All Publications

  • Emerging concepts in the science of vaccine adjuvants. Nature reviews. Drug discovery Pulendran, B., S Arunachalam, P., O'Hagan, D. T. 2021


    Adjuvants are vaccine components that enhance the magnitude, breadth and durability of the immune response. Following its introduction in the 1920s, alum remained the only adjuvant licensed for human use for the next 70 years. Since the 1990s, a further five adjuvants have been included in licensed vaccines, but the molecular mechanisms by which these adjuvants work remain only partially understood. However, a revolution in our understanding of the activation of the innate immune system through pattern recognition receptors (PRRs) is improving the mechanistic understanding of adjuvants, and recent conceptual advances highlight the notion that tissue damage, different forms of cell death, and metabolic and nutrient sensors can all modulate the innate immune system to activate adaptive immunity. Furthermore, recent advances in the use of systems biology to probe the molecular networks driving immune response to vaccines ('systems vaccinology') are revealing mechanistic insights and providing a new paradigm for the vaccine discovery and development process. Here, we review the 'known knowns' and 'known unknowns' of adjuvants, discuss these emerging concepts and highlight how our expanding knowledge about innate immunity and systems vaccinology are revitalizing the science and development of novel adjuvants for use in vaccines against COVID-19 and future pandemics.

    View details for DOI 10.1038/s41573-021-00163-y

    View details for PubMedID 33824489

  • 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


    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

  • 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. n., Bollimpelli, V. S., Scott, M. K., Wimmers, F. n., Burton, S. L., Labranche, C. C., Petitdemange, C. n., Gangadhara, S. n., Styles, T. M., Quarnstrom, C. F., Walter, K. A., Ketas, T. J., Legere, T. n., Jagadeesh Reddy, P. B., Kasturi, S. P., Tsai, A. n., Yeung, B. Z., Gupta, S. n., Tomai, M. n., Vasilakos, J. n., Shaw, G. M., Kang, C. Y., Moore, J. P., Subramaniam, S. n., Khatri, P. n., Montefiori, D. n., Kozlowski, P. A., Derdeyn, C. A., Hunter, E. n., Masopust, D. n., Amara, R. R., Pulendran, B. n. 2020


    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

  • Durability of immune responses to the booster mRNA vaccination against COVID-19. The Journal of clinical investigation Arunachalam, P. S., Lai, L., Samaha, H., Feng, Y., Hu, M., Hui, H. S., Wali, B., Ellis, M. L., Davis-Gardner, M. E., Huerta, C. M., Bechnak, K., Bechnak, S., Lee, M., Litvack, M. B., Losada, C., Grifoni, A., Sette, A., Zarnitsyna, V. I., Rouphael, N., Suthar, M. S., Pulendran, B. 2023


    Maintaining durable immunity to vaccination represents a major challenge, but whether booster mRNA vaccination improves durability is unknown.We measured antibody responses in 55 healthy adults who received a booster dose of Pfizer-BioNTech or Moderna vaccine against SARS-CoV-2 and calculated the half-life of antibody titers. We also measured memory B and T cell responses in a subset of 28 participants. In 13 volunteers who received a second booster, we measured serum antibody titers, and memory B and T cell responses.The booster (3rd immunization) dose at 6 - 10 months increased the half-life of serum neutralizing antibody (nAb) titers to 76 days from 56 - 66 days after the primary two-dose vaccination. A second booster dose (4th immunization) a year after the primary vaccination increased the half-life further to 88 days. However, despite this modestly improved durability in nAb responses against the ancestral (WA.1) strain, there was a loss in neutralization capacity against Omicron subvariants BA.2.75.2, BQ.1.1, and XBB.1.5 (48, 71, and 66-fold drop in titers respectively, relative to the WA.1 strain). While only 45 - 65% of participants demonstrated a detectable nAb titer against the newer variants after the booster (3rd dose), the response declined to below the detection limit in almost all individuals by 6 months. In contrast, booster vaccination induced antigen-specific memory B and T cells that persisted for at least 6 months.The durability of serum antibody responses improves only marginally following booster immunizations with the Pfizer-BioNTech or Moderna mRNA vaccines.

