Supplemental Information. Systems Scale Interactive Exploration. Reveals Quantitative and Qualitative Differences

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1 Immunity, Volume 38 Supplemental Information Systems Scale Interactive Exploration Reveals Quantitative and Qualitative Differences in Response to Influenza and Pneumococcal Vaccines Gerlinde Obermoser, Scott Presnell, Kelly Domico, Hui Xu, Yuanyuan Wang, Esperanza Anguiano, LuAnn Thompson-Snipes, Rajaram Ranganathan, Brad Zeitner, Anna Bjork, David Anderson, Cate Speake, Emily Ruchaud, Jason Skinner, Laia Alsina, Mamta Sharma, Helene Dutartre, Alma Cepika, Elisabeth Israelsson, Phuong Nguyen, Quynh-Anh Nguyen, A. Carson Harrod, Sandra M. Zurawski, Virginia Pascual, Hideki Ueno, Gerald T. Nepom, Charlie Quinn, Derek Blankenship, Karolina Palucka, Jacques Banchereau, and Damien Chaussabel 1. Supplemental Figures and Tables Figure S1, Related to Figure 7 Figure S2, Related to Figure 1 Figure S3, Related to Figure 1 Figure S4, Related to Figure 5 Table S1, Related to Figure 1 Table S2, Related to Figure 1 Table S3, Related to Figure 7 Table S4, Related to Figure 7 Table S5, Related to Figure 1 Table S6, Related to Figure 2 (see separate Excel file) 2. Supplemental Experimental Procedures 3. Supplemental References

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3 Figure S1. Related to Figure 7 A. Antibody and CBC response to influenza and pneumococcal vaccine. Antibody response to 2009 seasonal influenza vaccine. Fold change of serum HI and VN titers against the three vaccine component strains is shown for each individual. Red horizontal bar indicates 4-fold HI titer change. B: Antibody response to 23-valent pneumococcal vaccine. Fold change of binding titers against 14 pneumococcal polysaccharides is shown for each individual; horizontal bars indicate geometric means of fold increase. See Figure 7 for correlation patterns between serological profile and transcriptional response. C: Increase of total white blood cells and neutrophils on day 1 following pneumococcal vaccination. Complete blood counts were obtained from each subject and each time point of venicpuncture. Each error bar is constructed using one standard deviation from the mean (horizontal line). * P < 0.05 (Tukey-Kramer test).

4 Day 1 Fingerprint I II III Interferon Signature I II III Serum IP10 Finger stick Leukocytes Ab Secreting Cells I II II Blood Finger Stick Flow

5 Figure S2. Study Design, Related to Figure 1 Three independent cohorts have been recruited during the course of this study, for a total of 46 subjects enrolled and 897 samples collected. Transcriptional signatures were identified in cohort I (see Figure 1) and validated independently in cohorts II and III. Key findings were also validated in ad hoc sets of samples, collected at early time points via finger sticks (cohort II), or in samples from which leukocyte populations were isolated (cohort III). Furthermore, transcriptional signatures were validated at the protein level, via measurement of serum protein levels or by flow cytometry (plasmablasts).

6 Figure S3. Fold Change Comparison of Differentially Expressed Gene Probes and Modules across Cohorts, Related to Figure 1 Each scatter plot displays the fold change (log base 2) of probes or the mean fold change (log base 2) of all probes within a module determined to be statistically significant in at least one cohort by day and vaccine (for probe level and modular level analysis, see also Figures 1 and 2). The corresponding Pearson correlation coefficients and p-values are also displayed. All correlations for seasonal influenza and pneumococcal vaccine are above 0.70 and statistically significant. The module correlations for saline are neither high nor statistically significant and are therefore not displayed; also since only one module (M4.11) in the influenza vaccine cohort is significant on day 7, no scatter plot was generated for this time point.

