Dissecting Polyclonal Vaccine-Induced Humoral Immunity against HIV Using Systems Serology

Transcription

1 Cell Supplemental Information Dissecting Polyclonal Vaccine-Induced Humoral Immunity against HIV Using Systems Serology Amy W. Chung, Manu P. Kumar, Kelly B. Arnold, Wen Han Yu, Matthew K. Schoen, Laura J. Dunphy, Todd J. Suscovich, Nicole Frahm, Caitlyn Linde, Alison E. Mahan, Michelle Hoffner, Hendrik Streeck, Margaret E. Ackerman, M. Juliana McElrath, Hanneke Schuitemaker, Maria G. Pau, Lindsey R. Baden, Jerome H. Kim, Nelson L. Michael, Dan H. Barouch, Douglas A. Lauffenburger, and Galit Alter

2 Supplementary Experimental procedures: Vaccine Samples RV144 (Rerks-Ngarm et al., 2009): Plasma samples from 30 vaccinated subjects at week 26 (2 weeks post final vaccination) were provided by the MHRP. Vaccinated subjects were administered ALVAC vcp1521 prime, a recombinant canary pox vector genetically engineered to express CRF01_AE HIV-1 gp120 (92TH023) linked to the transmembrane anchoring portion of subtype B gp41 and HIV-1 gag and protease (weeks 0, 4, 12, 24), followed by a boost with AIDSVAX B/E containing bivalent rgp120 MN (clade B) and A244 (clade E) protein (week 12 and 24). RV144 case:control study data were provided by the RV144 study team (Haynes et al., 2012) (Yates et al., 2014) VAX003 (Pitisuttithum et al., 2006): Serum samples from 30 vaccinated subjects at month 30.5 (two weeks post final vaccination) were provided by GSID. Vaccinated subjects were administered AIDSVAX B/E at month 0, 1, 6, 12, 18, 24 and 30. HVTN204 (Churchyard et al., 2011): Serum samples from 30 vaccinated subjects taken at 2 weeks post final vaccination were provided by the HVTN. Subjects were administered a six-plasmid HIV-1 DNA prime (enva, envb, envc, gagb, polb, nefb) at month 0, 1, and 2 followed by a boost with recombinant adenovirus serotype-5 (rad5) expressing HIV-1 at month 6. IPCAVD 001 (Barouch et al., 2013): Serum samples from 30 vaccine subjects taken at 2 weeks post final vaccination were provided by Dan Barouch. Subjects were administered a single dose of rad26 encoding Clade A HIV-1 Env at week 0. All vaccine samples included in this analysis were balanced for sex and were collected from subjects years of age who provided signed, informed consent.

3 Antibody-Dependent Cellular Phagocytosis (ADCP) Assay The THP-1 phagocytosis assay was performed as previously described (Ackerman et al., 2011). Briefly, THP-1 cells were purchased from ATCC and cultured as recommended. Biotinylated rgp120 (clade specific for respective vaccination as mentioned previously) (Immune Technology) was used to saturate the binding sites on 1 µm fluorescent neutravidin beads (Invitrogen) overnight at 4 C. Excess antigen was removed by washing the pelleted beads, which were then incubated with patient Ab samples for 2 hr at 37 C. Following opsonization, THP-1 cells were added, and the cells were incubated overnight to allow phagocytosis. The cells were then fixed, and the extent of phagocytosis was measured via flow cytometry on a BD LSR II flow cytometer equipped with high-throughput sampler. The data are reported as a phagocytic score, which takes into account the proportion of effector cells that phagocytosed and the degree of phagocytosis (integrated MFI: frequency x MFI) (Darrah et al., 2007). Each Ab sample was tested over a range of concentrations ( µg/ml). Antibody-dependent cellular cytotoxicity (ADCC) assay The rapid fluorescent ADCC (RFADCC) assay was performed as previously described (Gomez-Roman et al., 2006). In brief, CEM-NKr cells were pulsed with vaccine cladespecific rgp120 proteins (6 µg/ml) and labeled with the intracellular dye CFSE and the membrane dye PKH26. NK cells were enriched directly from seronegative donor whole blood by negative selection using RosetteSep (Stem Cell Technologies). Purified IgG was added to the labeled, antigen-pulsed CEM-NKr cells after which fresh NK cells were added. The cells were incubated for 4 hr at 37 C and then fixed. The proportion of cells that maintained membrane expression of PKH26 but lost CFSE staining (i.e., lysed cells) were quantified via flow cytometry.

