Bali Pulendran

All Publications

• High titer, multi-target serum neutralizing antibody responses are associated with protection against autologous challenge in BG505 SOSIP immunized rhesus macaques Charles, T. P., Burton, S. L., Legere, T., Arunachalam, P. S., van Gils, M. J., Cottrell, C., Bollimpelli, V. S., Ward, A., Hunter, E., Amara, R. R., Pulendran, B., Derdeyn, C. A. WILEY. 2020: 249

  View details for Web of Science ID 000571653100065

• The science and medicine of human immunology. Science (New York, N.Y.) Pulendran, B., Davis, M. M. 2020; 369 (6511)

  Abstract

  Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.

  View details for DOI 10.1126/science.aay4014

  View details for PubMedID 32973003

• The Impact of the Microbiome on Immunity to Vaccination in Humans. Cell host & microbe de Jong, S. E., Olin, A., Pulendran, B. 2020; 28 (2): 169–79

  Abstract

  Vaccines are the most effective means available for preventing infectious diseases. However, vaccine-induced immune responses are highly variable between individuals and between populations in different regions of the world. Understanding the basis of this variation is, thus, of fundamental importance to human health. Although the factors that are associated with intra- and inter-population variation in vaccine responses are manifold, emerging evidence points to a key role for the gut microbiome in controlling immune responses to vaccination. Much of this evidence comes from studies in mice, and causal evidence for the impact of the microbiome on human immunity is sparse. However, recent studies on vaccination in subjects treated with broad-spectrum antibiotics have provided causal evidence and mechanistic insights into how the microbiota controls immune responses in humans.

  View details for DOI 10.1016/j.chom.2020.06.014

  View details for PubMedID 32791110

• Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science (New York, N.Y.) Arunachalam, P. S., Wimmers, F., Mok, C. K., Perera, R. A., Scott, M., Hagan, T., Sigal, N., Feng, Y., Bristow, L., Tak-Yin Tsang, O., Wagh, D., Coller, J., Pellegrini, K. L., Kazmin, D., Alaaeddine, G., Leung, W. S., Chan, J. M., Chik, T. S., Choi, C. Y., Huerta, C., Paine McCullough, M., Lv, H., Anderson, E., Edupuganti, S., Upadhyay, A. A., Bosinger, S. E., Maecker, H. T., Khatri, P., Rouphael, N., Peiris, M., Pulendran, B. 2020

  Abstract

  COVID-19 represents a global crisis, yet major knowledge gaps remain about human immunity to SARS-CoV-2. We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta. In PBMCs of COVID-19 patients, there was reduced expression of HLA-DR and pro-inflammatory cytokines by myeloid cells, and impaired mTOR-signaling and IFN-alpha production by plasmacytoid DCs. In contrast, there were enhanced plasma levels of inflammatory mediators, including EN-RAGE, TNFSF14, and oncostatin-M, which correlated with disease severity and increased bacterial products in human plasma. Single-cell transcriptomics revealed no type-I IFN, reduced HLA-DR in myeloid cells of severe patients, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics, and transient, low plasma IFN-alpha levels during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.

  View details for DOI 10.1126/science.abc6261

  View details for PubMedID 32788292

• Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humans. Proceedings of the National Academy of Sciences of the United States of America Ellebedy, A. H., Nachbagauer, R., Jackson, K. J., Dai, Y., Han, J., Alsoussi, W. B., Davis, C. W., Stadlbauer, D., Rouphael, N., Chromikova, V., McCausland, M., Chang, C. Y., Cortese, M., Bower, M., Chennareddy, C., Schmitz, A. J., Zarnitsyna, V. I., Lai, L., Rajabhathor, A., Kazemian, C., Antia, R., Mulligan, M. J., Ward, A. B., Fremont, D. H., Boyd, S. D., Pulendran, B., Krammer, F., Ahmed, R. 2020

  Abstract

  There is a need for improved influenza vaccines. In this study we compared the antibody responses in humans after vaccination with an AS03-adjuvanted versus nonadjuvanted H5N1 avian influenza virus inactivated vaccine. Healthy young adults received two doses of either formulation 3 wk apart. We found that AS03 significantly enhanced H5 hemagglutinin (HA)-specific plasmablast and antibody responses compared to the nonadjuvanted vaccine. Plasmablast response after the first immunization was exclusively directed to the conserved HA stem region and came from memory B cells. Monoclonal antibodies (mAbs) derived from these plasmablasts had high levels of somatic hypermutation (SHM) and recognized the HA stem region of multiple influenza virus subtypes. Second immunization induced a plasmablast response to the highly variable HA head region. mAbs derived from these plasmablasts exhibited minimal SHM (naive B cell origin) and largely recognized the HA head region of the immunizing H5N1 strain. Interestingly, the antibody response to H5 HA stem region was much lower after the second immunization, and this suppression was most likely due to blocking of these epitopes by stem-specific antibodies induced by the first immunization. Taken together, these findings show that an adjuvanted influenza vaccine can substantially increase antibody responses in humans by effectively recruiting preexisting memory B cells as well as naive B cells into the response. In addition, we show that high levels of preexisting antibody can have a negative effect on boosting. These findings have implications toward the development of a universal influenza vaccine.

  View details for DOI 10.1073/pnas.1906613117

  View details for PubMedID 32661157

• Squalene-based adjuvants stimulate CD8 T cell, but not antibody responses, through a RIPK3-dependent pathway. eLife Kim, E. H., Woodruff, M. C., Grigoryan, L., Maier, B., Lee, S. H., Mandal, P., Cortese, M., Natrajan, M. S., Ravindran, R., Ma, H., Merad, M., Gitlin, A. D., Mocarski, E. S., Jacob, J., Pulendran, B. 2020; 9

  Abstract

  The squalene-based oil-in-water emulsion (SE) vaccine adjuvant MF59 has been administered to more than 100 million people in more than 30 countries, in both seasonal and pandemic influenza vaccines. Despite its wide use and efficacy, its mechanisms of action remains unclear. In this study we demonstrate that immunization of mice with MF59 or its mimetic AddaVax (AV) plus soluble antigen results in robust antigen-specific antibody and CD8 T cell responses in lymph nodes and non-lymphoid tissues. Immunization triggered rapid RIPK3-kinase dependent necroptosis in the lymph node which peaked at 6 hours, followed by a sequential wave of apoptosis. Immunization with alum plus antigen did not induce RIPK3 kinase-dependent signaling. RIPK3-dependent signaling induced by MF59 or AV was essential for cross-presentation of antigen to CD8 T cells by Batf3-dependent CD8+ DCs. Consistent with this, RIPK3-kinase deficient or Batf3 deficient mice were impaired in their ability to mount adjuvant-enhanced CD8 T cell responses. However, CD8 T cell responses were unaffected in mice deficient in MLKL, a downstream mediator of necroptosis. Surprisingly, antibody responses were unaffected in RIPK3-kinase or Batf3 deficient mice. In contrast, antibody responses were impaired by in vivo administration of the pan-caspase inhibitor Z-VAD-FMK, but normal in caspase-1 deficient mice, suggesting a contribution from apoptotic caspases, in the induction of antibody responses. These results demonstrate that squalene-based vaccine adjuvants induce antigen-specific CD8 T cell and antibody responses, through RIPK3-dependent and-independent pathways, respectively.

  View details for DOI 10.7554/eLife.52687

  View details for PubMedID 32515732

• Emerging technologies for systems vaccinology - multi-omics integration and single-cell (epi)genomic profiling. Current opinion in immunology Wimmers, F., Pulendran, B. 2020; 65: 57–64

  Abstract

  Systems vaccinology leverages high-throughput 'omics' technologies, such as transcriptomics, metabolomics, and mass cytometry, coupled with computational approaches to construct a global map of the complex processes that occur during an immune response to vaccination. Its goal is to define the mechanisms of protective immunity and to identify cellular and molecular correlates of vaccine efficacy. Emerging technological advances including integration of multi-omics datasets, and single-cell genomic and epigenomic profiling of immune responses, have invigorated systems vaccinology, and provide new insights into the mechanisms by which the cellular and molecular information underlying immune memory is stored in the innate and adaptive immune systems. Here, we will review these emerging directions in systems vaccinology, with a particular focus on the epigenome, and its impact on modulating vaccination induced memory in the innate and adaptive immune systems.

  View details for DOI 10.1016/j.coi.2020.05.001

  View details for PubMedID 32504952

• Persistence of varicella zoster virus specific plasma cells in adult human bone marrow following childhood vaccination. Journal of virology Eberhardt, C. S., Wieland, A., Nasti, T. H., Grifoni, A., Wilson, E., Schmid, D. S., Pulendran, B., Sette, A., Waller, E. K., Rouphael, N., Ahmed, R. 2020

  Abstract

  Childhood immunization with the live-attenuated varicella zoster virus (VZV) vaccine induces protective immune responses. Routine VZV vaccination started only two decades ago and thus there are few studies examining the longevity of vaccine-induced immunity. Herein, we analyzed the quantity of VZV-specific plasma cells (PCs) and CD4 T cells in the bone marrow (BM) of healthy young adults (n=15) following childhood VZV immunization. Long-lived BM resident plasma cells constitutively secrete antibodies and we detected VZV-specific PCs in the BM of all subjects. Anti-VZV plasma antibody titers correlated positively with the number of VZV-specific BM PCs. Furthermore, we quantified the number of IFNgamma-producing CD4 T cells specific for VZV glycoprotein E and all other structural and non-structural VZV proteins in both BM and blood (PBMCs). The frequency of VZV-specific IFNgamma-producing CD4 T cells was significantly higher in PBMCs compared to BM. Our study shows that VZV-specific PCs and VZV-specific CD4 memory T cells persist up to 20 years after vaccination. These findings indicate that childhood VZV vaccination can elicit long-lived immune memory responses in the bone marrow.IMPORTANCE Childhood varicella zoster virus (VZV) immunization induces immune memory responses that protect against primary VZV infection, chickenpox. In the US, routine childhood VZV vaccination has been introduced only two decades ago. Hence, there is limited information on the longevity of B and CD4 T cell memory which are both important for protection. Here we show in fifteen healthy young adults that VZV-specific B and CD4 T cell responses are detectable in bone marrow (BM) and blood up to 20 years after vaccination. Specifically, we measured antibody-secreting plasma cells in the BM and VZV-specific CD4 T cells in BM and blood. These findings suggest that childhood VZV vaccination induces long-lived immunity.

  View details for DOI 10.1128/JVI.02127-19

  View details for PubMedID 32321817

• Systems Biological Analysis of Immune Response to Influenza Vaccination. Cold Spring Harbor perspectives in medicine Cortese, M., Sherman, A. C., Rouphael, N. G., Pulendran, B. 2020

  Abstract

  The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.

  View details for DOI 10.1101/cshperspect.a038596

  View details for PubMedID 32152245

• 3M-052, a synthetic TLR-7/8 agonist, induces durable HIV-1 envelope-specific plasma cells and humoral immunity in nonhuman primates. Science immunology Kasturi, S. P., Rasheed, M. A., Havenar-Daughton, C., Pham, M., Legere, T., Sher, Z. J., Kovalenkov, Y., Gumber, S., Huang, J. Y., Gottardo, R., Fulp, W., Sato, A., Sawant, S., Stanfield-Oakley, S., Yates, N., LaBranche, C., Alam, S. M., Tomaras, G., Ferrari, G., Montefiori, D., Wrammert, J., Villinger, F., Tomai, M., Vasilakos, J., Fox, C. B., Reed, S. G., Haynes, B. F., Crotty, S., Ahmed, R., Pulendran, B. 2020; 5 (48)

  Abstract

  A fundamental challenge in vaccinology is learning how to induce durable antibody responses. Live viral vaccines induce antibody responses that last a lifetime, but those induced with subunit vaccines wane rapidly. Studies in mice and humans have established that long-lived plasma cells (LLPCs) in the bone marrow (BM) are critical mediators of durable antibody responses. Here, we present data that adjuvanting an HIV-1 clade C 1086.C-derived gp140 immunogen (Env) with a novel synthetic Toll-like receptor (TLR)-7/8 agonist named 3M-052 formulated in poly(lactic-co-glycolic)acid or PLGA nanoparticles (NPs) or with alum, either alone or in combination with a TLR-4 agonist GLA, induces notably high and persistent (up to ~1 year) frequencies of Env-specific LLPCs in the BM and serum antibody responses in rhesus macaques. Up to 36 and 18% of Env-specific cells among total IgG-secreting BM-resident plasma cells were detected at peak and termination, respectively. In contrast, adjuvanting Env with alum or GLA in NP induced significantly lower (~<100-fold) LLPC and antibody responses. Immune responses induced by 3M-052 were also significantly higher than those induced by a combination of TLR-7/8 (R848) and TLR-4 (MPL) agonists. Adjuvanting Env with 3M-052 also induced robust activation of blood monocytes, strong plasmablast responses in blood, germinal center B cells, T follicular helper (TFH) cells, and persistent Env-specific plasma cells in draining lymph nodes. Overall, these results demonstrate efficacy of 3M-052 in promoting high magnitude and durability of antibody responses via robust stimulation of innate immunity and BM-resident LLPCs.

  View details for DOI 10.1126/sciimmunol.abb1025

  View details for PubMedID 32561559

• T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nature medicine Arunachalam, P. S., Charles, T. P., Joag, V., Bollimpelli, V. S., Scott, M. K., Wimmers, F., Burton, S. L., Labranche, C. C., Petitdemange, C., Gangadhara, S., Styles, T. M., Quarnstrom, C. F., Walter, K. A., Ketas, T. J., Legere, T., Jagadeesh Reddy, P. B., Kasturi, S. P., Tsai, A., Yeung, B. Z., Gupta, S., Tomai, M., Vasilakos, J., Shaw, G. M., Kang, C. Y., Moore, J. P., Subramaniam, S., Khatri, P., Montefiori, D., Kozlowski, P. A., Derdeyn, C. A., Hunter, E., Masopust, D., Amara, R. R., Pulendran, B. 2020

  Abstract

  Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular responses may be superior. Here, we immunized macaques with an HIV envelope trimer, either alone to induce nAbs, or together with a heterologous viral vector regimen to elicit nAbs and cellular immunity, including CD8+ tissue-resident memory T cells. After ten vaginal challenges with autologous virus, protection was observed in both vaccine groups at 53.3% and 66.7%, respectively. A nAb titer >300 was generally associated with protection but in the heterologous viral vector + nAb group, titers <300 were sufficient. In this group, protection was durable as the animals resisted six more challenges 5 months later. Antigen stimulation of T cells in ex vivo vaginal tissue cultures triggered antiviral responses in myeloid and CD4+ T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.

