Professional Education

  • Doctor of Philosophy, University of California San Diego (2015)
  • Bachelor of Science, University of Notre Dame (2010)


All Publications

  • 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

  • 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


    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

  • 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)


    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

  • 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-?


    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

  • 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


    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

  • 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


    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

  • Systems vaccinology: Enabling rational vaccine design with systems biological approaches VACCINE Hagan, T., Nakaya, H. I., Subramaniam, S., Pulendran, B. 2015; 33 (40): 5294–5301


    Vaccines have drastically reduced the mortality and morbidity of many diseases. However, vaccines have historically been developed empirically, and recent development of vaccines against current pandemics such as HIV and malaria has been met with difficulty. The advent of high-throughput technologies, coupled with systems biological methods of data analysis, has enabled researchers to interrogate the entire complement of a variety of molecular components within cells, and characterize the myriad interactions among them in order to model and understand the behavior of the system as a whole. In the context of vaccinology, these tools permit exploration of the molecular mechanisms by which vaccines induce protective immune responses. Here we review the recent advances, challenges, and potential of systems biological approaches in vaccinology. If the challenges facing this developing field can be overcome, systems vaccinology promises to empower the identification of early predictive signatures of vaccine response, as well as novel and robust correlates of protection from infection. Such discoveries, along with the improved understanding of immune responses to vaccination they impart, will play an instrumental role in development of the next generation of rationally designed vaccines.

    View details for DOI 10.1016/j.vaccine.2015.03.072

    View details for Web of Science ID 000362306100009

    View details for PubMedID 25858860

    View details for PubMedCentralID PMC4581890

  • Engineering cell-material interfaces for long-term expansion of human pluripotent stem cells BIOMATERIALS Chang, C., Hwang, Y., Brafman, D., Hagan, T., Phung, C., Varghese, S. 2013; 34 (4): 912–21


    Cost-effective and scalable synthetic matrices that support long-term expansion of human pluripotent stem cells (hPSCs) have many applications, ranging from drug screening platforms to regenerative medicine. Here, we report the development of a hydrogel-based matrix containing synthetic heparin-mimicking moieties that supports the long-term expansion of hPSCs (≥20 passages) in a chemically defined medium. HPSCs expanded on this synthetic matrix maintained their characteristic morphology, colony forming ability, karyotypic stability, and differentiation potential. We also used the synthetic matrix as a platform to investigate the effects of various physicochemical properties of the extracellular environment on the adhesion, growth, and self-renewal of hPSCs. The observed cellular responses can be explained in terms of matrix interface-mediated binding of extracellular matrix proteins, growth factors, and other cell-secreted factors, which create an instructive microenvironment to support self-renewal of hPSCs. These synthetic matrices, which comprise of "off-the-shelf" components and are easy to synthesize, provide an ideal tool to elucidate the molecular mechanisms that control stem cell fate.

    View details for DOI 10.1016/j.biomaterials.2012.10.020

    View details for Web of Science ID 000313155800007

    View details for PubMedID 23131532

    View details for PubMedCentralID PMC4160325

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