4 Antibody-dependent complement deposition (ADCD) Ab-dependent complement deposition was assessed by the measurement of complement component C3b on the surface of target cells. CD4-expressing target cells were pulsed with the relevant vaccine-specific gp120 protein (60 mg/ml), and incubated with purified Abs. Freshly isolated HIV negative donor plasma diluted with veronal buffer and 0.1% gelatin (1:10 dilution) was added, the cells were incubated for 20 min at 37 C. The cells were then washed with 15 mm EDTA in PBS, and complement deposition was detected via flow cytometry following staining for C3b (Cedarlane). Replicates using heat inactivated donor plasma were used as negative controls. Antibody-dependent NK cell activation Ab-dependent NK cell degranulation and cytokine/chemokine secretion was measured using the CEM-NKr CCR5+ T lymphoblast cell line pulsed with vaccine-specific gp120 (60 mg/ml), as previously described (Chung et al., 2014b). Fresh NK cells were isolated from whole blood from seronegative donors using negative selection with RosetteSep, as recommended by the manufacturer. The antigen-pulsed CEM-NKr cells and isolated primary NK cells were mixed at a ratio of 1:5, and purified Abs, anti-cd107a, brefeldin A (10 mg/ml) (Sigma), and GolgiStop (BD) were added and the cultures incubates for 5 hours at 37 C. The cells were then washed and stained for surface markers using anti- CD16, anti-cd56, and anti-cd3. The cells were then washed, fixed and permeabilized using Fix & Perm (Invitrogen), and then stained intracellularly with anti-ifn-γ and anti- MIP-1β. The cells were then fixed in 4% paraformaldehyde and analyzed using flow cytometry. NK cells were defined as CD3-negative and CD16- and/or CD56-positive. All antibodies for flow cytometry were purchased from BD.

5 FcγR Surface Plasmon Resonance (SPR) Antibody affinity for FCGRs was determined using surface plasmon resonance and a Biacore 3000 as previously described (Chung et al., 2014a). Briefly, research grade CM5 plasmon surface resonance chips were coated with recombinant FcGRIIa, IIb, IIIa or no protein. The subjects Abs were added at 125 ug/ml. The binding of Abs to the individual FCGRs was quantified as the relative response units of signal following each sample injection. Luminex Isotype Assay A Luminex isotype assay was used to quantify the relative concentration of each Ab isotype among the HIV-specific Abs as previously described (Brown et al., 2012). Briefly, Luminex microplex carboxlyated beads (Luminex) were coupled to the indicated proteins via covalent NHS-ester linkages by combining EDC and NHS (Thermo Scientific) in PBS, as recommending by the manufacturer. The coupled beads (50 µl of a 100 microspheres/µl solution in 0.1% BSA in PBS) were added to each well of a 96-well filter plate (Millipore). The purified IgGs (50 µl of each vaccine sample diluted to 200 µg IgG/ml) was added to five wells of the 96-well plate and incubated at 4 C overnight. The beads were washed three times with 100 µl of PBS-Tween, and individual IgG isotype detection reagents (i.e., bulk IgG, IgG1, IgG2, IgG3, and IgG4 for all vaccines plus IgA was assessed for the RV144 study from plasma samples) conjugated to PE (Southern Biotech) were added individually to each of one of the five wells. The 96-well plate was incubated with shaking for 2 hr, washed three times, and read on Bio-Plex 200. Importantly, to maintain complete objectivity, identical reagent sets/assays were performed on all vaccine samples. Thus, Ags were tested across all immunogenicity vaccine trial specimens, regardless of their inclusion in the trial s immunizing strategy.