  View details for DOI 10.1038/s41591-020-0858-8

  View details for PubMedID 32393800

• Systems Biological Approaches for Mucosal Vaccine Development MUCOSAL VACCINES: INNOVATION FOR PREVENTING INFECTIOUS DISEASES, 2ND EDITION Pulendran, B., Kiyono, H., Pascual, D. W. 2020: 753–72

  View details for DOI 10.1016/B978-0-12-811924-2.00045-6

  View details for Web of Science ID 000538933600046

• Vaccine innovations for emerging infectious diseases-a symposium report. Annals of the New York Academy of Sciences Cable, J., Srikantiah, P., Crowe, J. E., Pulendran, B., Hill, A., Ginsberg, A., Koff, W., Mathew, A., Ng, T., Jansen, K., Glenn, G., Permar, S., Wilson, I., Weiner, D. B., Weissman, D., Rappuoli, R. 2019

  Abstract

  Vaccines have been incredibly successful at stemming the morbidity and mortality of infectious diseases worldwide. However, there are still no effective vaccines for many serious and potentially preventable infectious diseases. Advances in vaccine technology, including new delivery methods and adjuvants, as well as progress in systems biology and an increased understanding of the human immune system, hold the potential to address these issues. In addition, maternal immunization has opened an avenue to address infectious diseases in neonates and very young infants. This report summarizes the presentations from a 1-day symposium at the New York Academy of Sciences entitled "Innovative Vaccines against Resistant Infectious Diseases and Emerging Threats," held on May 20, 2019.

  View details for DOI 10.1111/nyas.14235

  View details for PubMedID 31659752

• N6-Methyladenosine Modification Controls Circular RNA Immunity. Molecular cell Chen, Y. G., Chen, R., Ahmad, S., Verma, R., Kasturi, S. P., Amaya, L., Broughton, J. P., Kim, J., Cadena, C., Pulendran, B., Hur, S., Chang, H. Y. 2019

  Abstract

  Circular RNAs (circRNAs) are prevalent in eukaryotic cells and viral genomes. Mammalian cells possess innate immunity to detect foreign circRNAs, but the molecular basis of self versus foreign identity in circRNA immunity is unknown. Here, we show that N6-methyladenosine (m6A) RNA modification on human circRNAs inhibits innate immunity. Foreign circRNAs are potent adjuvants to induce antigen-specific Tcell activation, antibody production, and anti-tumor immunity invivo, and m6A modification abrogates immune gene activation and adjuvant activity. m6A reader YTHDF2 sequesters m6A-circRNA and is essential for suppression of innate immunity. Unmodified circRNA, but not m6A-modified circRNA, directly activates RNA pattern recognition receptor RIG-I in the presence of lysine-63-linked polyubiquitin chain to cause filamentation of the adaptor protein MAVS and activation of the downstream transcription factor IRF3. CircRNA immunity has considerable parallel to prokaryotic DNA restriction modification system that transforms nucleic acid chemical modification into organismal innate immunity.

  View details for DOI 10.1016/j.molcel.2019.07.016

  View details for PubMedID 31474572

• Understanding the immunology of the Zostavax shingles vaccine CURRENT OPINION IN IMMUNOLOGY Sullivan, N. L., Eberhardt, C. S., Wieland, A., Vora, K. A., Pulendran, B., Ahmed, R. 2019; 59: 25–30

  View details for DOI 10.1016/j.coi.2019.02.005

  View details for Web of Science ID 000491610600006

• ImmuneRegulation: a web-based tool for identifying human immune regulatory elements NUCLEIC ACIDS RESEARCH Kalayci, S., Selvan, M., Ramos, I., Cotsapas, C., Harris, E., Kim, E., Montgomery, R. R., Poland, G., Pulendran, B., Tsang, J. S., Klein, R. J., Gumus, Z. H. 2019; 47 (W1): W142–W150

  Abstract

  Humans vary considerably both in their baseline and activated immune phenotypes. We developed a user-friendly open-access web portal, ImmuneRegulation, that enables users to interactively explore immune regulatory elements that drive cell-type or cohort-specific gene expression levels. ImmuneRegulation currently provides the largest centrally integrated resource on human transcriptome regulation across whole blood and blood cell types, including (i) ∼43,000 genotyped individuals with associated gene expression data from ∼51,000 experiments, yielding genetic variant-gene expression associations on ∼220 million eQTLs; (ii) 14 million transcription factor (TF)-binding region hits extracted from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations. Users can interactively explore associations between queried gene(s) and their regulators (cis-eQTLs, trans-eQTLs or TFs) across multiple cohorts and studies. These regulators may explain genotype-dependent gene expression variations and be critical in selecting the ideal cohorts or cell types for follow-up studies or in developing predictive models. Overall, ImmuneRegulation significantly lowers the barriers between complex immune regulation data and researchers who want rapid, intuitive and high-quality access to the effects of regulatory elements on gene expression in multiple studies to empower investigators in translating these rich data into biological insights and clinical applications, and is freely available at https://immuneregulation.mssm.edu.

  View details for DOI 10.1093/nar/gkz450

  View details for Web of Science ID 000475901600021

  View details for PubMedID 31114925

  View details for PubMedCentralID PMC6602512

• Understanding the immunology of the Zostavax shingles vaccine. Current opinion in immunology Sullivan, N. L., Eberhardt, C. S., Wieland, A., Vora, K. A., Pulendran, B., Ahmed, R. 2019; 59: 25–30

  Abstract

  Zostavax is a live-attenuated varicella zoster virus (VZV) vaccine recommended for use in adults >50 years of age to prevent shingles. The main risk factor for the development of shingles is age, which correlates with decreasing cell-mediated immunity. These data suggest a predominant role of T cell immunity in controlling VZV latency. However, other components of the immune system may also contribute. In this review, we will discuss how the immune system responds to Zostavax, focusing on recent studies examining innate immunity, transcriptomics, metabolomics, cellular, and humoral immunity.

  View details for PubMedID 30970291

• Vaccine induction of antibodies and tissue-resident CD8(+) T cells enhances protection against mucosal SHIV-infection in young macaques JCI INSIGHT Petitdemange, C., Kasturi, S., Kozlowski, P. A., Nabi, R., Quarnstrom, C. F., Reddy, P., Derdeyn, C. A., Spicer, L. M., Patel, P., Legere, T., Kovalenkov, Y. O., Labranche, C. C., Villinger, F., Tomai, M., Vasilakos, J., Haynes, B., Kang, C., Gibbs, J. S., Yewdell, J. W., Barouch, D., Wrammert, J., Montefiori, D., Hunter, E., Amara, R. R., Masopust, D., Pulendran, B. 2019; 4 (4)

  View details for DOI 10.1172/jci.insight.126047

  View details for Web of Science ID 000459354800020

• West Nile Virus Infection Blocks Inflammatory Response and T Cell Costimulatory Capacity of Human Monocyte-Derived Dendritic Cells. Journal of virology Zimmerman, M. G., Bowen, J. R., McDonald, C. E., Pulendran, B., Suthar, M. S. 2019

  Abstract

  West Nile virus (WNV) is a neurotropic flavivirus and the leading cause of mosquito-borne encephalitis in the United States. Recent studies in humans have found that dysfunctional T cell responses strongly correlate with development of severe WNV neuroinvasive disease. However, the contributions of human dendritic cells (DCs) in priming WNV-specific T cell immunity remains poorly understood. Here, we demonstrate that human monocyte derived DCs (moDCs) support productive viral replication following infection with a pathogenic strain of WNV. Antiviral effector gene transcription was strongly induced during the log-phase viral growth, while secretion of type I interferons (IFN) occurred with delayed kinetics. Activation of RIG-I like receptor (RLR) or type I IFN signaling prior to log-phase viral growth significantly diminished viral replication, suggesting that early activation of antiviral programs can block WNV infection. In contrast to the induction of antiviral responses, WNV infection did not promote transcription or secretion of pro-inflammatory (IL-6, GM-CSF, CCL3, CCL5, CXCL9) or T cell modulatory cytokines (IL-4, IL-12, IL-15). There was also minimal induction of molecules associated with antigen presentation and T cell priming, including the co-stimulatory molecules CD80, CD86, and CD40. Functionally, WNV-infected moDCs dampened allogenic CD4 and CD8 T cell activation and proliferation. Combined, we propose a model where WNV subverts human DC activation to compromise priming of WNV-specific T cell immunity.IMPORTANCE West Nile virus (WNV) is an encephalitic flavivirus that remains endemic in the United States. Previous studies have found dysfunctional T cell responses correlate to severe disease outcomes during human WNV infection. Here, we sought to better understand the ability of WNV to program human dendritic cells (DCs) to prime WNV-specific T cell responses. While productive infection of monocyte-derived DCs activated antiviral and type I interferon responses, molecules associated with inflammation and programming of T cells were minimally induced. Functionally, WNV-infected DCs dampened T cell activation and proliferation during an allogeneic response. Combined, our data supports a model where WNV infection of human DCs compromises WNV-specific T cell immunity.

  View details for DOI 10.1128/JVI.00664-19

  View details for PubMedID 31534040

• Systems Vaccinology for a Live Attenuated Tularemia Vaccine Reveals Unique Transcriptional Signatures That Predict Humoral and Cellular Immune Responses. Vaccines Natrajan, M. S., Rouphael, N., Lai, L., Kazmin, D., Jensen, T. L., Weiss, D. S., Ibegbu, C., Sztein, M. B., Hooper, W. F., Hill, H., Anderson, E. J., Johnson, R., Sanz, P., Pulendran, B., Goll, J. B., Mulligan, M. J. 2019; 8 (1)

  Abstract

  Background: Tularemia is a potential biological weapon due to its high infectivity and ease of dissemination. This study aimed to characterize the innate and adaptive responses induced by two different lots of a live attenuated tularemia vaccine and compare them to other well-characterized viral vaccine immune responses. Methods: Microarray analyses were performed on human peripheral blood mononuclear cells (PBMCs) to determine changes in transcriptional activity that correlated with changes detected by cellular phenotyping, cytokine signaling, and serological assays. Transcriptional profiles after tularemia vaccination were compared with yellow fever [YF-17D], inactivated [TIV], and live attenuated [LAIV] influenza. Results: Tularemia vaccine lots produced strong innate immune responses by Day 2 after vaccination, with an increase in monocytes, NK cells, and cytokine signaling. T cell responses peaked at Day 14. Changes in gene expression, including upregulation of STAT1, GBP1, and IFIT2, predicted tularemia-specific antibody responses. Changes in CCL20 expression positively correlated with peak CD8+ T cell responses, but negatively correlated with peak CD4+ T cell activation. Tularemia vaccines elicited gene expression signatures similar to other replicating vaccines, inducing early upregulation of interferon-inducible genes. Conclusions: A systems vaccinology approach identified that tularemia vaccines induce a strong innate immune response early after vaccination, similar to the response seen after well-studied viral vaccines, and produce unique transcriptional signatures that are strongly correlated to the induction of T cell and antibody responses.

  View details for DOI 10.3390/vaccines8010004

  View details for PubMedID 31878161

• Vaccine induction of antibodies and tissue-resident CD8+ T cells enhances protection against mucosal SHIV-infection in young macaques. JCI insight Petitdemange, C., Kasturi, S. P., Kozlowski, P. A., Nabi, R., Quarnstrom, C. F., Reddy, P. B., Derdeyn, C. A., Spicer, L. M., Patel, P., Legere, T., Kovalenkov, Y. O., Labranche, C. C., Villinger, F., Tomai, M., Vasilakos, J., Haynes, B., Kang, C. Y., Gibbs, J. S., Yewdell, J. W., Barouch, D., Wrammert, J., Montefiori, D., Hunter, E., Amara, R. R., Masopust, D., Pulendran, B. 2019; 4 (4)

  Abstract

  Antibodies and cytotoxic T cells represent 2 arms of host defense against pathogens. We hypothesized that vaccines that induce both high-magnitude CD8+ T cell responses and antibody responses might confer enhanced protection against HIV. To test this hypothesis, we immunized 3 groups of nonhuman primates: (a) Group 1, which includes sequential immunization regimen involving heterologous viral vectors (HVVs) comprising vesicular stomatitis virus, vaccinia virus, and adenovirus serotype 5-expressing SIVmac239 Gag; (b) Group 2, which includes immunization with a clade C HIV-1 envelope (Env) gp140 protein adjuvanted with nanoparticles containing a TLR7/8 agonist (3M-052); and (c) Group 3, which includes a combination of both regimens. Immunization with HVVs induced very high-magnitude Gag-specific CD8+ T cell responses in blood and tissue-resident CD8+ memory T cells in vaginal mucosa. Immunization with 3M-052 adjuvanted Env protein induced robust and persistent antibody responses and long-lasting innate responses. Despite similar antibody titers in Groups 2 and 3, there was enhanced protection in the younger animals in Group 3, against intravaginal infection with a heterologous SHIV strain. This protection correlated with the magnitude of the serum and vaginal Env-specific antibody titers on the day of challenge. Thus, vaccination strategies that induce both CD8+ T cell and antibody responses can confer enhanced protection against infection.

  View details for PubMedID 30830870

• Immunology taught by vaccines. Science (New York, N.Y.) Pulendran, B. 2019; 366 (6469): 1074–75

  View details for DOI 10.1126/science.aau6975

  View details for PubMedID 31780544

• Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans. Cell Hagan, T., Cortese, M., Rouphael, N., Boudreau, C., Linde, C., Maddur, M. S., Das, J., Wang, H., Guthmiller, J., Zheng, N. Y., Huang, M., Uphadhyay, A. A., Gardinassi, L., Petitdemange, C., McCullough, M. P., Johnson, S. J., Gill, K., Cervasi, B., Zou, J., Bretin, A., Hahn, M., Gewirtz, A. T., Bosinger, S. E., Wilson, P. C., Li, S., Alter, G., Khurana, S., Golding, H., Pulendran, B. 2019; 178 (6): 1313–28.e13

  Abstract

  Emerging evidence indicates a central role for the microbiome in immunity. However, causal evidence in humans is sparse. Here, we administered broad-spectrum antibiotics to healthy adults prior and subsequent to seasonal influenza vaccination. Despite a 10,000-fold reduction in gut bacterial load and long-lasting diminution in bacterial diversity, antibody responses were not significantly affected. However, in a second trial of subjects with low pre-existing antibody titers, there was significant impairment in H1N1-specific neutralization and binding IgG1 and IgA responses. In addition, in both studies antibiotics treatment resulted in (1) enhanced inflammatory signatures (including AP-1/NR4A expression), observed previously in the elderly, and increased dendritic cell activation; (2) divergent metabolic trajectories, with a 1,000-fold reduction in serum secondary bile acids, which was highly correlated with AP-1/NR4A signaling and inflammasome activation. Multi-omics integration revealed significant associations between bacterial species and metabolic phenotypes, highlighting a key role for the microbiome in modulating human immunity.