7 Figure S4. Related to Figure 5 A. Cytokine and chemokine response to vaccination with seasonal influenza and pneumococcal vaccine or saline injections. Lg2 fold change of serum cytokines over baseline value were calculated based on pre-immunization levels (i.e. Lg2 (ObsConc DX)- Lg2 (ObsConc D0) and depicted as a heat map with yellow pixels indicating no change over baseline and red and blue indicating increased or decreased serum levels, respectively. B. Serum IP-10/ CXCL10 is significantly increased on day 1 following immunization with seasonal influenza vaccine. Log2 transformed cytokine concentrations were normalized to pre-vaccination levels and shown as box plots with whiskers indicating +/- 1.5 IQR and as a spider plot. *** P < 0.001, ** P < 0.01, * P < 0.05 (Tukey-Kramer test). See Figure 5 for concomitant profiling of transcriptional interferon response.

8 Table S1. Sampling Schedule and Assays First Vaccination Cohort, Related to Figure (Seasonal Influenza and Pneumococcal vaccines and Saline control) Days CBC Flow Cytometry Luminex Blood Microarray Finger Blood Microarray Serology x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x Table S2. Sampling Schedule and Assays Second Vaccination Cohort, Related to Figure 1 (Seasonal Influenza and Pneumococcal vaccines and Saline control) Days CBC x x x x x x x Flow Cytometry x x x x x x x x Luminex x x x x x Blood Microarray x x x x x x x x Serology x x x

9 Table S3. Haemagglutinin inhibition (HI) and virus neutralization (VN) antibody titers before and after 2009/10 seasonal influenza vaccination, Related to Figure 7 Brisbane H1N1 Brisbane H3N2 HI Antibody Titer HI Fold Increase Pre- Day 28 Mean Median vaccination B Brisbane Brisbane H1N1 Brisbane H3N2 VN Antibody Titer VN Fold Increase Pre- Day 28 Mean Median vaccination B Brisbane Values shown for HI and VN antibody titer are geometric means.

10 Table S4. Antibody Titers Before and After 23-Valent Pneumococcal Vaccination, Related to Figure 7 Serotype Antibody Titer ug/ ml Fold increase D28/BL Serotype 1 (1) Serotype 3 (3) Serotype 4 (4) Serotype 5 (5) Serotype8 (8) Serotype 9 (9N) Serotype 12 (12F) Serotype 14 (14) Serotype 19 (19F) Serotype 23 (23F) Serotype 26 (6B) Serotype 51 (7F) Serotype 56 (18C) Serotype 68 (9V) Prevaccination Day 28 Mean Median Values shown for titer are geometric means for each antigen; BL= baseline. Table S5. Sampling Schedule Finger Prick Samples in Second Vaccine Cohort, Related to Figure 1 Time D -7 H 0 H 1.5 H 3 H 6 H 9 H 12 H 15 H 24 H 36 H 48 Flu x x x x x x x x x x x

11 Supplemental Experimental Procedures Modular Analyses This analysis strategy has been described in detail elsewhere (Chaussabel et al., 2008). In that original manuscript peripheral blood leukocyte gene expression profiles were generated using Affymetrix GeneChips. Since that publication we have created a new set of transcriptional modules using whole blood samples and Illumina Hu6 V2 BeadChips, matching both the RNA source and platform used in this study. For the analysis of the vaccine signatures we used a set of 260 transcriptional modules generated through the analysis of 410 whole blood profiles. Briefly, nine datasets were used as input, including blood profiles generated from patients with HIV, tuberculosis, sepsis, systemic lupus erythematosus, systemic arthritis, and liver transplant. Each dataset was then clustered independently and the analysis of cluster membership of each gene across all the datasets was used to define transcriptional modules with varying degrees of stringency. Those modules with conserved expression across diseases (i.e. formed by transcripts that cluster together for all nine datasets) were selected in early rounds whereas modules with greater disease specificity (i.e. formed by transcripts that cluster together only in a subset of the nine datasets) were selected in later rounds. The top six rounds of modules defined by this approach (M1-M6, a total of 62 modules) represent a general yet powerful framework to analyze and interpret the datasets generated in the context of the present study. Functional analyses were carried out systematically across all modules and results are reported on a wiki page: A complete list of the genes forming the modules is provided as a supplementary file. The datasets used for module construction have been deposited in NCBI s Gene Expression Omnibus: GSE Supplemental References Chaussabel, D., Quinn, C., Shen, J., Patel, P., Glaser, C., Baldwin, N., Stichweh, D., Blankenship, D., Li, L., Munagala, I., et al. (2008). A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29,