6 Importantly, even though non-specific responses to Ags not included in the vaccine regimen, such as gp41, were rarely detected (Figure 2), these responses appeared in the network (Figure 4A), simply reflecting the previously reported presence of low-level cross-reactive responses to these peculiar Ags (Trama et al., 2014). Thus, excluding particular Ags that are not included in a particular vaccine trial at the time of the analysis may alter the objective nature of the analysis, the exclusion of these responses could be considered in subsequent supervised analyses. Identification of vaccine-specific signatures with LASSO and PLSDA Key features that contribute to profile differences, in multidimensional space, were defined using a combined feature selection (LASSO method) (Tibshirani, 1997) and partial least squares discriminant analysis (PLSDA) (Arnold et al., 2015; Lau et al., 2011), implemented using Matlab software (version 2014a, Mathworks, Natick, MA). K- fold cross-validation determined the optimum value of the tuning parameter ( s ), such that the resulting model had the lowest possible MSE for prediction and associated features were chosen as the minimum set of biomarkers. PLS (Partial Least Square) analytical approaches were specifically selected for these analyses, as the method was designed for small samples sizes relative to number of latent variables defined by weighting coefficients(haenlein and Kaplan, 2004; Janes et al., 2005). Partial least square discriminant analysis (PLSDA) (Arnold et al., 2015; Lau et al., 2011) assessed the predictive ability of LASSO-selected biomarkers for classifying vaccine groups. Prior to PLSDA analysis, the data was normalized with mean centering and variance scaling, and cross-validation was performed by iteratively excluding random subsets (in groups of 10%) during model calibration, then using excluded data samples to test model predictions. Orthogonal signal correction was used to improve model visualization and

7 interpretability. Quality of each PLS model was confirmed by posteriori cross-validation calculation, which was reported for each of our models in the associated figure legends.

8 Supplementary References: Ackerman, M.E., Moldt, B., Wyatt, R.T., Dugast, A.S., McAndrew, E., Tsoukas, S., Jost, S., Berger, C.T., Sciaranghella, G., Liu, Q., et al. (2011). A robust, high- throughput assay to determine the phagocytic activity of clinical antibody samples. Journal of immunological methods 366, Arnold, K.B., Burgener, A., Birse, K., Romas, L., Dunphy, L.J., Shahabi, K., Abou, M., Westmacott, G.R., McCorrister, S., Kwatampora, J., et al. (2015). Increased levels of inflammatory cytokines in the female reproductive tract are associated with altered expression of proteases, mucosal barrier proteins, and an influx of HIV- susceptible target cells. Mucosal immunology. Barouch, D.H., Liu, J., Peter, L., Abbink, P., Iampietro, M.J., Cheung, A., Alter, G., Chung, A., Dugast, A.S., Frahm, N., et al. (2013). Characterization of humoral and cellular immune responses elicited by a recombinant adenovirus serotype 26 HIV- 1 Env vaccine in healthy adults (IPCAVD 001). The Journal of infectious diseases 207, Brown, E.P., Licht, A.F., Dugast, A.S., Choi, I., Bailey- Kellogg, C., Alter, G., and Ackerman, M.E. (2012). High- throughput, multiplexed IgG subclassing of antigen- specific antibodies from clinical samples. Journal of immunological methods 386, Chung, A.W., Crispin, M., Pritchard, L., Robinson, H., Gorny, M.K., Yu, X., Bailey- Kellogg, C., Ackerman, M.E., Scanlan, C., Zolla- Pazner, S., et al. (2014a). Identification of antibody glycosylation structures that predict monoclonal antibody Fc- effector function. Aids 28, Chung, A.W., Ghebremichael, M., Robinson, H., Brown, E., Choi, I., Lane, S., Dugast, A.S., Schoen, M.K., Rolland, M., Suscovich, T.J., et al. (2014b). Polyfunctional Fc- effector profiles mediated by IgG subclass selection distinguish RV144 and VAX003 vaccines. Science translational medicine 6, 228ra238. Churchyard, G.J., Morgan, C., Adams, E., Hural, J., Graham, B.S., Moodie, Z., Grove, D., Gray, G., Bekker, L.G., McElrath, M.J., et al. (2011). A phase IIA randomized clinical trial of a multiclade HIV- 1 DNA prime followed by a multiclade rad5 HIV- 1 vaccine boost in healthy adults (HVTN204). PloS one 6, e Darrah, P.A., Patel, D.T., De Luca, P.M., Lindsay, R.W., Davey, D.F., Flynn, B.J., Hoff, S.T., Andersen, P., Reed, S.G., Morris, S.L., et al. (2007). Multifunctional TH1 cells define a correlate of vaccine- mediated protection against Leishmania major. Nature medicine 13, Gomez- Roman, V.R., Florese, R.H., Patterson, L.J., Peng, B., Venzon, D., Aldrich, K., and Robert- Guroff, M. (2006). A simplified method for the rapid fluorometric assessment of antibody- dependent cell- mediated cytotoxicity. Journal of immunological methods 308, Haenlein, M., and Kaplan, A.M. (2004). A beginner's guide to partial least squares analysis. Understanding Statistics 3, Haynes, B.F., Gilbert, P.B., McElrath, M.J., Zolla- Pazner, S., Tomaras, G.D., Alam, S.M., Evans, D.T., Montefiori, D.C., Karnasuta, C., Sutthent, R., et al. (2012). Immune-