  View details for DOI 10.1016/j.cell.2019.08.010

  View details for PubMedID 31491384

• STAT5: A Target of Antagonism by Neurotropic Flaviviruses. Journal of virology Zimmerman, M. G., Bowen, J. R., McDonald, C. E., Young, E., Baric, R. S., Pulendran, B., Suthar, M. S. 2019

  Abstract

  Flaviviruses are a diverse group of arthropod-borne viruses responsible for numerous significant public health threats; therefore, understanding the interactions between these viruses and the human immune response remains vital. West Nile virus (WNV) and Zika virus (ZIKV) infect human DCs and can block antiviral immune responses in DCs. Previously, we used mRNA sequencing and weighted gene co-expression network analysis (WGCNA) to define molecular signatures of antiviral DC responses following activation of innate immune signaling (RIG-I, MDA5, or type I IFN signaling) or infection with WNV. Using this approach, we found that several genes involved in T cell co-signaling and antigen processing were not enriched in DCs during WNV infection. Using cis-regulatory sequence analysis, STAT5 was identified as a regulator of DC activation and immune responses downstream of innate immune signaling that was not activated during either WNV or ZIKV infection. Mechanistically, WNV and ZIKV actively blocked STAT5 phosphorylation downstream of RIG-I, IFNβ, and IL-4, but not GM-CSF signaling. Unexpectedly, dengue virus serotypes 1-4 (DENV1-4) and the yellow fever 17D vaccine strain (YFV-17D) did not antagonize STAT5 phosphorylation. In contrast to WNV, ZIKV inhibited JAK1 and TYK2 phosphorylation following type I IFN treatment, suggesting divergent mechanisms used by these viruses to inhibit STAT5 activation. Combined, these findings identify STAT5 as a target of antagonism by specific pathogenic flaviviruses to subvert the immune response in infected DCs.IMPORTANCE Flaviviruses are a diverse group of insect-borne viruses responsible for numerous significant public health threats. Previously, we used a computational biology approach to define molecular signatures of antiviral DC responses following activation of innate immune signaling or infection with West Nile virus (WNV). In this work, we identify STAT5 as a regulator of DC activation and antiviral immune responses downstream of innate immune signaling that was not activated during either WNV or Zika virus (ZIKV) infection. WNV and ZIKV actively blocked STAT5 phosphorylation downstream of RIG-I, IFNβ, and IL-4, but not GM-CSF signaling. However, other related flaviviruses, dengue virus serotypes 1-4 and yellow fever 17D vaccine strain, did not antagonize STAT5 phosphorylation. Mechanistically, WNV and ZIKV showed differential inhibition of Jak kinases upstream of STAT5, suggesting divergent countermeasures to inhibit STAT5 activation. Combined, these findings identify STAT5 as a target of antagonism by specific pathogenic flaviviruses to subvert antiviral immune responses in human DCs.

  View details for DOI 10.1128/JVI.00665-19

  View details for PubMedID 31534033

• B Cell Competition for Restricted T Cell Help Suppresses Rare-Epitope Responses CELL REPORTS Woodruff, M., Kim, E., Luo, W., Pulendran, B. 2018; 25 (2): 321-+

  Abstract

  The immune system responds preferentially to particular antigenic-epitopes contained within complex immunogens, such as proteins or microbes. This poorly understood phenomenon, termed "immunodominance," remains an obstacle to achieving polyvalent immune responses against multiple antigenic-epitopes through vaccination. We observed profound suppression in the hapten-specific antibody response in mice immunized with hapten-protein conjugate, mixed with an excess of protein, relative to that in mice immunized with hapten-protein alone. The suppression was robust (100-fold and 10-fold with a 10- or 2-fold excess of protein, respectively), stable over a 6-log range in antigen dose, observed within 10 days of vaccination, and resistant to boosting and adjuvants. Furthermore, there were reduced frequencies of antigen-specific germinal-center B cells and long-lived bone-marrow plasma cells. The mechanism of this "antigen-competition" was mediated largely by early access to T-helper cells. These results offer mechanistic insights into B cell competition during an immune response and suggest vaccination strategies against HIV, influenza, and dengue.

  View details for PubMedID 30304673

• Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters JOURNAL OF CLINICAL INVESTIGATION Antunes, R., Babor, M., Carpenter, C., Khalil, N., Cortese, M., Mentzer, A. J., Seumois, G., Petro, C. D., Purcell, L. A., Vijayanand, P., Crotty, S., Pulendran, B., Peters, B., Sette, A. 2018; 128 (9): 3853–65

  Abstract

  In the mid-1990s, whole-cell pertussis (wP) vaccines were associated with local and systemic adverse events that prompted their replacement with acellular pertussis (aP) vaccines in many high-income countries. In the past decade, rates of pertussis disease have increased in children receiving only aP vaccines. We compared the immune responses to aP boosters in individuals who received their initial doses with either wP or aP vaccines using activation-induced marker (AIM) assays. Specifically, we examined pertussis-specific memory CD4+ T cell responses ex vivo, highlighting a type 2/Th2 versus type 1/Th1 and Th17 differential polarization as a function of childhood vaccination. Remarkably, after a contemporary aP booster, cells from donors originally primed with aP were (a) associated with increased IL-4, IL-5, IL-13, IL-9, and TGF-β and decreased IFN-γ and IL-17 production, (b) defective in their ex vivo capacity to expand memory cells, and (c) less capable of proliferating in vitro. These differences appeared to be T cell specific, since equivalent increases of antibody titers and plasmablasts after aP boost were seen in both groups. In conclusion, our data suggest that there are long-lasting effects and differences in polarization and proliferation of T cell responses in adults originally vaccinated with aP compared with those that initially received wP, despite repeated acellular boosters.

  View details for PubMedID 29920186

  View details for PubMedCentralID PMC6118631

• Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? From Data to Understanding through Systems Biology COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY Hagan, T., Pulendran, B. 2018; 10 (8)

  View details for DOI 10.1101/cshperspecta028894

  View details for Web of Science ID 000440493200007

• BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data GENOME MEDICINE Upadhyay, A. A., Kauffman, R. C., Wolabaugh, A. N., Cho, A., Patel, N. B., Reiss, S. M., Havenar-Daughton, C., Dawoud, R. A., Tharp, G. K., Sanz, I., Pulendran, B., Crotty, S., Lee, F., Wrammert, J., Bosinger, S. E. 2018; 10: 20

  Abstract

  B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer.BALDR is available at https://github.com/BosingerLab/BALDR .

  View details for PubMedID 29558968

• The potential of the microbiota to influence vaccine responses JOURNAL OF LEUKOCYTE BIOLOGY Lynn, D. J., Pulendran, B. 2018; 103 (2): 225–31

  Abstract

  After clean water, vaccines are the primary public health intervention providing protection against serious infectious diseases. Antigen-specific antibody-mediated responses play a critical role in the protection conferred by vaccination; however these responses are highly variable among individuals. In addition, vaccine immunogenicity is frequently impaired in developing world populations, for reasons that are poorly understood. Although the factors that are associated with interindividual variation in vaccine responses are likely manifold, emerging evidence from mouse models and studies in human populations now suggests that the gut microbiome plays a key role in shaping systemic immune responses to both orally and parenterally administered vaccines. Herein, we review the evidence to date that the microbiota can influence vaccine responses and discuss the potential mechanisms through which these effects may be mediated. In addition, we highlight the gaps in this evidence and suggest future directions for research.

  View details for PubMedID 28864446

  View details for PubMedCentralID PMC5921907

• Epitopes for neutralizing antibodies induced by HIV-1 envelope glycoprotein BG505 SOSIP trimers in rabbits and macaques PLOS PATHOGENS Klasse, P. J., Ketas, T. J., Cottrell, C. A., Ozorowski, G., Debnath, G., Camara, D., Francomano, E., Pugach, P., Ringe, R. P., LaBranche, C. C., van Gils, M. J., Bricault, C. A., Barouch, D. H., Crotty, S., Silvestri, G., Kasturi, S., Pulendran, B., Wilson, I. A., Montefiori, D. C., Sanders, R. W., Ward, A. B., Moore, J. P. 2018; 14 (2): e1006913

  Abstract

  The native-like, soluble SOSIP.664 trimer based on the BG505 clade A env gene of HIV-1 is immunogenic in various animal species, of which the most studied are rabbits and rhesus macaques. The trimer induces autologous neutralizing antibodies (NAbs) consistently but at a wide range of titers and with incompletely determined specificities. A precise delineation of immunogenic neutralization epitopes on native-like trimers could help strategies to extend the NAb response to heterologous HIV-1 strains. One autologous NAb epitope on the BG505 Env trimer is known to involve residues lining a hole in the glycan shield that is blocked by adding a glycan at either residue 241 or 289. This glycan-hole epitope accounts for the NAb response of most trimer-immunized rabbits but not for that of a substantial subset. Here, we have used a large panel of mutant BG505 Env-pseudotyped viruses to define additional sites. A frequently immunogenic epitope in rabbits is blocked by adding a glycan at residue 465 near the junction of the gp120 V5 loop and β24 strand and is influenced by amino-acid changes in the structurally nearby C3 region. We name this new site the "C3/465 epitope". Of note is that the C3 region was under selection pressure in the infected infant from whom the BG505 virus was isolated. A third NAb epitope is located in the V1 region of gp120, although it is rarely immunogenic. In macaques, NAb responses induced by BG505 SOSIP trimers are more often directed at the C3/465 epitope than the 241/289-glycan hole.

  View details for DOI 10.1371/journal.ppat.1006913

  View details for Web of Science ID 000426477000047

  View details for PubMedID 29474444

  View details for PubMedCentralID PMC5841823

• Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? From Data to Understanding through Systems Biology. Cold Spring Harbor perspectives in biology Hagan, T., Pulendran, B. 2018; 10 (8)

  Abstract

  The advent of high-throughput "omics" technologies, combined with the computational and statistical methods necessary to analyze such data, have revolutionized biology, enabling a global view of the complex molecular processes and interactions that occur within a biological system. Such systems-based approaches have begun to be used in the evaluation of immune responses to vaccination, with the promise of identifying predictive biomarkers capable of rapidly evaluating vaccine efficacy, transforming our understanding of the immune mechanisms responsible for protective responses to vaccination and contributing to a new generation of rationally designed vaccines. Here we present our opinion that systems biology does indeed have a critical role in the future of vaccinology. Such approaches have shown potential in identifying transcriptional and cellular signatures of responsiveness to vaccination using diverse vaccines, adjuvants, and human populations. These findings, coupled with further mechanistic evaluation in animal models, will guide development of targeted vaccine and adjuvant formulations designed to optimally induce protective responses in populations of differing immune status.

  View details for PubMedID 29038113

  View details for PubMedCentralID PMC5902663

• AS03-and MF59-Adjuvanted influenza vaccines in Children FRONTIERS IN IMMUNOLOGY Wilkins, A. L., Kazmin, D., Napolitani, G., Clutterbuck, E. A., Pulendran, B., Siegrist, C., Pollard, A. J. 2017; 8: 1760

  Abstract

  Influenza is a major cause of respiratory disease leading to hospitalization in young children. However, seasonal trivalent influenza vaccines (TIVs) have been shown to be ineffective and poorly immunogenic in this population. The development of live-attenuated influenza vaccines and adjuvanted vaccines are important advances in the prevention of influenza in young children. The oil-in-water emulsions MF59 and adjuvant systems 03 (AS03) have been used as adjuvants in both seasonal adjuvanted trivalent influenza vaccines (ATIVs) and pandemic monovalent influenza vaccines. Compared with non-adjuvanted vaccine responses, these vaccines induce a more robust and persistent antibody response for both homologous and heterologous influenza strains in infants and young children. Evidence of a significant improvement in vaccine efficacy with these adjuvanted vaccines resulted in the use of the monovalent (A/H1N1) AS03-adjuvanted vaccine in children in the 2009 influenza pandemic and the licensure of the seasonal MF59 ATIV for children aged 6 months to 2 years in Canada. The mechanism of action of MF59 and AS03 remains unclear. Adjuvants such as MF59 induce proinflammatory cytokines and chemokines, including CXCL10, but independently of type-1 interferon. This proinflammatory response is associated with improved recruitment, activation and maturation of antigen presenting cells at the injection site. In young children MF59 ATIV produced more homogenous and robust transcriptional responses, more similar to adult-like patterns, than did TIV. Early gene signatures characteristic of the innate immune response, which correlated with antibody titers were also identified. Differences were detected when comparing child and adult responses including opposite trends in gene set enrichment at day 3 postvaccination and, unlike adult data, a lack of correlation between magnitude of plasmablast response at day 7 and antibody titers at day 28 in children. These insights show the utility of novel approaches in understanding new adjuvants and their importance for developing improved influenza vaccines for children.

  View details for PubMedID 29326687

• Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses SCIENCE IMMUNOLOGY Avey, S., Cheung, F., Fermin, D., Frelinger, J., Gaujoux, R., Gottardo, R., Khatri, P., Kleinstein, S. H., Kotliarov, Y., Meng, H., Sauteraud, R., Shen-Orr, S. S., Tsang, J. S., Vallania, F., Anguiano, E., Baisch, J., Baldwin, N., Belshe, R. B., Blevins, T. P., Chaussabel, D., Davis, M. M., Fikrig, E., Grill, D. E., Hafler, D. A., Henrich, E., Joshi, S. R., Kaech, S. M., Kennedy, R. B., Mohanty, S., Montgomery, R. R., Oberg, A. L., Obermoser, G., Ovsyannikova, I. G., Palucka, A., Pascual, V., Poland, G. A., Pulendran, B., Reinherz, E. L., Shaw, A. C., Siconolfi, B., Stuart, K. D., Tsang, S., Ueda, I., Wilson, J., Zapata, H. J., HIPC-CHI Signatures Project Team, HIPC-I Consortium 2017; 2 (14)

  View details for Web of Science ID 000434326500001

• Metabolic Phenotypes of Response to Vaccination in Humans CELL Li, S., Sullivan, N. L., Rouphael, N., Yu, T., Banton, S., Maddur, M. S., McCausland, M., Chiu, C., Canniff, J., Dubey, S., Liu, K., ViLinh Tran, V., Hagan, T., Duraisingham, S., Wieland, A., Mehta, A. K., Whitaker, J. A., Subramaniam, S., Jones, D. P., Sette, A., Vora, K., Weinberg, A., Mulligan, M. J., Nakaya, H. I., Levin, M., Ahmed, R., Pulendran, B. 2017; 169 (5): 862-?

  Abstract

  Herpes zoster (shingles) causes significant morbidity in immune compromised hosts and older adults. Whereas a vaccine is available for prevention of shingles, its efficacy declines with age. To help to understand the mechanisms driving vaccinal responses, we constructed a multiscale, multifactorial response network (MMRN) of immunity in healthy young and older adults immunized with the live attenuated shingles vaccine Zostavax. Vaccination induces robust antigen-specific antibody, plasmablasts, and CD4+ T cells yet limited CD8+ T cell and antiviral responses. The MMRN reveals striking associations between orthogonal datasets, such as transcriptomic and metabolomics signatures, cell populations, and cytokine levels, and identifies immune and metabolic correlates of vaccine immunity. Networks associated with inositol phosphate, glycerophospholipids, and sterol metabolism are tightly coupled with immunity. Critically, the sterol regulatory binding protein 1 and its targets are key integrators of antibody and T follicular cell responses. Our approach is broadly applicable to study human immunity and can help to identify predictors of efficacy as well as mechanisms controlling immunity to vaccination.

