 1.503 | |
RPL3 | P39023 | 1.495 | |
RPL17 | P18621 | 1.449 | |
EEF1B2 | P24534 | 1.433 | |
RPS18 | P62269 | 1.428 | |
RPS27 | P42677 | 1.349 | |
RPL6 | Q02878 | 1.327 | |
EIF3I | Q13347 | 1.309 | |
GSE25123_WT_VS_PPARG_KO_MACROPHAGE_DN | |||
Assay | Gene | UniProt ID | Day 14 Fold Change |
2D DIGE/MS | ARHGDIB | P52566 | 1.504 |
LC MS/MS | SYNCRIP | O60506 | 2.136 |
SAMHD1 | Q9Y3Z3 | 2.118 | |
PSMA4 | P25789 | 1.814 | |
PTBP1 | P26599 | 1.635 | |
PSMA5 | P28066 | 1.595 | |
RPL5 | P46777 | 1.559 | |
RPL7 | P18124 | 1.555 | |
EEF1B2 | P24534 | 1.433 | |
SNX3 | O60493 | 1.247 | |
GSE37532_TREG_VS_TCONV_CD4_TCELL_FROM_LN_UP | |||
2D DIGE/MS | HSP90B1 | P14625 | 1.636 |
LC MS/MS | ATIC | P31939 | 2.222 |
NOP56 | O00567 | 2.169 | |
CCT3 | P49368 | 2.018 | |
HDGF | P51858 | 1.801 | |
EEF1D | P29692 | 1.578 | |
NOP58 | Q9Y2X3 | 1.525 | |
SMAP | O00193 | 1.452 | |
GSE37532_TREG_VS_TCONV_PPARG_KO_CD4_TCELL_FROM_LN_DN | |||
2D DIGE/MS | LCP1 | P13796 | 2.293 |
CALR | P27797 | 1.558 | |
HSPA5 | P11021 | 1.522 | |
P4HB | P07237 | 1.505 | |
GSE37532_WT_VS_PPARG_KO_VISCERAL_ADIPOSE_TISSUE_TREG_UP | |||
2D DIGE/MS | YWHAZ | P63104 | 1.848 |
LC MS/MS | HDGF | P51858 | 1.801 |
HMGB2 | P26583 | 1.757 | |
TCEA1 | P23193 | 1.661 | |
PPP6C | O00743 | 1.638 |
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Chang, Y.-H.; Duong, D.M.; Goll, J.B.; Wood, D.C.; Jensen, T.L.; Yin, L.; Gelber, C.E.; Seyfried, N.T.; Anderson, E.; Natrajan, M.S.; et al. Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine. Vaccines 2020, 8, 413. https://doi.org/10.3390/vaccines8030413
Chang Y-H, Duong DM, Goll JB, Wood DC, Jensen TL, Yin L, Gelber CE, Seyfried NT, Anderson E, Natrajan MS, et al. Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine. Vaccines. 2020; 8(3):413. https://doi.org/10.3390/vaccines8030413
Chicago/Turabian StyleChang, Yie-Hwa, Duc M. Duong, Johannes B. Goll, David C. Wood, Travis L. Jensen, Luming Yin, Casey E. Gelber, Nicholas T. Seyfried, Evan Anderson, Muktha S. Natrajan, and et al. 2020. "Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine" Vaccines 8, no. 3: 413. https://doi.org/10.3390/vaccines8030413
APA StyleChang, Y. -H., Duong, D. M., Goll, J. B., Wood, D. C., Jensen, T. L., Yin, L., Gelber, C. E., Seyfried, N. T., Anderson, E., Natrajan, M. S., Rouphael, N., Johnson, R. A., Sanz, P., Mulligan, M. J., & Hoft, D. F. (2020). Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine. Vaccines, 8(3), 413. https://doi.org/10.3390/vaccines8030413