9 correlates analysis of an HIV- 1 vaccine efficacy trial. The New England journal of medicine 366, Janes, K.A., Albeck, J.G., Gaudet, S., Sorger, P.K., Lauffenburger, D.A., and Yaffe, M.B. (2005). A systems model of signaling identifies a molecular basis set for cytokine- induced apoptosis. Science 310, Lau, K.S., Juchheim, A.M., Cavaliere, K.R., Philips, S.R., Lauffenburger, D.A., and Haigis, K.M. (2011). In vivo systems analysis identifies spatial and temporal aspects of the modulation of TNF- alpha- induced apoptosis and proliferation by MAPKs. Science signaling 4, ra16. Pitisuttithum, P., Gilbert, P., Gurwith, M., Heyward, W., Martin, M., van Griensven, F., Hu, D., Tappero, J.W., and Choopanya, K. (2006). Randomized, double- blind, placebo- controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV- 1 vaccine among injection drug users in Bangkok, Thailand. The Journal of infectious diseases 194, Rerks- Ngarm, S., Pitisuttithum, P., Nitayaphan, S., Kaewkungwal, J., Chiu, J., Paris, R., Premsri, N., Namwat, C., de Souza, M., Adams, E., et al. (2009). Vaccination with ALVAC and AIDSVAX to prevent HIV- 1 infection in Thailand. The New England journal of medicine 361, Tibshirani, R. (1997). The lasso method for variable selection in the Cox model. Statistics in medicine 16, Trama, A.M., Moody, M.A., Alam, S.M., Jaeger, F.H., Lockwood, B., Parks, R., Lloyd, K.E., Stolarchuk, C., Scearce, R., Foulger, A., et al. (2014). HIV- 1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross- reactivity with commensal bacteria. Cell host & microbe 16, Yates, N.L., Liao, H.X., Fong, Y., decamp, A., Vandergrift, N.A., Williams, W.T., Alam, S.M., Ferrari, G., Yang, Z.Y., Seaton, K.E., et al. (2014). Vaccine- induced Env V1- V2 IgG3 correlates with lower HIV- 1 infection risk and declines soon after vaccination. Science translational medicine 6, 228ra239.