  View details for DOI 10.1016/j.cell.2017.04.026

  View details for Web of Science ID 000401515900012

  View details for PubMedID 28502771

  View details for PubMedCentralID PMC5711477

• Systems analysis of protective immune responses to RTS, S malaria vaccination in humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kazmin, D., Nakaya, H. I., Lee, E. K., Johnson, M. J., van der Most, R., van den Berg, R. A., Ballou, W. R., Jongert, E., Wille-Reece, U., Ockenhouse, C., Aderem, A., Zak, D. E., Sadoff, J., Hendriks, J., Wrammert, J., Ahmed, R., Pulendran, B. 2017; 114 (9): 2425-2430

  Abstract

  RTS,S is an advanced malaria vaccine candidate and confers significant protection against Plasmodium falciparum infection in humans. Little is known about the molecular mechanisms driving vaccine immunity. Here, we applied a systems biology approach to study immune responses in subjects receiving three consecutive immunizations with RTS,S (RRR), or in those receiving two immunizations of RTS,S/AS01 following a primary immunization with adenovirus 35 (Ad35) (ARR) vector expressing circumsporozoite protein. Subsequent controlled human malaria challenge (CHMI) of the vaccinees with Plasmodium-infected mosquitoes, 3 wk after the final immunization, resulted in ∼50% protection in both groups of vaccinees. Circumsporozoite protein (CSP)-specific antibody titers, prechallenge, were associated with protection in the RRR group. In contrast, ARR-induced lower antibody responses, and protection was associated with polyfunctional CD4+ T-cell responses 2 wk after priming with Ad35. Molecular signatures of B and plasma cells detected in PBMCs were highly correlated with antibody titers prechallenge and protection in the RRR cohort. In contrast, early signatures of innate immunity and dendritic cell activation were highly associated with protection in the ARR cohort. For both vaccine regimens, natural killer (NK) cell signatures negatively correlated with and predicted protection. These results suggest that protective immunity against P. falciparum can be achieved via multiple mechanisms and highlight the utility of systems approaches in defining molecular correlates of protection to vaccination.

  View details for DOI 10.1073/pnas.1621489114

  View details for Web of Science ID 000395101200083

  View details for PubMedID 28193898

  View details for PubMedCentralID PMC5338562

• Adjuvanting a Simian Immunodeficiency Virus Vaccine with Toll-Like Receptor Ligands Encapsulated in Nanoparticles Induces Persistent Antibody Responses and Enhanced Protection in TRIM5 alpha Restrictive Macaques JOURNAL OF VIROLOGY Kasturi, S. P., Kozlowski, P. A., Nakaya, H. I., Burger, M. C., Russo, P., Pham, M., Kovalenkov, Y., Silveira, E. L., Havenar-Daughton, C., Burton, S. L., Kilgore, K. M., Johnson, M. J., Nabi, R., Legere, T., Sher, Z. J., Chen, X., Amara, R. R., Hunter, E., Bosinger, S. E., Spearman, P., Crotty, S., Villinger, F., Derdeyn, C. A., Wrammert, J., Pulendran, B. 2017; 91 (4)

  Abstract

  Our previous work has shown that antigens adjuvanted with ligands specific for Toll-like receptor 4 (TLR4) and TLR7/8 encapsulated in poly(lactic-co-glycolic) acid (PLGA)-based nanoparticles (NPs) induce robust and durable immune responses in mice and macaques. We investigated the efficacy of these NP adjuvants in inducing protective immunity against simian immunodeficiency virus (SIV). Rhesus macaques (RMs) were immunized with NPs containing TLR4 and TLR7/8 agonists mixed with soluble recombinant SIVmac239-derived envelope (Env) gp140 and Gag p55 (protein) or with virus-like particles (VLPs) containing SIVmac239 Env and Gag. NP-adjuvanted vaccines induced robust innate responses, antigen-specific antibody responses of a greater magnitude and persistence, and enhanced plasmablast responses compared to those achieved with alum-adjuvanted vaccines. NP-adjuvanted vaccines induced antigen-specific, long-lived plasma cells (LLPCs), which persisted in the bone marrow for several months after vaccination. NP-adjuvanted vaccines induced immune responses that were associated with enhanced protection against repeated low-dose, intravaginal challenges with heterologous SIVsmE660 in animals that carried TRIM5α restrictive alleles. The protection induced by immunization with protein-NP correlated with the prechallenge titers of Env-specific IgG antibodies in serum and vaginal secretions. However, no such correlate was apparent for immunization with VLP-NP or alum as the adjuvant. Transcriptional profiling of peripheral blood mononuclear cells isolated within the first few hours to days after primary vaccination revealed that NP-adjuvanted vaccines induced a molecular signature similar to that induced by the live attenuated yellow fever viral vaccine. This systems approach identified early blood transcriptional signatures that correlate with Env-specific antibody responses in vaginal secretions and protection against infection. These results demonstrate the adjuvanticity of the NP adjuvant in inducing persistent and protective antibody responses against SIV in RMs with implications for the design of vaccines against human immunodeficiency virus (HIV).The results of the RV144 HIV vaccine trial, which demonstrated a rapid waning of protective immunity with time, have underscored the need to develop strategies to enhance the durability of protective immune responses. Our recent work in mice has highlighted the capacity of nanoparticle-encapsulated TLR ligands (NP) to induce potent and durable antibody responses that last a lifetime in mice. In the present study, we evaluated the ability of these NP adjuvants to promote robust and durable protective immune responses against SIV in nonhuman primates. Our results demonstrate that immunization of rhesus macaques with NP adjuvants mixed with soluble SIV Env or a virus-like particle form of Env (VLP) induces potent and durable Env-specific antibody responses in the serum and in vaginal secretions. These responses were superior to those induced by alum adjuvant, and they resulted in enhanced protection against a low-dose intravaginal challenge with a heterologous strain of SIV in animals with TRIM5a restrictive alleles. These results highlight the potential for such NP TLR L adjuvants in promoting robust and durable antibody responses against HIV in the next generation of HIV immunogens currently being developed.

  View details for DOI 10.1128/JVI.01844-16

  View details for Web of Science ID 000393883300015

  View details for PubMedID 27928002

  View details for PubMedCentralID PMC5286877

• mTOR regulates metabolic adaptation of APCs in the lung and controls the outcome of allergic inflammation. Science (New York, N.Y.) Sinclair, C., Bommakanti, G., Gardinassi, L., Loebbermann, J., Johnson, M. J., Hakimpour, P., Hagan, T., Benitez, L., Todor, A., Machiah, D., Oriss, T., Ray, A., Bosinger, S., Ravindran, R., Li, S., Pulendran, B. 2017; 357 (6355): 1014–21

  Abstract

  Antigen-presenting cells (APCs) occupy diverse anatomical tissues, but their tissue-restricted homeostasis remains poorly understood. Here, working with mouse models of inflammation, we found that mechanistic target of rapamycin (mTOR)-dependent metabolic adaptation was required at discrete locations. mTOR was dispensable for dendritic cell (DC) homeostasis in secondary lymphoid tissues but necessary to regulate cellular metabolism and accumulation of CD103+ DCs and alveolar macrophages in lung. Moreover, while numbers of mTOR-deficient lung CD11b+ DCs were not changed, they were metabolically reprogrammed to skew allergic inflammation from eosinophilic T helper cell 2 (TH2) to neutrophilic TH17 polarity. The mechanism for this change was independent of translational control but dependent on inflammatory DCs, which produced interleukin-23 and increased fatty acid oxidation. mTOR therefore mediates metabolic adaptation of APCs in distinct tissues, influencing the immunological character of allergic inflammation.

  View details for PubMedID 28798047

  View details for PubMedCentralID PMC5746055

• Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response CELL HOST & MICROBE Reese, T. A., Bi, K., Kambal, A., Filali-Mouhim, A., Beura, L. K., Burger, M. C., Pulendran, B., Sekaly, R., Jameson, S. C., Masopust, D., Haining, W. N., Virgin, H. W. 2016; 19 (5): 713-719

  Abstract

  Immune responses differ between laboratory mice and humans. Chronic infection with viruses and parasites are common in humans, but are absent in laboratory mice, and thus represent potential contributors to inter-species differences in immunity. To test this, we sequentially infected laboratory mice with herpesviruses, influenza, and an intestinal helminth and compared their blood immune signatures to mock-infected mice before and after vaccination against yellow fever virus (YFV-17D). Sequential infection altered pre- and post-vaccination gene expression, cytokines, and antibodies in blood. Sequential pathogen exposure induced gene signatures that recapitulated those seen in blood from pet store-raised versus laboratory mice, and adult versus cord blood in humans. Therefore, basal and vaccine-induced murine immune responses are altered by infection with agents common outside of barrier facilities. This raises the possibility that we can improve mouse models of vaccination and immunity by selective microbial exposure of laboratory animals to mimic that of humans.

  View details for DOI 10.1016/j.chom.2016.04.003

  View details for PubMedID 27107939

• The amino acid sensor GCN2 controls gut inflammation by inhibiting inflammasome activation NATURE Ravindran, R., Loebbermann, J., Nakaya, H. I., Khan, N., Ma, H., Gama, L., Machiah, D. K., Lawson, B., Hakimpour, P., Wang, Y., Li, S., Sharma, P., Kaufman, R. J., Martinez, J., Pulendran, B. 2016; 531 (7595): 523-?

  Abstract

  The integrated stress response (ISR) is a homeostatic mechanism by which eukaryotic cells sense and respond to stress-inducing signals, such as amino acid starvation. General controlled non-repressed (GCN2) kinase is a key orchestrator of the ISR, and modulates protein synthesis in response to amino acid starvation. Here we demonstrate in mice that GCN2 controls intestinal inflammation by suppressing inflammasome activation. Enhanced activation of ISR was observed in intestinal antigen presenting cells (APCs) and epithelial cells during amino acid starvation, or intestinal inflammation. Genetic deletion of Gcn2 (also known as Eif2ka4) in CD11c(+) APCs or intestinal epithelial cells resulted in enhanced intestinal inflammation and T helper 17 cell (TH17) responses, owing to enhanced inflammasome activation and interleukin (IL)-1β production. This was caused by reduced autophagy in Gcn2(-/-) intestinal APCs and epithelial cells, leading to increased reactive oxygen species (ROS), a potent activator of inflammasomes. Thus, conditional ablation of Atg5 or Atg7 in intestinal APCs resulted in enhanced ROS and TH17 responses. Furthermore, in vivo blockade of ROS and IL-1β resulted in inhibition of TH17 responses and reduced inflammation in Gcn2(-/-) mice. Importantly, acute amino acid starvation suppressed intestinal inflammation via a mechanism dependent on GCN2. These results reveal a mechanism that couples amino acid sensing with control of intestinal inflammation via GCN2.

  View details for DOI 10.1038/nature17186

  View details for Web of Science ID 000372701300045

  View details for PubMedID 26982722

  View details for PubMedCentralID PMC4854628

• CXCL13 is a plasma biomarker of germinal center activity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Havenar-Daughton, C., Lindqvist, M., Heit, A., Wu, J. E., Reiss, S. M., Kendric, K., Belanger, S., Kasturi, S. P., Landais, E., Akondy, R. S., McGuire, H. M., Bothwell, M., Vagefi, P. A., Scully, E., Tomaras, G. D., Davis, M. M., Poignard, P., Ahmed, R., Walker, B. D., Pulendran, B., McElrath, M. J., Kaufmann, D. E., Crotty, S. 2016; 113 (10): 2702-2707

  Abstract

  Significantly higher levels of plasma CXCL13 [chemokine (C-X-C motif) ligand 13] were associated with the generation of broadly neutralizing antibodies (bnAbs) against HIV in a large longitudinal cohort of HIV-infected individuals. Germinal centers (GCs) perform the remarkable task of optimizing B-cell Ab responses. GCs are required for almost all B-cell receptor affinity maturation and will be a critical parameter to monitor if HIV bnAbs are to be induced by vaccination. However, lymphoid tissue is rarely available from immunized humans, making the monitoring of GC activity by direct assessment of GC B cells and germinal center CD4(+) T follicular helper (GC Tfh) cells problematic. The CXCL13-CXCR5 [chemokine (C-X-C motif) receptor 5] chemokine axis plays a central role in organizing both B-cell follicles and GCs. Because GC Tfh cells can produce CXCL13, we explored the potential use of CXCL13 as a blood biomarker to indicate GC activity. In a series of studies, we found that plasma CXCL13 levels correlated with GC activity in draining lymph nodes of immunized mice, immunized macaques, and HIV-infected humans. Furthermore, plasma CXCL13 levels in immunized humans correlated with the magnitude of Ab responses and the frequency of ICOS(+) (inducible T-cell costimulator) Tfh-like cells in blood. Together, these findings support the potential use of CXCL13 as a plasma biomarker of GC activity in human vaccine trials and other clinical settings.

  View details for DOI 10.1073/pnas.1520112113

  View details for PubMedID 26908875

• Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nakaya, H. I., Clutterbuck, E., Kazmin, D., Wang, L., Cortese, M., Bosinger, S. E., Patel, N. B., Zak, D. E., Aderemg, A., Dong, T., Del Giudice, G., Rappuoli, R., Cerundolo, V., Pollard, A. J., Pulendran, B., Siegrist, C. 2016; 113 (7): 1853-1858

  Abstract

  The dynamics and molecular mechanisms underlying vaccine immunity in early childhood remain poorly understood. Here we applied systems approaches to investigate the innate and adaptive responses to trivalent inactivated influenza vaccine (TIV) and MF59-adjuvanted TIV (ATIV) in 90 14- to 24-mo-old healthy children. MF59 enhanced the magnitude and kinetics of serum antibody titers following vaccination, and induced a greater frequency of vaccine specific, multicytokine-producing CD4(+) T cells. Compared with transcriptional responses to TIV vaccination previously reported in adults, responses to TIV in infants were markedly attenuated, limited to genes regulating antiviral and antigen presentation pathways, and observed only in a subset of vaccinees. In contrast, transcriptional responses to ATIV boost were more homogenous and robust. Interestingly, a day 1 gene signature characteristic of the innate response (antiviral IFN genes, dendritic cell, and monocyte responses) correlated with hemagglutination at day 28. These findings demonstrate that MF59 enhances the magnitude, kinetics, and consistency of the innate and adaptive response to vaccination with the seasonal influenza vaccine during early childhood, and identify potential molecular correlates of antibody responses.