    View details for DOI 10.1172/JCI167955

    View details for PubMedID 36951954

  • Adjuvanting a subunit SARS-CoV-2 vaccine with clinically relevant adjuvants induces durable protection in mice. NPJ vaccines Grigoryan, L., Lee, A., Walls, A. C., Lai, L., Franco, B., Arunachalam, P. S., Feng, Y., Luo, W., Vanderheiden, A., Floyd, K., Wrenn, S., Pettie, D., Miranda, M. C., Kepl, E., Ravichandran, R., Sydeman, C., Brunette, N., Murphy, M., Fiala, B., Carter, L., Coffman, R. L., Novack, D., Kleanthous, H., O'Hagan, D. T., van der Most, R., McLellan, J. S., Suthar, M., Veesler, D., King, N. P., Pulendran, B. 2022; 7 (1): 55


    Adjuvants enhance the magnitude and the durability of the immune response to vaccines. However, there is a paucity of comparative studies on the nature of the immune responses stimulated by leading adjuvant candidates. In this study, we compared five clinically relevant adjuvants in mice-alum, AS03 (a squalene-based adjuvant supplemented with α-tocopherol), AS37 (a TLR7 ligand emulsified in alum), CpG1018 (a TLR9 ligand emulsified in alum), O/W 1849101 (a squalene-based adjuvant)-for their capacity to stimulate immune responses when combined with a subunit vaccine under clinical development. We found that all four of the adjuvant candidates surpassed alum with respect to their capacity to induce enhanced and durable antigen-specific antibody responses. The TLR-agonist-based adjuvants CpG1018 (TLR9) and AS37 (TLR7) induced Th1-skewed CD4+ T cell responses, while alum, O/W, and AS03 induced a balanced Th1/Th2 response. Consistent with this, adjuvants induced distinct patterns of early innate responses. Finally, vaccines adjuvanted with AS03, AS37, and CpG1018/alum-induced durable neutralizing-antibody responses and significant protection against the B.1.351 variant 7 months following immunization. These results, together with our recent results from an identical study in non-human primates (NHPs), provide a comparative benchmarking of five clinically relevant vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV-2 subunit vaccines to provide durable protection against the B.1.351 variant. Furthermore, these results reveal differences between the widely-used C57BL/6 mouse strain and NHP animal models, highlighting the importance of species selection for future vaccine and adjuvant studies.

    View details for DOI 10.1038/s41541-022-00472-2

    View details for PubMedID 35606518

  • Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine. Nature immunology Li, C., Lee, A., Grigoryan, L., Arunachalam, P. S., Scott, M. K., Trisal, M., Wimmers, F., Sanyal, M., Weidenbacher, P. A., Feng, Y., Adamska, J. Z., Valore, E., Wang, Y., Verma, R., Reis, N., Dunham, D., O'Hara, R., Park, H., Luo, W., Gitlin, A. D., Kim, P., Khatri, P., Nadeau, K. C., Pulendran, B. 2022


    Despite the success of the BNT162b2 mRNA vaccine, the immunological mechanisms that underlie its efficacy are poorly understood. Here we analyzed the innate and adaptive responses to BNT162b2 in mice, and show that immunization stimulated potent antibody and antigen-specific T cell responses, as well as strikingly enhanced innate responses after secondary immunization, which was concurrent with enhanced serum interferon (IFN)-gamma levels 1d following secondary immunization. Notably, we found that natural killer cells and CD8+ T cells in the draining lymph nodes are the major producers of this circulating IFN-gamma. Analysis of knockout mice revealed that induction of antibody and T cell responses to BNT162b2 was not dependent on signaling via Toll-like receptors 2, 3, 4, 5 and 7 nor inflammasome activation, nor the necroptosis or pyroptosis cell death pathways. Rather, the CD8+ T cell response induced by BNT162b2 was dependent on type I interferon-dependent MDA5 signaling. These results provide insights into the molecular mechanisms by which the BNT162b2 vaccine stimulates immune responses.