10 Table S1: Features Included in Systems Serology Analysis Feature name Feature description 1 IgG gp140 B1 Bulk IgG gp140 CFI (Clade B) 2 IgG V1V2 B Bulk IgG gp70 V1V2 case A2 (Clade B) 3 IgG p24 B Bulk IgG p24 HXBc2 (Clade B) 4 IgG gp140 B2 Bulk IgG gp140 Concensus B (Clade B) 5 IgG gp41 Bulk IgG gp41hxbc2 (Clade B) 6 IgG gp120 AE Bulk IgG gp120 A244 (Clade AE) 7 IgG gp140 AE Bulk IgG gp140 A244 (Clade AE) 8 IgG p24 E Bulk IgG p24 clade E 9 IgG gp120 B2 Bulk IgG gp120 MN (Clade B) 10 IgG V1V2 AE Bulk IgG gp70 V1V2 A244 (Clade AE) 11 IgG gp120 A Bulk IgG gp120 92RW020 (Clade A) 12 IgG1 gp140 B1 IgG1 gp140 CFI (Clade B) 13 IgG1 V1V2 B IgG1 gp70 V1V2 case A2 (Clade B) 14 IgG1 p24 B IgG1 p24 HXBc2 (Clade B) 15 IgG1 gp140 B2 IgG1 gp140 Concensus B (Clade B) 16 IgG1 gp41 IgG1 gp41hxbc2 (Clade B) 17 IgG1 gp120 AE IgG1 gp120 A244 (Clade AE) 18 IgG1 gp140 AE IgG1 gp140 A244 (Clade AE) 19 IgG1 p24 E IgG1 p24 clade E 20 IgG1 gp120 B2 IgG1 gp120 MN (Clade B) 21 IgG1 V1V2 AE IgG1 gp70 V1V2 A244 (Clade AE) 22 IgG1 gp120 A IgG1 gp120 92RW020 (Clade A) 23 IgG2 gp140 B1 IgG2 gp140 CFI (Clade B) 24 IgG2 V1V2 B IgG2 gp70 V1V2 case A2 (Clade B) 25 IgG2 p24 B IgG2 p24 HXBc2 (Clade B) 26 IgG2 gp140 B2 IgG2 gp140 Concensus B (Clade B) 27 IgG2 gp41 IgG2 gp41hxbc2 (Clade B) 28 IgG2 gp120 AE IgG2 gp120 A244 (Clade AE) 29 IgG2 gp140 AE IgG2 gp140 A244 (Clade AE) 30 IgG2 p24 E IgG2 p24 clade E 31 IgG2 gp120 B2 IgG2 gp120 MN (Clade B) 32 IgG2 V1V2 AE IgG2 gp70 V1V2 A244 (Clade AE) 33 IgG2 gp120 A IgG2 gp120 92RW020 (Clade A) 34 IgG3 gp140 B1 IgG3 gp140 CFI (Clade B) 35 IgG3 V1V2 B IgG3 gp70 V1V2 case A2 (Clade B) 36 IgG3 p24 B IgG3 p24 HXBc2 (Clade B) 37 IgG3 gp140 B2 IgG3 gp140 Concensus B (Clade B) 38 IgG3 gp41 IgG3 gp41hxbc2 (Clade B) 39 IgG3 gp120 AE IgG3 gp120 A244 (Clade AE) 40 IgG3 gp140 AE IgG3 gp140 A244 (Clade AE)

11 41 IgG3 p24 E IgG3 p24 clade E 42 IgG3 gp120 B2 IgG3 gp120 MN (Clade B) 43 IgG3 V1V2 AE IgG3 gp70 V1V2 A244 (Clade AE) 44 IgG3 gp120 A IgG3 gp120 92RW020 (Clade A) 45 IgG4 gp140 B1 IgG4 gp140 CFI (Clade B) 46 IgG4 V1V2 B IgG4 gp70 V1V2 case A2 (Clade B) 47 IgG4 p24 B IgG4 p24 HXBc2 (Clade B) 48 IgG4 gp140 B2 IgG4 gp140 Concensus B (Clade B) 49 IgG4 gp41 IgG4 gp41hxbc2 (Clade B) 50 IgG4 gp120 AE IgG4 gp120 A244 (Clade AE) 51 IgG4 gp140 AE IgG4 gp140 A244 (Clade AE) 52 IgG4 p24 E IgG4 p24 clade E 53 IgG4 gp120 B2 IgG4 gp120 MN (Clade B) 54 IgG4 V1V2 AE IgG4 gp70 V1V2 A244 (Clade AE) 55 IgG4 gp120 A IgG4 gp120 92RW020 (Clade A) 56 FcR2a FcγR2a 57 FcR2b FcγR2b 58 FcR3a FcγR3a 59 ADCC Antibody Dependent Cellular Cytotoxicity 60 ADCD Antibody Dependent Complement Deposition 61 IFNγ Antibody Dependent NK cell IFNγ secretion 62 MIP1β Antibody Dependent NK cell MIP1β secretion 63 CD107a Antibody Dependent NK cell CD107a activation 64 ADCP Antibody Dependent Cellular Phagocytosis 65 IgA gp140 B1 Bulk IgA gp140 CFI (Clade B)* 2 IgA V1V2 B Bulk IgA gp70 V1V2 case A2 (Clade B) * 3 IgA p24 B Bulk IgA p24 HXBc2 (Clade B) * 4 IgA gp140 B2 Bulk IgA gp140 Concensus B (Clade B) * 5 IgA gp41 Bulk IgA gp41hxbc2 (Clade B) * 6 IgA gp120 AE Bulk IgA gp120 A244 (Clade AE) * 7 IgA gp140 AE Bulk IgA gp140 A244 (Clade AE) * 9 IgA gp120 B2 Bulk IgA gp120 MN (Clade B) * 10 IgA V1V2 AE Bulk IgA gp70 V1V2 A244 (Clade AE) * * denotes features only included with RV144 specific analyses (Figure 5)