  View details for DOI 10.1073/pnas.1519690113

  View details for Web of Science ID 000370220000053

  View details for PubMedID 26755593

  View details for PubMedCentralID PMC4763735

• Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures IMMUNITY Nakaya, H. I., Hagan, T., Duraisingham, S. S., Lee, E. K., Kwissa, M., Rouphael, N., Frasca, D., Gersten, M., Mehta, A. K., Gaujoux, R., Li, G., Gupta, S., Ahmed, R., Mulligan, M. J., Shen-Orr, S., Blomberg, B. B., Subramaniam, S., Pulendran, B. 2015; 43 (6): 1186-1198

  Abstract

  Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans. Whether such signatures are similar across multiple seasons and in diverse populations is unknown. We applied systems approaches to study immune responses in young, elderly, and diabetic subjects vaccinated with the seasonal influenza vaccine across five consecutive seasons. Signatures of innate immunity and plasmablasts correlated with and predicted influenza antibody titers at 1 month after vaccination with >80% accuracy across multiple seasons but were not associated with the longevity of the response. Baseline signatures of lymphocyte and monocyte inflammation were positively and negatively correlated, respectively, with antibody responses at 1 month. Finally, integrative analysis of microRNAs and transcriptomic profiling revealed potential regulators of vaccine immunity. These results identify shared vaccine-induced signatures across multiple seasons and in diverse populations and might help guide the development of next-generation vaccines that provide persistent immunity against influenza.

  View details for DOI 10.1016/j.immuni.2015.11.012

  View details for Web of Science ID 000366846600021

  View details for PubMedID 26682988

  View details for PubMedCentralID PMC4859820

• Vaccinology in the era of high-throughput biology PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Nakaya, H. I., Pulendran, B. 2015; 370 (1671)

  Abstract

  Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced 'experimental challenge models' in humans.

  View details for DOI 10.1098/rstb.2014.0146

  View details for Web of Science ID 000355575800010

  View details for PubMedID 25964458

  View details for PubMedCentralID PMC4527391

• The Varieties of Immunological Experience; Of Pathogens, Stress, and Dendritic Cells ANNUAL REVIEW OF IMMUNOLOGY VOL 33 Pulendran, B. 2015; 33: 563-606

  Abstract

  In the 40 years since their discovery, dendritic cells (DCs) have been recognized as central players in immune regulation. DCs sense microbial stimuli through pathogen-recognition receptors (PRRs) and decode, integrate, and present information derived from such stimuli to T cells, thus stimulating immune responses. DCs can also regulate the quality of immune responses. Several functionally specialized subsets of DCs exist, but DCs also display functional plasticity in response to diverse stimuli. In addition to sensing pathogens via PRRs, emerging evidence suggests that DCs can also sense stress signals, such as amino acid starvation, through ancient stress and nutrient sensing pathways, to stimulate adaptive immunity. Here, I discuss these exciting advances in the context of a historic perspective on the discovery of DCs and their role in immune regulation. I conclude with a discussion of emerging areas in DC biology in the systems immunology era and suggest that the impact of DCs on immunity can be usefully contextualized in a hierarchy-of-organization model in which DCs, their receptors and signaling networks, cell-cell interactions, tissue microenvironment, and the host macroenvironment represent different levels of the hierarchy. Immunity or tolerance can then be represented as a complex function of each of these hierarchies.

  View details for DOI 10.1146/annurev-immunol-020711-075049

  View details for Web of Science ID 000352911900019

  View details for PubMedID 25665078

• Activation of Toll-like Receptor-2 by Endogenous Matrix Metalloproteinase-2 Modulates Dendritic-Cell-Mediated Inflammatory Responses CELL REPORTS Godefroy, E., Gallois, A., Idoyaga, J., Merad, M., Tung, N., Monu, N., Saenger, Y., Fu, Y., Ravindran, R., Pulendran, B., Jotereau, F., Trombetta, S., Bhardwaj, N. 2014; 9 (5): 1856-1870

  Abstract

  Matrix metalloproteinase-2 (MMP-2) is involved in several physiological mechanisms, including wound healing and tumor progression. We show that MMP-2 directly stimulates dendritic cells (DCs) to both upregulate OX40L on the cell surface and secrete inflammatory cytokines. The mechanism underlying DC activation includes physical association with Toll-like receptor-2 (TLR2), leading to NF-κB activation, OX40L upregulation on DCs, and ensuing TH2 differentiation. Significantly, MMP-2 polarizes T cells toward type 2 responses in vivo, in a TLR2-dependent manner. MMP-2-dependent type 2 polarization may represent a key immune regulatory mechanism for protection against a broad array of disorders, such as inflammatory, infectious, and autoimmune diseases, which can be hijacked by tumors to evade immunity.

  View details for DOI 10.1016/j.celrep.2014.10.067

  View details for Web of Science ID 000346851900027

  View details for PubMedID 25466255

  View details for PubMedCentralID PMC4336179

• Emerging functions of the unfolded protein response in immunity NATURE IMMUNOLOGY Janssens, S., Pulendran, B., Lambrecht, B. N. 2014; 15 (10): 910-919

  Abstract

  The unfolded protein response (UPR) has traditionally been viewed as an adaptive response triggered by the accumulation of unfolded proteins in the endoplasmic reticulum (ER) and aimed at restoring ER function. The UPR can also be an anticipatory response that is activated well before the disruption of protein homeostasis. UPR signaling intersects at many levels with the innate and adaptive immune responses. In some types of cells of the immune system, such as dendritic cells (DCs) and B cells, particular sensors that detect the UPR seem to be constitutively active in the absence of induction of the traditional UPR gene program and are necessary for antigen presentation and immunoglobulin synthesis. The UPR also influences signaling via Toll-like receptors (TLRs) and activation of the transcription factor NF-κB, and some pathogens subvert the UPR. This Review summarizes these emerging noncanonical functions of the UPR in immunity.

  View details for DOI 10.1038/ni.2991

  View details for Web of Science ID 000342564800006

  View details for PubMedID 25232821

  View details for PubMedCentralID PMC4388558

• TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination IMMUNITY Oh, J. Z., Ravindran, R., Chassaing, B., Carvalho, F. A., Maddur, M. S., Bower, M., Hakimpour, P., Gill, K. P., Nakaya, H. I., Yarovinsky, F., Sartor, R. b., Gewirtz, A. T., Pulendran, B. 2014; 41 (3): 478-492

  Abstract

  Systems biological analysis of immunity to the trivalent inactivated influenza vaccine (TIV) in humans revealed a correlation between early expression of TLR5 and the magnitude of the antibody response. Vaccination of Trl5(-/-) mice resulted in reduced antibody titers and lower frequencies of plasma cells, demonstrating a role for TLR5 in immunity to TIV. This was due to a failure to sense host microbiota. Thus, antibody responses in germ-free or antibiotic-treated mice were impaired, but restored by oral reconstitution with a flagellated, but not aflagellated, strain of E. coli. TLR5-mediated sensing of flagellin promoted plasma cell differentiation directly and by stimulating lymph node macrophages to produce plasma cell growth factors. Finally, TLR5-mediated sensing of the microbiota also impacted antibody responses to the inactivated polio vaccine, but not to adjuvanted vaccines or the live-attenuated yellow fever vaccine. These results reveal an unappreciated role for gut microbiota in promoting immunity to vaccination.

  View details for DOI 10.1016/j.immuni.2014.08.009

  View details for Web of Science ID 000342626500017

  View details for PubMedID 25220212

  View details for PubMedCentralID PMC4169736

• Systems vaccinology: Probing humanity's diverse immune systems with vaccines PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pulendran, B. 2014; 111 (34): 12300-12306

  Abstract

  Homo sapiens are genetically diverse, but dramatic demographic and socioeconomic changes during the past century have created further diversification with respect to age, nutritional status, and the incidence of associated chronic inflammatory disorders and chronic infections. These shifting demographics pose new challenges for vaccination, as emerging evidence suggests that age, the metabolic state, and chronic infections can exert major influences on the immune system. Thus, a key public health challenge is learning how to reprogram suboptimal immune systems to induce effective vaccine immunity. Recent advances have applied systems biological analysis to define molecular signatures induced early after vaccination that correlate with and predict the later adaptive immune responses in humans. Such "systems vaccinology" approaches offer an integrated picture of the molecular networks driving vaccine immunity, and are beginning to yield novel insights about the immune system. Here we discuss the promise of systems vaccinology in probing humanity's diverse immune systems, and in delineating the impact of genes, the environment, and the microbiome on protective immunity induced by vaccination. Such insights will be critical in reengineering suboptimal immune systems in immunocompromised populations.

  View details for DOI 10.1073/pnas.1400476111

  View details for Web of Science ID 000340780300021

  View details for PubMedID 25136102

  View details for PubMedCentralID PMC4151766

• Dengue Virus Infection Induces Expansion of a CD14(+)CD16(+) Monocyte Population that Stimulates Plasmablast Differentiation CELL HOST & MICROBE Kwissa, M., Nakaya, H. I., Onlamoon, N., Wrammert, J., Villinger, F., Perng, G. C., Yoksan, S., Pattanapanyasat, K., Chokephaibulkit, K., Ahmed, R., Pulendran, B. 2014; 16 (1): 115-127

  Abstract

  Dengue virus (DENV) infection induces the expansion of plasmablasts, which produce antibodies that can neutralize DENV but also enhance disease upon secondary infection with another DENV serotype. To understand how these immune responses are generated, we used a systems biological approach to analyze immune responses to dengue in humans. Transcriptomic analysis of whole blood revealed that genes encoding proinflammatory mediators and type I interferon-related proteins were associated with high DENV levels during initial symptomatic disease. Additionally, CD14(+)CD16(+) monocytes increased in the blood. Similarly, in a nonhuman primate model, DENV infection boosted CD14(+)CD16(+) monocyte numbers in the blood and lymph nodes. Upon DENV infection in vitro, monocytes upregulated CD16 and mediated differentiation of resting B cells to plasmablasts as well as immunoglobulin G (IgG) and IgM secretion. These findings provide a detailed picture of innate responses to dengue and highlight a role for CD14(+)CD16(+) monocytes in promoting plasmablast differentiation and anti-DENV antibody responses.

  View details for DOI 10.1016/j.chom.2014.06.001

  View details for Web of Science ID 000341142600014

  View details for PubMedID 24981333

  View details for PubMedCentralID PMC4116428

• Molecular signatures of antibody responses derived from a systems biology study of five human vaccines NATURE IMMUNOLOGY Li, S., Rouphael, N., Duraisingham, S., Romero-Steiner, S., Presnell, S., Davis, C., Schmidt, D. S., Johnson, S. E., Milton, A., Rajam, G., Kasturi, S., Carlone, G. M., Quinn, C., Chaussabel, D., Palucka, A. K., Mulligan, M. J., Ahmed, R., Stephens, D. S., Nakaya, H. I., Pulendran, B. 2014; 15 (2): 195-204

  Abstract

  Many vaccines induce protective immunity via antibodies. Systems biology approaches have been used to determine signatures that can be used to predict vaccine-induced immunity in humans, but whether there is a 'universal signature' that can be used to predict antibody responses to any vaccine is unknown. Here we did systems analyses of immune responses to the polysaccharide and conjugate vaccines against meningococcus in healthy adults, in the broader context of published studies of vaccines against yellow fever virus and influenza virus. To achieve this, we did a large-scale network integration of publicly available human blood transcriptomes and systems-scale databases in specific biological contexts and deduced a set of transcription modules in blood. Those modules revealed distinct transcriptional signatures of antibody responses to different classes of vaccines, which provided key insights into primary viral, protein recall and anti-polysaccharide responses. Our results elucidate the early transcriptional programs that orchestrate vaccine immunity in humans and demonstrate the power of integrative network modeling.

  View details for DOI 10.1038/ni.2789

  View details for Web of Science ID 000330150600014

  View details for PubMedID 24336226

  View details for PubMedCentralID PMC3946932

• Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium NATURE BIOTECHNOLOGY Brusic, V., Gottardo, R., Kleinstein, S. H., Davis, M. M., HIPC Steering Comm 2014; 32 (2): 146–48

  View details for DOI 10.1038/nbt.2777

  View details for Web of Science ID 000331074000019

  View details for PubMedID 24441472

  View details for PubMedCentralID PMC4294529

• Vaccine Activation of the Nutrient Sensor GCN2 in Dendritic Cells Enhances Antigen Presentation SCIENCE Ravindran, R., Khan, N., Nakaya, H. I., Li, S., Loebbermann, J., Maddur, M. S., Park, Y., Jones, D. P., Chappert, P., Davoust, J., Weiss, D. S., Virgin, H. W., Ron, D., Pulendran, B. 2014; 343 (6168): 313-317

  Abstract

  The yellow fever vaccine YF-17D is one of the most successful vaccines ever developed in humans. Despite its efficacy and widespread use in more than 600 million people, the mechanisms by which it stimulates protective immunity remain poorly understood. Recent studies using systems biology approaches in humans have revealed that YF-17D-induced early expression of general control nonderepressible 2 kinase (GCN2) in the blood strongly correlates with the magnitude of the later CD8(+) T cell response. We demonstrate a key role for virus-induced GCN2 activation in programming dendritic cells to initiate autophagy and enhanced antigen presentation to both CD4(+) and CD8(+) T cells. These results reveal an unappreciated link between virus-induced integrated stress response in dendritic cells and the adaptive immune response.

  View details for DOI 10.1126/science.1246829

  View details for Web of Science ID 000329718600040

  View details for PubMedID 24310610

  View details for PubMedCentralID PMC4048998

• Chronic but Not Acute Virus Infection Induces Sustained Expansion of Myeloid Suppressor Cell Numbers that Inhibit Viral-Specific T Cell Immunity IMMUNITY Norris, B. A., Uebelhoer, L. S., Nakaya, H. I., Price, A. A., Grakoui, A., Pulendran, B. 2013; 38 (2): 309-321

  Abstract

  Resolution of acute and chronic viral infections requires activation of innate cells to initiate and maintain adaptive immune responses. Here we report that infection with acute Armstrong (ARM) or chronic Clone 13 (C13) strains of lymphocytic choriomeningitis virus (LCMV) led to two distinct phases of innate immune response. During the first 72 hr of infection, dendritic cells upregulated activation markers and stimulated antiviral CD8(+) T cells, independent of viral strain. Seven days after infection, there was an increase in Ly6C(hi) monocytic and Gr-1(hi) neutrophilic cells in lymphoid organs and blood. This expansion in cell numbers was enhanced and sustained in C13 infection, whereas it occurred only transiently with ARM infection. These cells resembled myeloid-derived suppressor cells and potently suppressed T cell proliferation. The reduction of monocytic cells in Ccr2(-/-) mice or after Gr-1 antibody depletion enhanced antiviral T cell function. Thus, innate cells have an important immunomodulatory role throughout chronic infection.