    View details for DOI 10.1038/s41590-022-01163-9

    View details for PubMedID 35288714

  • A molecular atlas of innate immunity to adjuvanted and live attenuated vaccines, in mice. Nature communications Lee, A., Scott, M. K., Wimmers, F., Arunachalam, P. S., Luo, W., Fox, C. B., Tomai, M., Khatri, P., Pulendran, B. 1800; 13 (1): 549


    Adjuvants hold great potential in enhancing vaccine efficacy, making the understanding and improving of adjuvants critical goals in vaccinology. The TLR7/8 agonist, 3M-052, induces long-lived humoral immunity in non-human primates and is currently being evaluated in human clinical trials. However, the innate mechanisms of 3M-052 have not been fully characterized. Here, we perform flow cytometry, single cell RNA-seq and ATAC-seq to profile the kinetics, transcriptomics and epigenomics of innate immune cells in murine draining lymph nodes following 3M-052-Alum/Ovalbumin immunization. We find that 3M-052-Alum/OVA induces a robust antiviral and interferon gene program, similar to the yellow fever vaccine, which is known to confer long-lasting protection. Activation of myeloid cells in dLNs persists through day 28 and single cell analysis reveals putative TF-gene regulatory programs in distinct myeloid cells and heterogeneity of monocytes. This study provides a comprehensive characterization of the transcriptomics and epigenomics of innate populations in the dLNs after vaccination.

    View details for DOI 10.1038/s41467-022-28197-9

    View details for PubMedID 35087093

  • Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Science translational medicine Sievers, B. L., Chakraborty, S., Xue, Y., Gelbart, T., Gonzalez, J. C., Cassidy, A. G., Golan, Y., Prahl, M., Gaw, S. L., Arunachalam, P. S., Blish, C. A., Boyd, S. D., Davis, M. M., Jagannathan, P., Nadeau, K. C., Pulendran, B., Singh, U., Scheuermann, R. H., Frieman, M. B., Vashee, S., Wang, T. T., Tan, G. S. 1800: eabn7842


    Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that possess mutations associated with increased transmission and antibody escape have arisen over the course of the current pandemic. Although the current vaccines have largely been effective against past variants, the number of mutations found on the Omicron (B.1.1.529) spike protein appear to diminish the protection conferred by pre-existing immunity. Using vesicular stomatitis virus (VSV) pseudoparticles expressing the spike protein of several SARS-CoV-2 variants, we evaluated the magnitude and breadth of the neutralizing antibody response over time in individuals after infection and in mRNA-vaccinated individuals. We observed that boosting increases the magnitude of the antibody response to wildtype (D614), Beta, Delta, and Omicron variants; however, the Omicron variant was the most resistant to neutralization. We further observed that vaccinated healthy adults had robust and broad antibody responses whereas responses may have been reduced in vaccinated pregnant women, underscoring the importance of learning how to maximize mRNA vaccine responses in pregnant populations. Findings from this study show substantial heterogeneity in the magnitude and breadth of responses after infection and mRNA vaccination and may support the addition of more conserved viral antigens to existing SARS-CoV-2 vaccines.

    View details for DOI 10.1126/scitranslmed.abn7842

    View details for PubMedID 35025672

  • Toll-Like Receptor 9 Activation Rescues Impaired Antibody Response in Needle-free Intradermal DNA Vaccination SCIENTIFIC REPORTS Arunachalam, P. S., Mishra, R., Badarinath, K., Selvam, D., Payeli, S. K., Stout, R. R., Ranga, U. 2016; 6


    The delivery of plasmid DNA to the skin can target distinct subsets of dermal dendritic cells to confer a superior immune response. The needle-free immunization technology offers a reliable, safe and efficient means to administer intradermal (ID) injections. We report here that the ID injection of DNA vectors using an NF device (NF-ID) elicits a superior cell-mediated immune response, at much lesser DNA dosage, comparable in magnitude to the traditional intramuscular immunization. However, the humoral response is significantly impaired, possibly at the stage of B cell isotype switching. We found that the NF-ID administration deposits the DNA primarily on the epidermis resulting in a rapid loss of the DNA as well as the synthesized antigen due to the faster regeneration rate of the skin layers. Therefore, despite the immune-rich nature of the skin, the NF-ID immunization of DNA vectors may be limited by the impaired humoral response. Additional booster injections are required to augment the antibody response. As an alternative and a viable solution, we rescued the IgG response by coadministration of a Toll-like receptor 9 agonist, among other adjuvants examined. Our work has important implication for the optimization of the emerging needle-free technology for ID immunization.

    View details for DOI 10.1038/srep33564

    View details for Web of Science ID 000383946000001

    View details for PubMedID 27658623

    View details for PubMedCentralID PMC5034244