12 Table S2: Heatmap Features Feature group Function FcR IgG4 IgG3 IgG2 IgG1 Feature name ADCP CD107a MIP1B IFNg ADCD ADCC FcR3a FcR2b FcR2a IgG4 gp120 A IgG4 V1V2 AE IgG4 gp120 B2 IgG4 p24 E IgG4 gp140 AE IgG4 gp120 AE IgG4 gp41 IgG4 gp140 B2 IgG4 p24 B IgG4 V1V2 B IgG4 gp140 B1 IgG3 gp120 A IgG3 V1V2 AE IgG3 gp120 B2 IgG3 p24 E IgG3 gp140 AE IgG3 gp120 AE IgG3 gp41 IgG3 gp140 B2 IgG3 p24 B IgG3 V1V2 B IgG3 gp140 B1 IgG2 gp120 A IgG2 V1V2 AE IgG2 gp120 B2 IgG2 p24 E IgG2 gp140 AE IgG2 gp120 AE IgG2 gp41 IgG2 gp140 B2 IgG2 p24 B IgG2 V1V2 B IgG2 gp140 B1 IgG1 gp120 A IgG1 V1V2 AE IgG1 gp120 B2 IgG1 p24 E IgG1 gp140 AE IgG1 gp120 AE

13 IgG IgG1 gp41 IgG1 gp140 B2 IgG1 p24 B IgG1 V1V2 B IgG1 gp140 B1 IgG gp120 A IgG V1V2 AE IgG gp120 B2 IgG p24 E IgG gp140 AE IgG gp120 AE IgG gp41 IgG gp140 B2 IgG p24 B IgG V1V2 B IgG gp140 B1

14 Table S3. RV144 Case Control Study Analysis Features Feature name primary_iga_score_tomaras primary_avidity_a244_gdneg_delta11_alam primary_adcc_luc_92th023_evans primary_nab_tzmbl_a3r5_auc_afrims_siriraj_montefiori primary_v2_gp70_v1v2_zollapazner toggle_iga_gdneg_delta11_tomaras toggle_avidity_mn_gdneg_alam toggle_adcc_gp120coated_a244_ferrari toggle_nab_tzmbl_aucmb_siriraj toggle_nab_tzmbl_aucmb_afrims toggle_nab_tzmbl_a3r5_montefiori toggle_v2_cyclic_peptide_42aa secondary_gt_iga_main_breadth secondary_gt_iga_gd secondary_gt_iga_a244_gdneg_d11 secondary_gt_iga_a244_gdpos_293t secondary_gt_iga_a244_gdpos_chogsid secondary_gt_iga_92th023_gdpos_293t secondary_gt_iga_92th023_gdpos_chogsid secondary_gt_iga_gne8 secondary_gt_iga_bconenv03140cf secondary_gt_iga_cconenv03140cf secondary_gt_iga_con6gp120b secondary_gt_iga_consgp140cfi secondary_gt_igg_main secondary_gt_igg_toggle secondary_gt_igg_main_breadth secondary_gt_igg_main_vac secondary_gt_igg_k178 secondary_gt_igg_gd secondary_gt_igg_c1biotin secondary_gt_igg_244_gdneg Specific details about each of these features and methods describing their collection are detailed in (Haynes et al., 2012-Supplementary materials)