  View details for DOI 10.1016/j.immuni.2012.10.022

  View details for Web of Science ID 000330940800013

  View details for PubMedID 23438822

  View details for PubMedCentralID PMC3869405

• Systems Biology of Vaccination in the Elderly SYSTEMS BIOLOGY Duraisingham, S. S., Rouphael, N., Cavanagh, M. M., Nakaya, H. I., Goronzy, J. J., Pulendran, B. 2013; 363: 117-142

  Abstract

  Aging population demographics, combined with suboptimal vaccine responses in the elderly, make the improvement of vaccination strategies in the elderly a developing public health issue. The immune system changes with age, with innate and adaptive cell components becoming increasingly dysfunctional. As such, vaccine responses in the elderly are impaired in ways that differ depending on the type of vaccine (e.g., live attenuated, polysaccharide, conjugate, or subunit) and the mediators of protection (e.g., antibody and/or T cell). The rapidly progressing field of systems biology has been shown to be useful in predicting immunogenicity and offering insights into potential mechanisms of protection in young adults. Future application of systems biology to vaccination in the elderly may help to identify gene signatures that predict suboptimal responses and help to identify more accurate correlates of protection. Moreover, the identification of specific defects may be used to target novel vaccination strategies that improve efficacy in elderly populations.

  View details for DOI 10.1007/82_2012_250

  View details for Web of Science ID 000330590200008

  View details for PubMedID 22903566

• A Blueprint for HIV Vaccine Discovery CELL HOST & MICROBE Burton, D. R., Ahmed, R., Barouch, D. H., Butera, S. T., Crotty, S., Godzik, A., Kaufmann, D. E., McElrath, M. J., Nussenzweig, M. C., Pulendran, B., Scanlan, C. N., Schief, W. R., Silvestri, G., Streeck, H., Walker, B. D., Walker, L. M., Ward, A. B., Wilson, I. A., Wyatt, R. 2012; 12 (4): 396-407

  Abstract

  Despite numerous attempts over many years to develop an HIV vaccine based on classical strategies, none has convincingly succeeded to date. A number of approaches are being pursued in the field, including building upon possible efficacy indicated by the recent RV144 clinical trial, which combined two HIV vaccines. Here, we argue for an approach based, in part, on understanding the HIV envelope spike and its interaction with broadly neutralizing antibodies (bnAbs) at the molecular level and using this understanding to design immunogens as possible vaccines. BnAbs can protect against virus challenge in animal models, and many such antibodies have been isolated recently. We further propose that studies focused on how best to provide T cell help to B cells that produce bnAbs are crucial for optimal immunization strategies. The synthesis of rational immunogen design and immunization strategies, together with iterative improvements, offers great promise for advancing toward an HIV vaccine.

  View details for DOI 10.1016/j.chom.2012.09.008

  View details for Web of Science ID 000310719700004

  View details for PubMedID 23084910

  View details for PubMedCentralID PMC3513329

• New Paradigms in Type 2 Immunity SCIENCE Pulendran, B., Artis, D. 2012; 337 (6093): 431-435

  Abstract

  Nearly half of the world's population harbors helminth infections or suffers from allergic disorders. A common feature of this population is the so-called "type 2 immune response," which confers protection against helminths, but also promotes pathologic responses associated with allergic inflammation. However, the mechanisms that initiate and control type 2 responses remain enigmatic. Recent advances have revealed a role for the innate immune system in orchestrating type 2 responses against a bewildering array of stimuli, from nanometer-sized allergens to 20-meter-long helminth parasites. Here, we review these advances and suggest that the human immune system has evolved multiple mechanisms of sensing such stimuli, from recognition of molecular patterns via innate immune receptors to detecting metabolic changes and tissue damage caused by these stimuli.

  View details for DOI 10.1126/science.1221064

  View details for Web of Science ID 000306802300033

  View details for PubMedID 22837519

  View details for PubMedCentralID PMC4078898

• Distinct TLR adjuvants differentially stimulate systemic and local innate immune responses in nonhuman primates BLOOD Kwissa, M., Nakaya, H. I., Oluoch, H., Pulendran, B. 2012; 119 (9): 2044-2055

  Abstract

  TLR ligands (TLR-Ls) represent novel vaccine adjuvants, but their immunologic effects in humans remain poorly defined in vivo. In the present study, we analyzed the innate responses stimulated by different TLR-Ls in rhesus macaques. MPL (TLR4-L), R-848 (TLR7/8-L), or cytosine-phosphate-guanine oligodeoxynucleotide (TLR9-L) induced a rapid and robust expansion of blood neutrophils, with a concomitant reduction in PBMCs. Furthermore, all TLR-Ls induced rapid (3-8 hours) expansion of CD14(+) monocytes, but only TLR7/8-L and TLR9-L mobilized the CD14(+)CD16(+) and CD14(dim)CD16(++) monocytes, and only TLR7/8-L and TLR9-L induced activation of myeloid dendritic cells (mDCs) and plasmacytoid DCs (pDCs), production of IP-10 and type-I IFN, and expression of type-I IFN-related and chemokine genes in the blood. In the draining lymph nodes (LNs), consistent with the effects in blood, all TLR-Ls induced expansion of CD14(+) monocytes, but only TLR7/8-L and TLR9-L expanded the activated CD14(+)CD16(+) cells. TLR4-L and TLR9-L differentially induced the expansion of mDCs and pDCs (1-3 days), but did not activate DCs. In contrast, TLR7/8-L did not induce DC expansion, but did activate mDCs. Finally, both TLR9-L and TLR7/8-L induced the expression of genes related to chemokines and type-I IFNs in LNs. Thus different TLR-Ls mediate distinct signatures of early innate responses both locally and systemically.

  View details for DOI 10.1182/blood-2011-10-388579

  View details for Web of Science ID 000300949500014

  View details for PubMedID 22246032

  View details for PubMedCentralID PMC3311246

• Learning vaccinology from viral infections JOURNAL OF EXPERIMENTAL MEDICINE Ahmed, R., Pulendran, B. 2011; 208 (12): 2347-2349

  Abstract

  This issue of the Journal of Experimental Medicine celebrates and honors the life of Ralph Steinman (1943-2011), winner of the 2011 Nobel Prize in Physiology or Medicine. Ralph's science was rooted in fundamental discovery with the goal of translating these findings into clinical medicine. He recognized the power of immunology in treating human disease and passionately championed studies on vaccine design, immune therapy, and human immunology. One particular collaborative effort between the Steinman and Sekaly laboratories resulted in a paper published in this issue of the journal.

  View details for DOI 10.1084/jem.20112321

  View details for Web of Science ID 000297870700003

  View details for PubMedID 22110181

  View details for PubMedCentralID PMC3256975

• Systems biology of vaccination for seasonal influenza in humans NATURE IMMUNOLOGY Nakaya, H. I., Wrammert, J., Lee, E. K., Racioppi, L., Marie-Kunze, S., Haining, W. N., Means, A. R., Kasturi, S. P., Khan, N., Li, G., McCausland, M., Kanchan, V., Kokko, K. E., Li, S., Elbein, R., Mehta, A. K., Aderem, A., Subbarao, K., Ahmed, R., Pulendran, B. 2011; 12 (8): 786-U149

  Abstract

  Here we have used a systems biology approach to study innate and adaptive responses to vaccination against influenza in humans during three consecutive influenza seasons. We studied healthy adults vaccinated with trivalent inactivated influenza vaccine (TIV) or live attenuated influenza vaccine (LAIV). TIV induced higher antibody titers and more plasmablasts than LAIV did. In subjects vaccinated with TIV, early molecular signatures correlated with and could be used to accurately predict later antibody titers in two independent trials. Notably, expression of the kinase CaMKIV at day 3 was inversely correlated with later antibody titers. Vaccination of CaMKIV-deficient mice with TIV induced enhanced antigen-specific antibody titers, which demonstrated an unappreciated role for CaMKIV in the regulation of antibody responses. Thus, systems approaches can be used to predict immunogenicity and provide new mechanistic insights about vaccines.

  View details for DOI 10.1038/ni.2067

  View details for Web of Science ID 000292870700017

  View details for PubMedID 21743478

  View details for PubMedCentralID PMC3140559

• Functional Specializations of Intestinal Dendritic Cell and Macrophage Subsets That Control Th17 and Regulatory T Cell Responses Are Dependent on the T Cell/APC Ratio, Source of Mouse Strain, and Regional Localization JOURNAL OF IMMUNOLOGY Denning, T. L., Norris, B. A., Medina-Contreras, O., Manicassamy, S., Geem, D., Madan, R., Karp, C. L., Pulendran, B. 2011; 187 (2): 733-747

  Abstract

  Although several subsets of intestinal APCs have been described, there has been no systematic evaluation of their phenotypes, functions, and regional localization to date. In this article, we used 10-color flow cytometry to define the major APC subsets in the small and large intestine lamina propria. Lamina propria APCs could be subdivided into CD11c(+)CD11b(-), CD11c(+)CD11b(+), and CD11c(dull)CD11b(+) subsets. CD11c(+)CD11b(-) cells were largely CD103(+)F4/80(-) dendritic cells (DCs), whereas the CD11c(+)CD11b(+) subset comprised CD11c(+)CD11b(+)CD103(+)F4/80(-) DCs and CD11c(+)CD11b(+)CD103(-)F4/80(+) macrophage-like cells. The majority of CD11c(dull)CD11b(+) cells were CD103(-)F4/80(+) macrophages. Although macrophages were more efficient at inducing Foxp3(+) regulatory T (T(reg)) cells than DCs, at higher T cell/APC ratios, all of the DC subsets efficiently induced Foxp3(+) T(reg) cells. In contrast, only CD11c(+)CD11b(+)CD103(+) DCs efficiently induced Th17 cells. Consistent with this, the regional distribution of CD11c(+)CD11b(+)CD103(+) DCs correlated with that of Th17 cells, with duodenum > jejunum > ileum > colon. Conversely, CD11c(+)CD11b(-)CD103(+) DCs, macrophages, and Foxp3(+) T(reg) cells were most abundant in the colon and scarce in the duodenum. Importantly, however, the ability of DC and macrophage subsets to induce Foxp3(+) T(reg) cells versus Th17 cells was strikingly dependent on the source of the mouse strain. Thus, DCs from C57BL/6 mice from Charles River Laboratories (that have segmented filamentous bacteria, which induce robust levels of Th17 cells in situ) were more efficient at inducing Th17 cells and less efficient at inducing Foxp3(+) T(reg) cells than DCs from B6 mice from The Jackson Laboratory. Thus, the functional specializations of APC subsets in the intestine are dependent on the T cell/APC ratio, regional localization, and source of the mouse strain.

  View details for DOI 10.4049/jimmunol.1002701

  View details for Web of Science ID 000292451000020

  View details for PubMedID 21666057

  View details for PubMedCentralID PMC3131424

• Immunological mechanisms of vaccination NATURE IMMUNOLOGY Pulendran, B., Ahmed, R. 2011; 12 (6): 509-517

  Abstract

  Vaccines represent one of the greatest triumphs of modern medicine. Despite the common origins of vaccinology and immunology more than 200 years ago, the two disciplines have evolved along such different trajectories that most of the highly successful vaccines have been made empirically, with little or no immunological insight. Recent advances in innate immunity have offered new insights about the mechanisms of vaccine-induced immunity and have facilitated a more rational approach to vaccine design. Here we will discuss these advances and emerging themes on the immunology of vaccination.

  View details for DOI 10.1038/ni.2039

  View details for Web of Science ID 000290707100009

  View details for PubMedID 21739679

  View details for PubMedCentralID PMC3253344

• Dendritic cell control of tolerogenic responses IMMUNOLOGICAL REVIEWS Manicassamy, S., Pulendran, B. 2011; 241: 206-227

  Abstract

  One of the most fundamental problems in immunology is the seemingly schizophrenic ability of the immune system to launch robust immunity against pathogens, while acquiring and maintaining a state of tolerance to the body's own tissues and the trillions of commensal microorganisms and food antigens that confront it every day. A fundamental role for the innate immune system, particularly dendritic cells (DCs), in orchestrating immunological tolerance has been appreciated, but emerging studies have highlighted the nature of the innate receptors and the signaling pathways that program DCs to a tolerogenic state. Furthermore, several studies have emphasized the major role played by cellular interactions and the microenvironment in programming tolerogenic DCs. Here, we review these studies and suggest that the innate control of tolerogenic responses can be viewed as different hierarchies of organization, in which DCs, their innate receptors and signaling networks, and their interactions with other cells and local microenvironments represent different levels of the hierarchy.

  View details for DOI 10.1111/j.1600-065X.2011.01015.x

  View details for Web of Science ID 000289468700014

  View details for PubMedID 21488899

  View details for PubMedCentralID PMC3094730

• Programming the magnitude and persistence of antibody responses with innate immunity NATURE Kasturi, S. P., Skountzou, I., Albrecht, R. A., Koutsonanos, D., Hua, T., Nakaya, H. I., Ravindran, R., Stewart, S., Alam, M., Kwissa, M., Villinger, F., Murthy, N., Steel, J., Jacob, J., Hogan, R. J., Garcia-Sastre, A., Compans, R., Pulendran, B. 2011; 470 (7335): 543-U136

  Abstract

  Many successful vaccines induce persistent antibody responses that can last a lifetime. The mechanisms by which they do so remain unclear, but emerging evidence indicates that they activate dendritic cells via Toll-like receptors (TLRs). For example, the yellow fever vaccine YF-17D, one of the most successful empiric vaccines ever developed, activates dendritic cells via multiple TLRs to stimulate proinflammatory cytokines. Triggering specific combinations of TLRs in dendritic cells can induce synergistic production of cytokines, which results in enhanced T-cell responses, but its impact on antibody responses remain unknown. Learning the critical parameters of innate immunity that program such antibody responses remains a major challenge in vaccinology. Here we demonstrate that immunization of mice with synthetic nanoparticles containing antigens plus ligands that signal through TLR4 and TLR7 induces synergistic increases in antigen-specific, neutralizing antibodies compared to immunization with nanoparticles containing antigens plus a single TLR ligand. Consistent with this there was enhanced persistence of germinal centres and of plasma-cell responses, which persisted in the lymph nodes for >1.5 years. Surprisingly, there was no enhancement of the early short-lived plasma-cell response relative to that observed with single TLR ligands. Molecular profiling of activated B cells, isolated 7 days after immunization, indicated that there was early programming towards B-cell memory. Antibody responses were dependent on direct triggering of both TLRs on B cells and dendritic cells, as well as on T-cell help. Immunization protected completely against lethal avian and swine influenza virus strains in mice, and induced robust immunity against pandemic H1N1 influenza in rhesus macaques.

  View details for DOI 10.1038/nature09737

  View details for Web of Science ID 000287652900044

  View details for PubMedID 21350488

  View details for PubMedCentralID PMC3057367

• Systems Vaccinology IMMUNITY Pulendran, B., Li, S., Nakaya, H. I. 2010; 33 (4): 516-529

  Abstract

  Vaccination is one of the greatest triumphs of modern medicine, yet we remain largely ignorant of the mechanisms by which successful vaccines stimulate protective immunity. Two recent advances are beginning to illuminate such mechanisms: realization of the pivotal role of the innate immune system in sensing microbes and stimulating adaptive immunity, and advances in systems biology. Recent studies have used systems biology approaches to obtain a global picture of the immune responses to vaccination in humans. This has enabled the identification of early innate signatures that predict the immunogenicity of vaccines, and identification of potentially novel mechanisms of immune regulation. Here, we review these advances and critically examine the potential opportunities and challenges posed by systems biology in vaccine development.

  View details for DOI 10.1016/j.immuni.2010.10.006

  View details for Web of Science ID 000284300200008

  View details for PubMedID 21029962

  View details for PubMedCentralID PMC3001343

• Activation of beta-Catenin in Dendritic Cells Regulates Immunity Versus Tolerance in the Intestine SCIENCE Manicassamy, S., Reizis, B., Ravindran, R., Nakaya, H., Salazar-Gonzalez, R. M., Wang, Y., Pulendran, B. 2010; 329 (5993): 849-853

  Abstract

  Dendritic cells (DCs) play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens. However, the intracellular signaling networks that program DCs to become tolerogenic remain unknown. We report here that the Wnt-beta-catenin signaling in intestinal dendritic cells regulates the balance between inflammatory versus regulatory responses in the gut. beta-catenin in intestinal dendritic cells was required for the expression of anti-inflammatory mediators such as retinoic acid-metabolizing enzymes, interleukin-10, and transforming growth factor-beta, and the stimulation of regulatory T cell induction while suppressing inflammatory effector T cells. Furthermore, ablation of beta-catenin expression in DCs enhanced inflammatory responses and disease in a mouse model of inflammatory bowel disease. Thus, beta-catenin signaling programs DCs to a tolerogenic state, limiting the inflammatory response.

  View details for DOI 10.1126/science.1188510

  View details for Web of Science ID 000280809900053

  View details for PubMedID 20705860

  View details for PubMedCentralID PMC3732486

• Programming dendritic cells to induce T(H)2 and tolerogenic responses NATURE IMMUNOLOGY Pulendran, B., Tang, H., Manicassamy, S. 2010; 11 (8): 647-655

  Abstract

  A fundamental puzzle in immunology is how the immune system decides what types of immune responses to launch against different stimuli. Although much is known about control of T helper type 1 (T(H)1) and T(H)17 responses, the mechanisms that initiate T(H)2 and T regulatory (T(reg)) responses remain obscure. Emerging studies suggest a fundamental role for the innate immune system, particularly dendritic cells (DCs), in this process. We review these studies, and suggest that the innate control of T(H)2 and T(reg) responses can be viewed as different hierarchies of organization, in which DCs, their innate receptors and signaling networks, and their interactions with other cells and local microenvironments represent different levels of the hierarchy.

  View details for DOI 10.1038/ni.1894

  View details for Web of Science ID 000280149400002

  View details for PubMedID 20644570

• The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling NATURE IMMUNOLOGY Tang, H., Cao, W., Kasturi, S. P., Ravindran, R., Nakaya, H. I., Kundu, K., Murthy, N., Kepler, T. B., Malissen, B., Pulendran, B. 2010; 11 (7): 608-U80

  Abstract

  The mechanisms that initiate T helper type 2 (T(H)2) responses are poorly understood. Here we demonstrate that cysteine protease-induced T(H)2 responses occur via 'cooperation' between migratory dermal dendritic cells (DCs) and basophils positive for interleukin 4 (IL-4). Subcutaneous immunization with papain plus antigen induced reactive oxygen species (ROS) in lymph node DCs and in dermal DCs and epithelial cells of the skin. ROS orchestrated T(H)2 responses by inducing oxidized lipids that triggered the induction of thymic stromal lymphopoietin (TSLP) by epithelial cells mediated by Toll-like receptor 4 (TLR4) and the adaptor protein TRIF; by suppressing production of the T(H)1-inducing molecules IL-12 and CD70 in lymph node DCs; and by inducing the DC-derived chemokine CCL7, which mediated recruitment of IL-4(+) basophils to the lymph node. Thus, the T(H)2 response to cysteine proteases requires DC-basophil cooperation via ROS-mediated signaling.

  View details for DOI 10.1038/ni.1883

  View details for Web of Science ID 000278926400017

  View details for PubMedID 20495560

  View details for PubMedCentralID PMC3145206

• Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology NATURE REVIEWS IMMUNOLOGY Pulendran, B. 2009; 9 (10): 741-747

  Abstract

  Despite their great success, we understand little about how effective vaccines stimulate protective immune responses. Two recent developments promise to yield such understanding: the appreciation of the crucial role of the innate immune system in sensing microorganisms and tuning immune responses, and advances in systems biology. Here I review how these developments are yielding insights into the mechanism of action of the yellow fever vaccine, one of the most successful vaccines ever developed, and the broader implications for vaccinology.

  View details for DOI 10.1038/nri2629

  View details for Web of Science ID 000270133000018

  View details for PubMedID 19763148

• Toll-like receptor 2-dependent induction of vitamin A-metabolizing enzymes in dendritic cells promotes T regulatory responses and inhibits autoimmunity NATURE MEDICINE Manicassamy, S., Ravindran, R., Deng, J., Oluoch, H., Denning, T. L., Kasturi, S. P., Rosenthal, K. M., Evavold, B. D., Pulendran, B. 2009; 15 (4): 401-409

  Abstract

  Immune sensing of a microbe occurs via multiple receptors. How signals from different receptors are coordinated to yield a specific immune response is poorly understood. We show that two pathogen recognition receptors, Toll-like receptor 2 (TLR2) and dectin-1, recognizing the same microbial stimulus, stimulate distinct innate and adaptive responses. TLR2 signaling induced splenic dendritic cells (DCs) to express the retinoic acid metabolizing enzyme retinaldehyde dehydrogenase type 2 and interleukin-10 (IL-10) and to metabolize vitamin A and stimulate Foxp3(+) T regulatory cells (T(reg) cells). Retinoic acid acted on DCs to induce suppressor of cytokine signaling-3 expression, which suppressed activation of p38 mitogen-activated protein kinase and proinflammatory cytokines. Consistent with this finding, TLR2 signaling induced T(reg) cells and suppressed IL-23 and T helper type 17 (T(H)17) and T(H)1-mediated autoimmune responses in vivo. In contrast, dectin-1 signaling mostly induced IL-23 and proinflammatory cytokines and augmented T(H)17 and T(H)1-mediated autoimmune responses in vivo. These data define a new mechanism for the systemic induction of retinoic acid and immune suppression against autoimmunity.

  View details for DOI 10.1038/nm.1925

  View details for Web of Science ID 000264937200027

  View details for PubMedID 19252500

  View details for PubMedCentralID PMC2768543

• Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans NATURE IMMUNOLOGY Querec, T. D., Akondy, R. S., Lee, E. K., Cao, W., Nakaya, H. I., Teuwen, D., Pirani, A., Gernert, K., Deng, J., Marzolf, B., Kennedy, K., Wu, H., Bennouna, S., Oluoch, H., Miller, J., Vencio, R. Z., Mulligan, M., Aderem, A., Ahmed, R., Pulendran, B. 2009; 10 (1): 116-125

  Abstract

  A major challenge in vaccinology is to prospectively determine vaccine efficacy. Here we have used a systems biology approach to identify early gene 'signatures' that predicted immune responses in humans vaccinated with yellow fever vaccine YF-17D. Vaccination induced genes that regulate virus innate sensing and type I interferon production. Computational analyses identified a gene signature, including complement protein C1qB and eukaryotic translation initiation factor 2 alpha kinase 4-an orchestrator of the integrated stress response-that correlated with and predicted YF-17D CD8(+) T cell responses with up to 90% accuracy in an independent, blinded trial. A distinct signature, including B cell growth factor TNFRS17, predicted the neutralizing antibody response with up to 100% accuracy. These data highlight the utility of systems biology approaches in predicting vaccine efficacy.

  View details for DOI 10.1038/ni.1688

  View details for Web of Science ID 000261788800019

  View details for PubMedID 19029902

  View details for PubMedCentralID PMC4049462

• Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses NATURE IMMUNOLOGY Denning, T. L., Wang, Y., Patel, S. R., Williams, I. R., Pulendran, B. 2007; 8 (10): 1086-1094

  Abstract

  The intestinal immune system must elicit robust immunity against harmful pathogens but must also restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood. Here we describe a population of CD11b+F4/80+CD11c- macrophages in the lamina propria that expressed several anti-inflammatory molecules, including interleukin 10 (IL-10), but little or no proinflammatory cytokines, even after stimulation with Toll-like receptor ligands. These macrophages induced, by a mechanism dependent on IL-10, retinoic acid and exogenous transforming growth factor-beta, the differentiation of Foxp3+ regulatory T cells. In contrast, lamina propria CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by lamina propria macrophages, indicating that a dynamic interaction between these subsets may influence the balance between immune activation and tolerance.

  View details for DOI 10.1038/ni1511

  View details for Web of Science ID 000249691400023

  View details for PubMedID 17873879

• Translating innate immunity into immunological memory: Implications for vaccine development CELL Pulendran, B., Ahmed, R. 2006; 124 (4): 849-863

  Abstract

  Vaccination is the most effective means of preventing infectious diseases. Despite the success of many vaccines, there is presently little knowledge of the immunological mechanisms that mediate their efficacy. Such information will be critical in the design of future vaccines against old and new infectious diseases. Recent advances in immunology are beginning to provide an intellectual framework with which to address fundamental questions about how the innate immune system shapes adaptive immunity. In this review, we summarize current knowledge about how the innate immune system modulates the quantity and quality of long-term T and B cell memory and protective immune responses to pathogens. In addition, we point out unanswered questions and identify critical challenges, the solution of which, we believe, will greatly facilitate the rational design of novel vaccines against a multitude of emerging infections.

  View details for DOI 10.1016/j.cell.2006.02.019

  View details for Web of Science ID 000237240900026

  View details for PubMedID 16497593

• Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity JOURNAL OF EXPERIMENTAL MEDICINE Querec, T., Bennouna, S., Alkan, S. K., Laouar, Y., Gorden, K., Flavell, R., Akira, S., Ahmed, R., Pulendran, B. 2006; 203 (2): 413-424

  Abstract

  The live attenuated yellow fever vaccine 17D (YF-17D) is one of the most effective vaccines available, with a 65-yr history of use in >400 million people globally. Despite this efficacy, there is presently no information about the immunological mechanisms by which YF-17D acts. Here, we present data that suggest that YF-17D activates multiple Toll-like receptors (TLRs) on dendritic cells (DCs) to elicit a broad spectrum of innate and adaptive immune responses. Specifically, YF-17D activates multiple DC subsets via TLRs 2, 7, 8, and 9 to elicit the proinflammatory cytokines interleukin (IL)-12p40, IL-6, and interferon-alpha. Interestingly, the resulting adaptive immune responses are characterized by a mixed T helper cell (Th)1/Th2 cytokine profile and antigen-specific CD8+ T cells. Furthermore, distinct TLRs appear to differentially control the Th1/Th2 balance; thus, whilst MyD88-deficient mice show a profound impairment of Th1 cytokines, TLR2-deficient mice show greatly enhanced Th1 and Tc1 responses to YF-17D. Together, these data enhance our understanding of the molecular mechanism of action of YF-17D, and highlight the potential of vaccination strategies that use combinations of different TLR ligands to stimulate polyvalent immune responses.

  View details for DOI 10.1084/jem.20051720

  View details for Web of Science ID 000235707700020

  View details for PubMedID 16461338

  View details for PubMedCentralID PMC2118210

• Cutting edge: Different toll-like receptor agonists instruct dendritic cells to induce distinct th responses via differential modulation of extracellular signal-regulated kinase-mitogen-activated protein kinase and c-fos JOURNAL OF IMMUNOLOGY Agrawal, S., Agrawal, A., Doughty, B., Gerwitz, A., Blenis, J., Van Dyke, T., Pulendran, B. 2003; 171 (10): 4984-4989

  Abstract

  Dendritic cells (DCs) are pivotal in determining the class of an adaptive immune response. However, the molecular mechanisms within DCs that determine this decision-making process are unknown. Here, we demonstrate that distinct Toll-like receptor (TLR) ligands instruct human DCs to induce distinct Th cell responses by differentially modulating mitogen-activated protein kinase signaling. Thus, Escherichia coli LPS and flagellin, which trigger TLR4 and TLR5, respectively, instruct DCs to stimulate Th1 responses via IL-12p70 production, which depends on the phosphorylation of p38 and c-Jun N-terminal kinase 1/2. In contrast, the TLR2 agonist, Pam3cys, and the Th2 stimulus, schistosome egg Ags: 1) barely induce IL-12p70; 2) stimulate sustained duration and magnitude of extracellular signal-regulated kinase 1/2 phosphorylation, which results in stabilization of the transcription factor c-Fos, a suppressor of IL-12; and 3) yield a Th2 bias. Thus, distinct TLR agonists differentially modulate extracellular signal-regulated kinase signaling, c-Fos activity, and cytokine responses in DCs to stimulate different Th responses.

  View details for Web of Science ID 000186643300007

  View details for PubMedID 14607893

• Impairment of dendritic cells and adaptive immunity by anthrax lethal toxin NATURE Agrawal, A., Lingappa, J., Leppla, S. H., Agrawal, S., Jabbar, A., Quinn, C., Pulendran, B. 2003; 424 (6946): 329-334

  Abstract

  Anthrax poses a clear and present danger as an agent of biological terrorism. Infection with Bacillus anthracis, the causative agent of anthrax, if untreated can result in rampant bacteraemia, multisystem dysfunction and death. Anthrax lethal toxin (LT) is a critical virulence factor of B. anthracis, which occurs as a complex of protective antigen and lethal factor. Here we demonstrate that LT severely impairs the function of dendritic cells--which are pivotal to the establishment of immunity against pathogens--and host immune responses by disrupting the mitogen-activated protein (MAP) kinase intracellular signalling network. Dendritic cells exposed to LT and then stimulated with lipopolysaccharide do not upregulate co-stimulatory molecules, secrete greatly diminished amounts of proinflammatory cytokines, and do not effectively stimulate antigen-specific T cells in vivo. Furthermore, injections of LT induce a profound impairment of antigen-specific T- and B-cell immunity. These data suggest a role for LT in suppressing host immunity during B. anthracis infections, and represent an immune evasion strategy, where a microbe targets MAP kinases in dendritic cells to disarm the immune response.

  View details for DOI 10.1038/nature01794

  View details for Web of Science ID 000184183900046

  View details for PubMedID 12867985

• Cutting edge: impairment of dendritic cells and adaptive immunity by Ebola and Lassa viruses. Journal of immunology Mahanty, S., Hutchinson, K., Agarwal, S., McRae, M., Rollin, P. E., Pulendran, B. 2003; 170 (6): 2797-2801

  Abstract

  Acute infection of humans with Ebola and Lassa viruses, two principal etiologic agents of hemorrhagic fevers, often results in a paradoxical pattern of immune responses: early infection, characterized by an outpouring of inflammatory mediators such as TNF-alpha, IL-1 beta, and IL-6, vs late stage infections, which are associated with poor immune responses. The mechanisms underlying these diverse outcomes are poorly understood. In particular, the role played by cells of the innate immune system, such as dendritic cells (DC), is not known. In this study, we show that Ebola and Lassa viruses infect human monocyte-derived DC and impair their function. Monocyte-derived DC exposed to either virus fail to secrete proinflammatory cytokines, do not up-regulate costimulatory molecules, and are poor stimulators of T cells. These data represent the first evidence for a mechanism by which Ebola and Lassa viruses target DC to impair adaptive immunity.

  View details for PubMedID 12626527

• Lipopolysaccharides from distinct pathogens induce different classes of immune responses in vivo JOURNAL OF IMMUNOLOGY Pulendran, B., Kumar, P., Cutler, C. W., Mohamadzadeh, M., Van Dyke, T., Banchereau, J. 2001; 167 (9): 5067-5076

  Abstract

  The adaptive immune system has evolved distinct responses against different pathogens, but the mechanism(s) by which a particular response is initiated is poorly understood. In this study, we investigated the type of Ag-specific CD4(+) Th and CD8(+) T cell responses elicited in vivo, in response to soluble OVA, coinjected with LPS from two different pathogens. We used Escherichia coli LPS, which signals through Toll-like receptor 4 (TLR4) and LPS from the oral pathogen Porphyromonas gingivalis, which does not appear to require TLR4 for signaling. Coinjections of E. coli LPS + OVA or P. gingivalis LPS + OVA induced similar clonal expansions of OVA-specific CD4(+) and CD8(+) T cells, but strikingly different cytokine profiles. E. coli LPS induced a Th1-like response with abundant IFN-gamma, but little or no IL-4, IL-13, and IL-5. In contrast, P. gingivalis LPS induced Th and T cell responses characterized by significant levels of IL-13, IL-5, and IL-10, but lower levels of IFN-gamma. Consistent with these results, E. coli LPS induced IL-12(p70) in the CD8alpha(+) dendritic cell (DC) subset, while P. gingivalis LPS did not. Both LPS, however, activated the two DC subsets to up-regulate costimulatory molecules and produce IL-6 and TNF-alpha. Interestingly, these LPS appeared to have differences in their ability to signal through TLR4; proliferation of splenocytes and cytokine secretion by splenocytes or DCs from TLR4-deficient C3H/HeJ mice were greatly impaired in response to E. coli LPS, but not P. gingivalis LPS. Therefore, LPS from different bacteria activate DC subsets to produce different cytokines, and induce distinct types of adaptive immunity in vivo.

  View details for Web of Science ID 000171858500037

  View details for PubMedID 11673516

  View details for PubMedCentralID PMC3739327

• Sensing pathogens and tuning immune responses SCIENCE Pulendran, B., Palucka, K., Banchereau, J. 2001; 293 (5528): 253-256

  Abstract

  The immune system is capable of making qualitatively distinct responses against different microbial infections, and recent advances are starting to reveal how it manages this complex task. An integral component of the immune system is a network of cells known as dendritic cells (DCs), which sense different microbial stimuli and convey this information to lymphocytes. A better understanding of DC biology has allowed a model to be constructed in which the type of immune response to an infection is viewed as a function of several determinants, including the subpopulation of DCs, the nature of the microbe, microbe recognition receptors, and the cytokine microenvironment.

  View details for Web of Science ID 000169875200046

  View details for PubMedID 11452116

• Flt3-ligand and granulocyte colony-stimulating factor mobilize distinct human dendritic cell subsets in vivo JOURNAL OF IMMUNOLOGY Pulendran, B., Banchereau, J., Burkeholder, S., Kraus, E., Guinet, E., Chalouni, C., Caron, D., Maliszewski, C., DAVOUST, J., Fay, J., Palucka, K. 2000; 165 (1): 566-572

  Abstract

  Dendritic cells (DCs) have a unique ability to stimulate naive T cells. Recent evidence suggests that distinct DC subsets direct different classes of immune responses in vitro and in vivo. In humans, the monocyte-derived CD11c+ DCs induce T cells to produce Th1 cytokines in vitro, whereas the CD11c- plasmacytoid T cell-derived DCs elicit the production of Th2 cytokines. In this paper we report that administration of either Flt3-ligand (FL) or G-CSF to healthy human volunteers dramatically increases distinct DC subsets, or DC precursors, in the blood. FL increases both the CD11c+ DC subset (48-fold) and the CD11c- IL-3R+ DC precursors (13-fold). In contrast, G-CSF only increases the CD11c- precursors (>7-fold). Freshly sorted CD11c+ but not CD11c- cells stimulate CD4+ T cells in an allogeneic MLR, whereas only the CD11c- cells can be induced to secrete high levels of IFN-alpha, in response to influenza virus. CD11c+ and CD11c- cells can mature in vitro with GM-CSF + TNF-alpha or with IL-3 + CD40 ligand, respectively. These two subsets up-regulate MHC class II costimulatory molecules as well as the DC maturation marker DC-lysosome-associated membrane protein, and they stimulate naive, allogeneic CD4+ T cells efficiently. These two DC subsets elicit distinct cytokine profiles in CD4+ T cells, with the CD11c- subset inducing higher levels of the Th2 cytokine IL-10. The differential mobilization of distinct DC subsets or DC precursors by in vivo administration of FL and G-CSF offers a novel strategy to manipulate immune responses in humans.

  View details for Web of Science ID 000087816800072

  View details for PubMedID 10861097

• Polyethylene glycol-modified GM-CSF expands CD11b(high)CD11c(high) but not CD11b(low)CD11c(high) murine dendritic cells in vivo: A comparative analysis with Flt3 ligand JOURNAL OF IMMUNOLOGY Daro, E., Pulendran, N., Brasel, K., Teepe, M., Pettit, D., Lynch, D. H., Vremec, D., Robb, L., Shortman, K., McKenna, H. J., Maliszewski, C. R., Maraskovsky, E. 2000; 165 (1): 49-58

  Abstract

  Dendritic cells (DC) are potent APCs that can be characterized in the murine spleen as CD11b(high)CD11c(high) or CD11b(low)CD11c(high). Daily injection of mice of Flt3 ligand (FL) into mice transiently expands both subsets of DC in vivo, but the effect of administration of GM-CSF on the expansion of DC in vivo is not well defined. To gain further insight into the role of GM-CSF in DC development and function in vivo, we treated mice with polyethylene glycol-modified GM-CSF (pGM-CSF) which has an increased half-life in vivo. Administration of pGM-CSF to mice for 5 days led to a 5- to 10-fold expansion of CD11b(high)CD11c(high) but not CD11b(low)CD11c(high) DC. DC from pGM-CSF-treated mice captured and processed Ag more efficiently than DC from FL-treated mice. Although both FL- and pGM-CSF-generated CD11b(high)CD11c(high) DC were CD8alpha-, a greater proportion of these DC from pGM-CSF-treated mice were 33D1+ than from FL-treated mice. CD11b(low)CD11c(high) DC from FL-treated mice expressed high levels of intracellular MHC class II. DC from both pGM-CSF- and FL-treated mice expressed high levels of surface class II, low levels of the costimulatory molecules CD40, CD80, and CD86 and were equally efficient at stimulating allogeneic and Ag-specific T cell proliferation in vitro. The data demonstrate that treatment with pGM-CSF in vivo preferentially expands CD11b(high)CD11c(high) DC that share phenotypic and functional characteristics with FL-generated CD11b(high)CD11c(high) DC but can be distinguished from FL-generated DC on the basis of Ag capture and surface expression of 33D1.

  View details for Web of Science ID 000087816800009

  View details for PubMedID 10861034

• Mice lacking flt3 ligand have deficient hematopoiesis affecting hematopoietic progenitor cells, dendritic cells, and natural killer cells BLOOD McKenna, H. J., Stocking, K. L., MILLER, R. E., Brasel, K., De Smedt, T., Maraskovsky, E., Maliszewski, C. R., Lynch, D. H., Smith, J., Pulendran, B., Roux, E. R., Teepe, M., Lyman, S. D., Peschon, J. J. 2000; 95 (11): 3489-3497

  Abstract

  The ligand for the receptor tyrosine kinase fms-like tyrosine kinase 3 (flt3), also referred to as fetal liver kinase-2 (flk-2), has an important role in hematopoiesis. The flt3 ligand (flt3L) is a growth factor for hematopoietic progenitors and induces hematopoietic progenitor and stem cell mobilization in vivo. In addition, when mice are treated with flt3L immature B cells, natural killer (NK) cells and dendritic cells (DC) are expanded in vivo. To further elucidate the role of flt3L in hematopoiesis, mice lacking flt3L (flt3L-/-) were generated by targeted gene disruption. Leukocyte cellularity was reduced in the bone marrow, peripheral blood, lymph nodes (LN), and spleen. Thymic cellularity, blood hematocrit, and platelet numbers were not affected. Significantly reduced numbers of myeloid and B-lymphoid progenitors were noted in the BM of flt3L-/- mice. In addition a marked deficiency of NK cells in the spleen was noted. DC numbers were also reduced in the spleen, LN, and thymus. Both myeloid-related (CD11c(++) CD8alpha(-)) and lymphoid-related (CD11c(++) CD8alpha(+)) DC numbers were affected. We conclude that flt3L has an important role in the expansion of early hematopoietic progenitors and in the generation of mature peripheral leukocytes.

  View details for Web of Science ID 000087351600030

  View details for PubMedID 10828034

• Distinct dendritic cell subsets differentially regulate the class of immune response in vivo PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pulendran, B., Smith, J. L., Caspary, G., Brasel, K., Pettit, D., Maraskovsky, E., Maliszewski, C. R. 1999; 96 (3): 1036-1041

  Abstract

  Dendritic cells (DCs) are unique in their ability to stimulate T cells and initiate adaptive immunity. Injection of mice with the cytokine Flt3-ligand (FL) dramatically expands mature lymphoid and myeloid-related DC subsets. In contrast, injection of a polyethylene glycol-modified form of granulocyte/macrophage colony-stimulating factor (GM-CSF) into mice only expands the myeloid-related DC subset. These DC subsets differ in the cytokine profiles they induce in T cells in vivo. The lymphoid-related subset induces high levels of the Th1 cytokines interferon gamma and interleukin (IL)-2 but little or no Th2 cytokines. In contrast, the myeloid-related subset induces large amounts of the Th2 cytokines IL-4 and IL-10, in addition to interferon gamma and IL-2. FL- or GM-CSF-treated mice injected with soluble ovalbumin display dramatic increases in antigen-specific antibody titers, but the isotype profiles seem critically dependent on the cytokine used. Although FL treatment induces up to a 10, 000-fold increase in ovalbumin-specific IgG2a and a more modest increase in IgG1 titers, GM-CSF treatment favors a predominantly IgG1 response with little increase in IgG2a levels. These data suggest that distinct DC subsets have strikingly different influences on the type of immune response generated in vivo and may thus be targets for pharmacological intervention.

  View details for Web of Science ID 000078484100044

  View details for PubMedID 9927689

  View details for PubMedCentralID PMC15346

• Developmental pathways of dendritic cells in vivo - Distinct function, phenotype, and localization of dendritic cell subsets in FLT3 ligand-treated mice JOURNAL OF IMMUNOLOGY Pulendran, B., Lingappa, J., Kennedy, M. K., Smith, J., Teepe, M., Rudensky, A., Maliszewski, C. R., Maraskovsky, E. 1997; 159 (5): 2222-2231

  Abstract

  We have recently shown that Flt3 ligand administration dramatically increases dendritic cell (DC) numbers in various mouse tissues. This has enabled the identification of distinct mature DC subpopulations. These have been designated: population C (CD11c(bright) CD11b(bright)), D (CD11c(bright) CD11b(dull)), and E (CD11c(bright) CD11b(negative)) This report demonstrates that the mature DC subsets (C, D, and E) from Flt3 ligand-treated mice differ with respect to phenotype, geographic localization, and function. The myeloid Ags CD11b, F4/80, and Ly-6C are predominantly expressed by population C, but not D or E. In addition, a subset of population C-type DC expresses 33D1 and CD4. In contrast, DC within population D and E selectively express the lymphoid-related DC markers CD8alpha, DEC 205, CD1d, as well as CD23, elevated levels of CD117 (c-kit), CD24 (HSA), CD13, and CD54. Immunohistology indicates that the different DC subsets reside in distinct microenvironments, with populations D and E residing in the T cell areas of the white pulp, while DC within population C localize in the marginal zones. These DC subpopulations showed different capacities to phagocytose FITC-zymosan and to secrete IL-12 upon stimulation with Staphylococcus aureus cowan I strain + IFN-gamma + granulocyte-macrophage-CSF. Population C-type DC were more phagocytic but secreted little inducible IL-12 while population D- and E-type DC showed poor phagocytic capacity and secreted considerably higher levels of IL-12. These results underscore the importance of viewing DC development in vivo, as an interplay between distinct lineages and a maturational dependence on specific microenvironmental signals.

  View details for Web of Science ID A1997XR80200021

  View details for PubMedID 9278310

• SOLUBLE-ANTIGEN CAN CAUSE ENHANCED APOPTOSIS OF GERMINAL-CENTER B-CELLS NATURE Pulendran, B., Kannourakis, G., Nouri, S., Smith, K. G., Nossal, G. J. 1995; 375 (6529): 331-334

  Abstract

  Germinal centres are dynamic microenvironments of B-lymphocyte differentiation, which develop in secondary lymphoid tissues during immune responses. Within germinal centres, activated B lymphocytes proliferate and point mutations are rapidly introduced into the genes encoding their immunoglobulin receptors. As a result, new specificities of B cells are created, including those with a heightened capacity to bind the immunizing antigen. Immunoglobulin gene mutation can also lead to reactivity to self antigens. It has been suggested that any newly formed self-reactive B cells are eliminated within the germinal centre in order to avoid autoimmunity. Here we present evidence that antigen-specific, high-affinity, germinal-centre B cells are rapidly killed by apoptosis in situ when they encounter soluble antigen. The effect seems to act directly on the B cells, rather than through helper T cells. Furthermore, the apoptosis is unique to germinal-centre cells, and is only incompletely impeded by constitutive expression of the proto-oncogene bcl-2. This phenomenon may reflect clonal deletion of self-reactive B cells within germinal centres.

  View details for Web of Science ID A1995RA03000055

  View details for PubMedID 7753199